Timestamp 18-Jul-2025 00:12:39
pMakeSCFGModels: Looking for motifs in C:\Users\zirbel\Documents\JAR3D\Motifs\J4_3.48\mat
pMakeSCFGModels: Found 65 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 J4_01665.1
    {'> J4_01665.1  5J7L G  142 C  221'}    {'GAG*CAUAACG*CCAAAG*UGC'}

pCalculateTransitions:  processing J4_04237.1
    {'> J4_04237.1  4WSM G    7 C   77'}    {'GUGGUGGAAUUGGUAGACACGC*GUG*CUUA*UC'}

pCalculateTransitions:  processing J4_04930.2
  Columns 1 through 5

    {'> J4_04930.2  4…'}    {'CAAAG*CUGAC*GGG…'}    {'> J4_04930.2  5…'}    {'CGAAG*UUGAC*GGU…'}    {'> J4_04930.2  4…'}

  Columns 6 through 10

    {'CAAAG*UUGAC*GGG…'}    {'> J4_04930.2  7…'}    {'CAAAG*UUGAC*GGG…'}    {'> J4_04930.2  5…'}    {'CUAAG*UUGAU*ACC…'}

  Columns 11 through 12

    {'> J4_04930.2  4…'}    {'CUAUG*UUGAC*GAC…'}

pCalculateTransitions:  processing J4_07491.1
  Columns 1 through 5

    {'> J4_07491.1  4…'}    {'AUAAU*AG*CC*GAUU'}    {'> J4_07491.1  1…'}    {'AUAAU*AG*CC*GAUU'}    {'> J4_07491.1  1…'}

  Columns 6 through 10

    {'AUAAU*AG*CC*GACU'}    {'> J4_07491.1  4…'}    {'AUAAU*AG*CC*GACU'}    {'> J4_07491.1  3…'}    {'AUAAC*GG*CC*GACU'}

  Columns 11 through 15

    {'> J4_07491.1  3…'}    {'AUAAU*AG*CC*GACU'}    {'> J4_07491.1  3…'}    {'AUAAC*GG*CC*GACU'}    {'> J4_07491.1  3…'}

  Columns 16 through 18

    {'ACAGG*UG*CC*GACU'}    {'> J4_07491.1  3…'}    {'ACAGG*UG*CC*GACU'}

pCalculateTransitions:  processing J4_10313.2
  Columns 1 through 5

    {'> J4_10313.2  4…'}    {'UC*GGUUAG*CU*AC…'}    {'> J4_10313.2  4…'}    {'UC*GGUUAG*CC*GC…'}    {'> J4_10313.2  4…'}

  Columns 6 through 10

    {'UC*GGUUAG*CC*GU…'}    {'> J4_10313.2  7…'}    {'UC*GGAAAG*CC*GC…'}    {'> J4_10313.2  5…'}    {'UC*GGUGAG*CU*AA…'}

pCalculateTransitions:  processing J4_10408.3
    {'> J4_10408.3  6OF1 G    5…'}    {'GAUUAG*CAC*GGGGUCG*CAUC'}    {'> J4_10408.3  6GSK A    5…'}    {'AUAUAG*CGC*GAGGUCG*CUAU'}

pCalculateTransitions:  processing J4_10571.1
    {'> J4_10571.1  2ZNI U    7 A   66'}    {'UGG*CAC*GCAGG*UA'}

pCalculateTransitions:  processing J4_11418.1
    {'> J4_11418.1  4V9F A  302 U  349'}    {'ACGAAG*CGUG*CAG*CGUACU'}

pCalculateTransitions:  processing J4_12209.1
    {'> J4_12209.1  1U9S C  119 G  222'}    {'CACAGAGAAGAGAC*GGUGAAACG*CG*CACG'}

pCalculateTransitions:  processing J4_16596.1
  Columns 1 through 5

    {'> J4_16596.1  4…'}    {'GGAAAG*CAGA*UAC…'}    {'> J4_16596.1  4…'}    {'GGAAAG*CACA*UAC…'}    {'> J4_16596.1  4…'}

  Column 6

    {'GGGAAG*CACG*CAC…'}

pCalculateTransitions:  processing J4_19572.1
    {'> J4_19572.1  1U9S C  119 G  222'}    {'CACAGAGAAGAGAC*GGUGAAACG*CGC*GGCACG'}

pCalculateTransitions:  processing J4_22413.2
  Columns 1 through 5

    {'> J4_22413.2  1…'}    {'UUAA*UAG*UCUAGU…'}    {'> J4_22413.2  2…'}    {'GUAG*CAU*AGUGUC…'}    {'> J4_22413.2  5…'}

  Column 6

    {'GUAG*CAC*GGUGUC…'}

pCalculateTransitions:  processing J4_24220.1
    {'> J4_24220.1  4FEN A   21 U   75'}    {'AUAUAC*GAG*CC*GACU'}

pCalculateTransitions:  processing J4_26776.1
    {'> J4_26776.1  4RUM C   16 G   88'}    {'CAG*CGGG*CAA*UGGG'}

pCalculateTransitions:  processing J4_26796.1
    {'> J4_26796.1  4V88 C   99 G  384'}    {'CAUUAAAUC*GCC*GUAAC*GG'}

pCalculateTransitions:  processing J4_28426.1
    {'> J4_28426.1  4OQU C    5 G   67'}    {'CACGAG*CG*UCAC*GG'}

pCalculateTransitions:  processing J4_28473.1
    {'> J4_28473.1  4V9F G 2679 C 2806'}    {'GAAC*GG*CACG*CAC'}

pCalculateTransitions:  processing J4_34476.1
    {'> J4_34476.1  4V9F G 1828…'}    {'GACUG*CAUAG*UGAAU*AUUAAC'}    {'> J4_34476.1  5TBW G 2130…'}    {'GACUG*CAUAG*UGAUU*AUUAAC'}

pCalculateTransitions:  processing J4_35578.2
  Columns 1 through 5

    {'> J4_35578.2  4…'}    {'GAGUAACG*UC*GUA…'}    {'> J4_35578.2  5…'}    {'GAGUAAUG*UG*CUA…'}    {'> J4_35578.2  6…'}

  Column 6

    {'GAGUAACG*UC*GUA…'}

pCalculateTransitions:  processing J4_36296.1
  Columns 1 through 5

    {'> J4_36296.1  2…'}    {'GUAG*CGG*CAGGUC…'}    {'> J4_36296.1  3…'}    {'GUAG*CAC*GGUGUC…'}    {'> J4_36296.1  4…'}

  Columns 6 through 10

    {'AUAG*CAG*CGUGUC…'}    {'> J4_36296.1  1…'}    {'AUCG*CAC*GCAUUC…'}    {'> J4_36296.1  1…'}    {'UUAA*UAG*UCUAGU…'}

pCalculateTransitions:  processing J4_36540.1
    {'> J4_36540.1  3F2X G   32…'}    {'GG*CGAA*UUGAU*AACC'}    {'> J4_36540.1  6DN2 G   32…'}    {'GG*CGAA*UUGAU*AACC'}

pCalculateTransitions:  processing J4_36568.1
    {'> J4_36568.1  6CZR G  137…'}    {'GAG*CAUGUG*CAAAG*CGC'}    {'> J4_36568.1  4LFB G  142…'}    {'GAG*CAUGUG*CAAAG*CGC'}

pCalculateTransitions:  processing J4_40439.2
  Columns 1 through 5

    {'> J4_40439.2  4…'}    {'CAAGAG*CA*UAAAU…'}    {'> J4_40439.2  5…'}    {'CAAGAG*CG*CAAUU…'}    {'> J4_40439.2  4…'}

  Column 6

    {'CAAGAG*CG*CAAUU…'}

pCalculateTransitions:  processing J4_43687.1
    {'> J4_43687.1  7KKV U  490…'}    {'UC*UAA*UGC*UA'}    {'> J4_43687.1  2A64 G  136…'}    {'GAC*GCC*GCG*GC'}

pCalculateTransitions:  processing J4_44058.1
    {'> J4_44058.1  6VMY G  245 C  309'}    {'GGAAA*UGCG*CAC*GGAUAC'}

pCalculateTransitions:  processing J4_45582.1
    {'> J4_45582.1  4Y1M C   17 G   94'}    {'CGA*UG*CGG*CAG'}

pCalculateTransitions:  processing J4_45801.2
  Columns 1 through 5

    {'> J4_45801.2  7…'}    {'CC*GAGUAG*UGAAU…'}    {'> J4_45801.2  4…'}    {'CC*GAGUAG*CGAAU…'}    {'> J4_45801.2  5…'}

  Columns 6 through 10

    {'CC*GAGUAG*UGAAU…'}    {'> J4_45801.2  4…'}    {'CC*GAGUAC*GGAAU…'}    {'> J4_45801.2  4…'}    {'CU*GAGUAC*GGAAU…'}

  Columns 11 through 12

    {'> J4_45801.2  5…'}    {'UC*GAGUCG*CUAAG…'}

pCalculateTransitions:  processing J4_46448.1
    {'> J4_46448.1  6CB3 C   15 G   90'}    {'CGU*AA*UG*UUAG'}

pCalculateTransitions:  processing J4_47478.1
    {'> J4_47478.1  1KH6 G    5 C   49'}    {'GAAC*GA*UUG*CC'}

pCalculateTransitions:  processing J4_48692.1
    {'> J4_48692.1  5SWD A   21 U   75'}    {'AUAAU*AG*CC*GAUU'}

pCalculateTransitions:  processing J4_48907.1
    {'> J4_48907.1  1NBS G   90…'}    {'GC*GG*CG*CC'}    {'> J4_48907.1  1U9S G   79…'}    {'GC*GG*CG*CC'}

pCalculateTransitions:  processing J4_51403.1
    {'> J4_51403.1  5TBW C  185 G  231'}    {'CUAUG*CGUC*GAG*CGUGUG'}

pCalculateTransitions:  processing J4_54165.1
    {'> J4_54165.1  7A0S G 2622 C 2751'}    {'GAGU*AAC*GGAACG*CAGC'}

pCalculateTransitions:  processing J4_57327.1
    {'> J4_57327.1  4V7M U    6 A   66'}    {'UAUCGCC*GGCAC*GCUUUCC*GUA'}

pCalculateTransitions:  processing J4_57344.1
    {'> J4_57344.1  5UD5 C    7 G   66'}    {'CUG*CG*CAGC*GG'}

pCalculateTransitions:  processing J4_59634.1
    {'> J4_59634.1  4V8N U    7 A   68'}    {'UUAGCU*AGCG*UGGGCG*CA'}

pCalculateTransitions:  processing J4_59845.1
    {'> J4_59845.1  6CK5 A    5…'}    {'AGU*AG*CACAC*GAUAGGU'}    {'> J4_59845.1  6DLR A    5…'}    {'AGU*AG*UACAC*GGUAGGU'}

pCalculateTransitions:  processing J4_60168.1
    {'> J4_60168.1  4WF9 C  644…'}    {'CAAG*CGUAG*CGAGU*GCGUUUAG'}    {'> J4_60168.1  5J7L C  601…'}    {'CAAG*CGAAG*CGAG*CGUUAAG'}

pCalculateTransitions:  processing J4_61477.2
  Columns 1 through 5

    {'> J4_61477.2  5…'}    {'AACUG*CACAG*UGA…'}    {'> J4_61477.2  4…'}    {'GACUG*CACAG*CGA…'}    {'> J4_61477.2  4…'}

  Columns 6 through 8

    {'GACUG*CACAG*UGA…'}    {'> J4_61477.2  7…'}    {'GACUG*CACAG*UGA…'}

pCalculateTransitions:  processing J4_61885.2
  Columns 1 through 5

    {'> J4_61885.2  4…'}    {'GGG*CGAAAG*CCCU…'}    {'> J4_61885.2  6…'}    {'GGG*CGAAAG*CCCU…'}    {'> J4_61885.2  5…'}

  Columns 6 through 8

    {'GCG*CGAAAG*CCGU…'}    {'> J4_61885.2  4…'}    {'AAG*CGAAAG*CCAU…'}

pCalculateTransitions:  processing J4_63076.1
    {'> J4_63076.1  3HHN A   54…'}    {'AC*GCAG*CC*GU'}    {'> J4_63076.1  3IVK A   54…'}    {'AC*GCAG*CC*GU'}

pCalculateTransitions:  processing J4_64075.1
  Columns 1 through 5

    {'> J4_64075.1  5…'}    {'CUG*CG*CCUAAGGU…'}    {'> J4_64075.1  4…'}    {'UUG*CG*CCUAAGGU…'}    {'> J4_64075.1  5…'}

  Columns 6 through 8

    {'CUG*CG*CUUAAGGU…'}    {'> J4_64075.1  4…'}    {'CUG*CG*CUUAAGGU…'}

pCalculateTransitions:  processing J4_64571.2
  Columns 1 through 5

    {'> J4_64571.2  5…'}    {'CGAUAAA*UC*GCUU…'}    {'> J4_64571.2  7…'}    {'CGAUAAA*UC*GCGC…'}    {'> J4_64571.2  4…'}

  Columns 6 through 8

    {'CGAUAAA*UC*GCGC…'}    {'> J4_64571.2  4…'}    {'CGAAAG*CC*GAGC*GG'}

pCalculateTransitions:  processing J4_65052.1
    {'> J4_65052.1  6N2V C   16 G   86'}    {'CUG*CGC*GA*UCUG'}

pCalculateTransitions:  processing J4_65285.1
    {'> J4_65285.1  2DU3 G  907…'}    {'GUGG*CGGC*GCUUUACC*GC'}    {'> J4_65285.1  5WWT A    7…'}    {'AUAG*CAUU*AGAGGUCC*GU'}

pCalculateTransitions:  processing J4_69051.2
  Columns 1 through 5

    {'> J4_69051.2  5…'}    {'GGUUC*GGUUAG*CC…'}    {'> J4_69051.2  4…'}    {'GGUUC*GGUUAG*CC…'}    {'> J4_69051.2  5…'}

  Columns 6 through 10

    {'GGUUC*GGUGAG*CU…'}    {'> J4_69051.2  4…'}    {'GGUUC*GGUUAG*CU…'}    {'> J4_69051.2  4…'}    {'GUUUC*GGUUAG*CC…'}

  Columns 11 through 12

    {'> J4_69051.2  7…'}    {'GGUUC*GGAAAG*CC…'}

pCalculateTransitions:  processing J4_69073.1
    {'> J4_69073.1  6U8D G  153 C  239'}    {'GAAC*GA*UUG*CC'}

pCalculateTransitions:  processing J4_69568.1
    {'> J4_69568.1  5TBW C 1451 G 2353'}    {'CAAAUAU*AG*UGAU*AG'}

pCalculateTransitions:  processing J4_70449.12
  Columns 1 through 5

    {'> J4_70449.12  …'}    {'GUAG*CGC*GAGGCC…'}    {'> J4_70449.12  …'}    {'GUAG*UAC*GGGGUC…'}    {'> J4_70449.12  …'}

  Columns 6 through 10

    {'GUAG*CAC*GGGGUC…'}    {'> J4_70449.12  …'}    {'AUAG*CGC*GAGGUC…'}    {'> J4_70449.12  …'}    {'UUAG*CGC*GAGGUC…'}

  Columns 11 through 15

    {'> J4_70449.12  …'}    {'AUAG*CAU*AGGGUC…'}    {'> J4_70449.12  …'}    {'CUAG*CGC*GAGGUC…'}    {'> J4_70449.12  …'}

  Columns 16 through 20

    {'GUGG*CGC*GAUGUC…'}    {'> J4_70449.12  …'}    {'GUAG*CAU*AGUGUC…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUC…'}

  Columns 21 through 25

    {'> J4_70449.12  …'}    {'GUAG*CGU*AAGGUC…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUC…'}    {'> J4_70449.12  …'}

  Columns 26 through 30

    {'AUAG*CAA*UGGGUC…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUU…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUC…'}

  Columns 31 through 35

    {'> J4_70449.12  …'}    {'GUAG*CGC*GAGGUC…'}    {'> J4_70449.12  …'}    {'AUAG*CAU*AGGGUC…'}    {'> J4_70449.12  …'}

  Columns 36 through 40

    {'GUAG*UAC*GCGGUC…'}    {'> J4_70449.12  …'}    {'GUAG*CAC*GGGGUC…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUC…'}

  Columns 41 through 45

    {'> J4_70449.12  …'}    {'GUAG*CAC*GGGGGC…'}    {'> J4_70449.12  …'}    {'GUAG*CGG*CAGGUC…'}    {'> J4_70449.12  …'}

  Columns 46 through 50

    {'UUCG*CAC*GUAACA…'}    {'> J4_70449.12  …'}    {'GUAG*CAG*UAGGUC…'}    {'> J4_70449.12  …'}    {'GUAG*CAC*GGGGUC…'}

  Columns 51 through 55

    {'> J4_70449.12  …'}    {'GUAG*CGC*GCGGUC…'}    {'> J4_70449.12  …'}    {'GUAG*CGG*CAUGUC…'}    {'> J4_70449.12  …'}

  Columns 56 through 60

    {'GUGG*CGU*AAGAUC…'}    {'> J4_70449.12  …'}    {'UUGG*CAC*GGGGUC…'}    {'> J4_70449.12  …'}    {'UUAG*CAG*UUGGUC…'}

  Columns 61 through 65

    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGGUC…'}    {'> J4_70449.12  …'}    {'AUAG*CAG*CGGGUC…'}    {'> J4_70449.12  …'}

  Columns 66 through 70

    {'AUAG*UGG*CAGAUC…'}    {'> J4_70449.12  …'}    {'GUAG*CAC*GGGGUC…'}    {'> J4_70449.12  …'}    {'GUGG*CGU*AAGAUU…'}

  Columns 71 through 75

    {'> J4_70449.12  …'}    {'AUGG*CAG*UUGGUC…'}    {'> J4_70449.12  …'}    {'AUCG*CGC*GAAACG…'}    {'> J4_70449.12  …'}

  Columns 76 through 80

    {'UUCG*CAC*GUAACA…'}    {'> J4_70449.12  …'}    {'UUCG*CAC*GUAACA…'}    {'> J4_70449.12  …'}    {'AUAG*CAG*CGUGUC…'}

  Columns 81 through 84

    {'> J4_70449.12  …'}    {'UUAG*CAG*UUGGUC…'}    {'> J4_70449.12  …'}    {'AUAG*CAU*AGGGUC…'}

pCalculateTransitions:  processing J4_70672.1
    {'> J4_70672.1  6DN2 C    8…'}    {'CGGGGCAG*CGACC*GAC*GGAUGA…'}    {'> J4_70672.1  3F2X C    8…'}    {'CGGGGCAG*CGACC*GAC*GGAUGA…'}

pCalculateTransitions:  processing J4_71729.2
  Columns 1 through 5

    {'> J4_71729.2  4…'}    {'CGAAG*CGCC*GAG*…'}    {'> J4_71729.2  4…'}    {'CGAAU*AAUC*GAA*…'}    {'> J4_71729.2  5…'}

  Columns 6 through 8

    {'GGAAG*CGCG*CAG*…'}    {'> J4_71729.2  7…'}    {'CGAAG*CACC*GAA*…'}

pCalculateTransitions:  processing J4_72305.3
  Columns 1 through 5

    {'> J4_72305.3  4…'}    {'CUGG*UG*CGACC*GG'}    {'> J4_72305.3  5…'}    {'CUGG*UG*CGACC*GG'}    {'> J4_72305.3  2…'}

  Columns 6 through 10

    {'GUGG*UG*CGACA*UC'}    {'> J4_72305.3  3…'}    {'GUCG*CG*UGGUG*CC'}    {'> J4_72305.3  6…'}    {'GUAG*CG*UUGUUG*UC'}

  Columns 11 through 12

    {'> J4_72305.3  5…'}    {'GUAG*CA*UGUCG*CC'}

pCalculateTransitions:  processing J4_75852.1
    {'> J4_75852.1  6DME A    4 U   99'}    {'AGU*AG*UACAC*GCAAGU'}

pCalculateTransitions:  processing J4_75971.1
    {'> J4_75971.1  5TBW U 3010 G 3136'}    {'UAA*UC*GCU*AUG'}

pCalculateTransitions:  processing J4_76405.1
    {'> J4_76405.1  2QUS U   11 A   54'}    {'UCA*UC*GAG*CAAAA'}

pCalculateTransitions:  processing J4_77044.1
  Columns 1 through 5

    {'> J4_77044.1  5…'}    {'GGGC*GAC*GGAAG*…'}    {'> J4_77044.1  4…'}    {'GGGC*GAC*GGAAG*…'}    {'> J4_77044.1  4…'}

  Column 6

    {'GAGC*GAC*GGACG*…'}

pCalculateTransitions:  processing J4_78628.1
  Columns 1 through 6

    {'> J4_78628.1  5…'}    {'GG*UU*AC*GC'}    {'> J4_78628.1  5…'}    {'AG*UC*GG*CU'}    {'> J4_78628.1  4…'}    {'GAC*GC*GG*CC'}

  Columns 7 through 8

    {'> J4_78628.1  4…'}    {'GG*CG*CG*UC'}

pCalculateTransitions:  processing J4_80682.1
    {'> J4_80682.1  3ICQ U    7…'}    {'UUAAC*GCGC*GAGGUCC*GA'}    {'> J4_80682.1  5X6B G    7…'}    {'GUAGU*GCAGC*GCCUUACG*CC'}

pCalculateTransitions:  processing J4_89787.1
    {'> J4_89787.1  4V9F C 1374 G 2051'}    {'CAGCGAUAG*CG*CUGUC*GG'}

pCalculateTransitions:  processing J4_91813.1
    {'> J4_91813.1  7A0S A 1458 U 1563'}    {'AUG*UU*GGGAG*CGAAGU'}

pCalculateTransitions:  processing J4_91882.1
    {'> J4_91882.1  2AKE G    7…'}    {'GUGG*CGU*AAGGUUG*UC'}    {'> J4_91882.1  2ZZN G    7…'}    {'GUAG*CAG*CCUUACG*CC'}

pCalculateTransitions:  processing J4_94519.1
    {'> J4_94519.1  4V90 A    7…'}    {'AUAG*CAGG*CCGUGUCC*GU'}    {'> J4_94519.1  1QF6 A    7…'}    {'AUAG*CAGC*GAAGGUCG*UU'}

pCalculateTransitions:  processing J4_97835.1
    {'> J4_97835.1  6ORD U    6 A   67'}    {'UAUAG*CGC*GAGGUCA*UUA'}

pCalculateTransitions:  processing J4_98739.1
    {'> J4_98739.1  7A0S C  611 G  669'}    {'CGAG*CGGAG*CGAGU*GGCGGCAUUAG'}

pCalculateTransitions:  processing J4_99897.1
    {'> J4_99897.1  3SUX G    8 C   89'}    {'GUAG*CGC*GUAG*CGC'}

pCalculateTransitions:  cWW basepair probabilities for CG, GC, AU, UA, GU, UG are

cWW_M =

    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

pCalculateTransitions:  initial distribution for A, C, G, U is

initial_M =

    0.3005
    0.0960
    0.3106
    0.2929

pCalculateTransitions:  initial transition matrix is

initialTransition_M =

    0.2909    0.0909    0.1273    0.4909
    0.4017    0.0769    0.4017    0.1197
    0.2765    0.1176    0.3000    0.3059
    0.1667    0.0741    0.3333    0.4259

pCalculateTransitions:  interior transition matrix is

transition_M =

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

Timestamp 18-Jul-2025 00:12:41
pMakeSCFGModels: Making JAR3D model for motif group J4_01665.1, number 1 of 65
pMakeSCFGModels: Loaded C:\Users\zirbel\Documents\JAR3D\Motifs\J4_3.48\mat\J4_01665.1.mat, looks like:
Search = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

         motif_id: 'J4_01665.1'
       Candidates: [1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17 18 19 1]
    consensusEdge: [18×18 double]
     bp_signature: 'cWW-tWH-F-tWH-cWW-tSS-F-tHW-tSS-cWW-cWW'
        Signature: 'cWW-tWH-F-tWH-cWW-tSS-F-tHW-tSS-cWW-cWW'
       chainbreak: {3×1 cell}
         loop_ids: {'J4_5J7L_002'}
         Truncate: [3×1 double]
            Query: [1×1 struct]
       MaxDiffMat: [1 1 1 1 1 1 1 1 1 1 1 1 1 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 Inf 0 Inf 0 Inf 0 0 … ]
             File: [1×1 struct]
         NumFixed: 0


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

         Backbone: [19×19 double]
    BasePhosphate: [19×19 double]
       BaseRibose: [19×19 double]
       BestChains: {{3×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [19×19 double]
         Covalent: [19×19 double]
         Crossing: [19×19 double]
         Distance: []
             Edge: [57×58 double]
         Filename: '5J7L'
            Flank: [19×19 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [3068 5965]
         Modified: 0
               NT: [1×19 struct]
            NumNT: 19
      PDBFilename: '5J7L.pdb'
            PDBID: '5J7L'
            Range: [19×19 double]
        Redundant: [19×19 double]


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

         Backbone: [19×19 double]
    BasePhosphate: [19×19 double]
       BaseRibose: [19×19 double]
       BestChains: {{3×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [19×19 double]
         Covalent: [19×19 double]
         Crossing: [19×19 double]
         Distance: []
             Edge: [57×58 double]
         Filename: '5J7L'
            Flank: [19×19 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [3068 5965]
         Modified: 0
               NT: [1×19 struct]
            NumNT: 19
      PDBFilename: '5J7L.pdb'
            PDBID: '5J7L'
            Range: [19×19 double]
        Redundant: [19×19 double]

pMakeNodes starting loop:     a=5J7L|1|AA|G|142 B=5J7L|1|AA|C|221
  2 Basepair   142  221 GC cWW 
No need to probe because of interaction between a=5J7L|1|AA|A|143 B=5J7L|1|AA|G|220
  3 Basepair   143  220 AG cSW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|G|144 B=5J7L|1|AA|U|219
pMakeNodes probed for insert:  a=5J7L|1|AA|G|144 B=5J7L|1|AA|U|219
pMakeNodesJunction: a=5J7L|1|AA|G|144 r=5J7L|1|AA|G|144 s=5J7L|1|AA|C|178 t=5J7L|1|AA|A|179 u=B=5J7L|1|AA|U|219
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|AA|G|144 and 5J7L|1|AA|C|178 and between 5J7L|1|AA|A|179 and 5J7L|1|AA|U|219
pMakeNodesJunction: about to make a junction: a=5J7L|1|AA|G|144 s=5J7L|1|AA|C|178 t=5J7L|1|AA|A|179 B=5J7L|1|AA|U|219
pMakeNodesJunction: first branch starts at   5J7L|1|AA|G|144
pMakeNodesJunction: first branch ends around 5J7L|1|AA|C|178
pMakeNodesJunction: second branch starts at  5J7L|1|AA|A|179
pMakeNodesJunction: junction ends at         5J7L|1|AA|U|219
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|AA|G|144
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|AA|C|178
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|AA|G|184
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|AA|U|219

Junction with 2 loops, call it J8147
Actual Branch 1 of junction J8147 - Nucleotides 5J7L|1|AA|G|144 to 5J7L|1|AA|C|178, length   2
Actual Branch 2 of junction J8147 - Nucleotides 5J7L|1|AA|A|179 to 5J7L|1|AA|U|219, length  12
  4 Junction

2B Branch 1 of 2 of junction J8147 - Nucleotides   144 to   178, length   2
pMakeNodes starting loop:     a=5J7L|1|AA|G|144 B=5J7L|1|AA|C|178
  6 Basepair   144  178 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J8147 - Nucleotides   179 to   219, length  12
pMakeNodes starting loop:     a=5J7L|1|AA|A|179 B=5J7L|1|AA|U|219
  8 Initial    179 (0 insertion) and  219 (0 insertion)
pMakeNodesJunction: a=5J7L|1|AA|A|179 r=5J7L|1|AA|A|179 s=5J7L|1|AA|A|196 t=5J7L|1|AA|A|197 u=B=5J7L|1|AA|U|219
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|AA|A|179 and 5J7L|1|AA|A|196 and between 5J7L|1|AA|A|197 and 5J7L|1|AA|U|219
pMakeNodesJunction: about to make a junction: a=5J7L|1|AA|A|179 s=5J7L|1|AA|A|196 t=5J7L|1|AA|A|197 B=5J7L|1|AA|U|219
pMakeNodesJunction: first branch starts at   5J7L|1|AA|A|179
pMakeNodesJunction: first branch ends around 5J7L|1|AA|A|196
pMakeNodesJunction: second branch starts at  5J7L|1|AA|A|197
pMakeNodesJunction: junction ends at         5J7L|1|AA|U|219
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|AA|G|184
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|AA|C|193
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|AA|G|198
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|AA|U|219

Junction with 2 loops, call it J9057
Actual Branch 1 of junction J9057 - Nucleotides 5J7L|1|AA|A|179 to 5J7L|1|AA|A|196, length   9
Actual Branch 2 of junction J9057 - Nucleotides 5J7L|1|AA|A|197 to 5J7L|1|AA|U|219, length   3
  9 Junction

2B Branch 1 of 2 of junction J9057 - Nucleotides   179 to   196, length   9
pMakeNodes starting loop:     a=5J7L|1|AA|A|179 B=5J7L|1|AA|A|196
 11 Basepair   179  196 AA tWH 
No need to probe because of interaction between a=5J7L|1|AA|U|180 B=5J7L|1|AA|A|195
 12 Basepair   180  195 UA tWH 
pMakeNodes probe for inserts:  a=5J7L|1|AA|A|181 B=5J7L|1|AA|C|194
    Insertion on left  5J7L|1|AA|A|181
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|A|182 interacts with 5J7L|1|AA|C|194
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|C|194 interacts with 5J7L|1|AA|A|182
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|C|194 interacts with 5J7L|1|AA|A|182
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|AA|A|182 B=5J7L|1|AA|C|194
 13 Basepair   182  194 AC tHW 
No need to probe because of interaction between a=5J7L|1|AA|G|184 B=5J7L|1|AA|C|193
 14 Basepair   184  193 GC cWW 
 15 Hairpin type *

2B Branch 2 of 2 of junction J9057 - Nucleotides   197 to   219, length   3
pMakeNodes starting loop:     a=5J7L|1|AA|A|197 B=5J7L|1|AA|U|219
    Insertion on left  5J7L|1|AA|A|197
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|G|198 interacts with 5J7L|1|AA|U|219
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|U|219 interacts with 5J7L|1|AA|G|198
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|U|219 interacts with 5J7L|1|AA|G|198
 16 Initial    197 (1 insertion) and  219 (0 insertion)
 17 Basepair   198  219 GU cWW 
 18 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  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  15   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  16   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  17  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  18   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|181
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|196
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: []
           numbranches: []
              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 G142 - C221 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A143 - G220 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]
           numbranches: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: 'J8147'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G144 - U219 ID J8147'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J8147'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             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 G144 - C178 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 7

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: []
           numbranches: []
              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: 16
             Insertion: []
                    id: 'J8147'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|AA|A|179 - 5J7L|1|AA|U|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 16]
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: 'J9057'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A179 - U219 ID J9057'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: 'J9057'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             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 A179 - A196 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]
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             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: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U180 - A195 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]
           numbranches: []
              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 5J7L|1|AA|A|181'
              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]
           numbranches: []
              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: '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]
           numbranches: []
              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: 'C'
               Comment: ' // Basepair A182 - C194 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]
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G184 - C193 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: 'J9057'
        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|AA|A|197 - 5J7L|1|AA|U|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             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 5J7L|1|AA|A|196'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G198 - U219 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 12
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
pMakeMotifModelFromSSF:  18   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  19     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  20   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  21  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  22   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J8147'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: 'J8147'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|AA|A|179 - 5J7L|1|AA|U|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_01665.1. Nodes 5 and 8 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: 'J9057'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: 'J9057'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|AA|A|197 - 5J7L|1|AA|U|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_01665.1. Nodes 10 and 18 both model an insertion before position 14. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 13
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 13 and 18
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 14 and 17
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 13
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 13 and 18
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 14 and 17
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_01665.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.3190

Timestamp 18-Jul-2025 00:12:42
pMakeSCFGModels: Making JAR3D model for motif group J4_04237.1, number 2 of 65
pMakeNodes starting loop:     a=4WSM|1|1K|G|7 B=4WSM|1|1K|C|77
  2 Basepair     7   77 GC cWW 
pMakeNodes probe for inserts:  a=4WSM|1|1K|U|8 B=4WSM|1|1K|U|76
pMakeNodes probed for insert:  a=4WSM|1|1K|U|8 B=4WSM|1|1K|U|76
pMakeNodesJunction: a=4WSM|1|1K|U|8 r=4WSM|1|1K|U|8 s=4WSM|1|1K|U|45 t=4WSM|1|1K|G|46 u=B=4WSM|1|1K|U|76
pMakeNodesJunction: a:s count 4
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4WSM|1|1K|U|8 and 4WSM|1|1K|U|45 and between 4WSM|1|1K|G|46 and 4WSM|1|1K|U|76
pMakeNodesJunction: about to make a junction: a=4WSM|1|1K|U|8 s=4WSM|1|1K|U|45 t=4WSM|1|1K|G|46 B=4WSM|1|1K|U|76
pMakeNodesJunction: first branch starts at   4WSM|1|1K|U|8
pMakeNodesJunction: first branch ends around 4WSM|1|1K|U|45
pMakeNodesJunction: second branch starts at  4WSM|1|1K|G|46
pMakeNodesJunction: junction ends at         4WSM|1|1K|U|76
pMakeNodesJunction: first branch strand start goes up to  4WSM|1|1K|G|13
pMakeNodesJunction: first branch strand end goes down to  4WSM|1|1K|G|44
pMakeNodesJunction: second branch strand start goes up to 4WSM|1|1K|G|46
pMakeNodesJunction: last strand of junction goes down to  4WSM|1|1K|U|76

Junction with 2 loops, call it J1269
Actual Branch 1 of junction J1269 - Nucleotides 4WSM|1|1K|U|8 to 4WSM|1|1K|U|45, length  21
Actual Branch 2 of junction J1269 - Nucleotides 4WSM|1|1K|G|46 to 4WSM|1|1K|U|76, length   6
  3 Junction

2B Branch 1 of 2 of junction J1269 - Nucleotides     8 to    45, length  21
pMakeNodes starting loop:     a=4WSM|1|1K|U|8 B=4WSM|1|1K|U|45
pMakeNodesProbeForInsertions:  a 4WSM|1|1K|U|8 interacts with 4WSM|1|1K|G|22
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|45 interacts with 4WSM|1|1K|G|27
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|45 interacts with 4WSM|1|1K|G|27
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial      8 (0 insertion) and   45 (0 insertion)
pMakeNodes making a cluster near strand break a=4WSM|1|1K|U|8 B=4WSM|1|1K|U|45
pMakeNodesCluster: amax is 20 bmin is 21, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 19 and then 22 to 22
aa is 19 bb is 22
  5 Cluster   4WSM|1|1K|U|8:4WSM|1|1K|G|27 4WSM|1|1K|U|45:4WSM|1|1K|U|45
    LR Inter  4WSM|1|1K|G|27 4WSM|1|1K|U|45 tWW 
    LL Inter  4WSM|1|1K|G|9 4WSM|1|1K|G|12 cWH 
    LL Inter  4WSM|1|1K|U|8 4WSM|1|1K|A|14 tWH 
    LL Inter  4WSM|1|1K|U|8 4WSM|1|1K|G|22 tSS 
    LL Inter  4WSM|1|1K|U|11 4WSM|1|1K|A|25 cWW 
    Left  strand conserved insertion 4WSM|1|1K|G|10 at position 3
    Left  strand conserved insertion 4WSM|1|1K|G|13 at position 6
    Left  strand conserved insertion 4WSM|1|1K|A|15 at position 8
    Left  strand conserved insertion 4WSM|1|1K|U|16 at position 9
    Left  strand conserved insertion 4WSM|1|1K|G|19 at position 10
    Left  strand conserved insertion 4WSM|1|1K|U|20 at position 11
    Left  strand conserved insertion 4WSM|1|1K|A|21 at position 12
    Left  strand conserved insertion 4WSM|1|1K|A|23 at position 14
    Left  strand conserved insertion 4WSM|1|1K|C|24 at position 15
    Left  strand conserved insertion 4WSM|1|1K|C|26 at position 17
pMakeNodesCluster a=20 B=21 at the end
pMakeNodesCluster a=20 B=21 at the end
No need to probe because of interaction between a=4WSM|1|1K|C|28 B=4WSM|1|1K|G|44
  6 Basepair    28   44 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1269 - Nucleotides    46 to    76, length   6
pMakeNodes starting loop:     a=4WSM|1|1K|G|46 B=4WSM|1|1K|U|76
  8 Initial     46 (0 insertion) and   76 (0 insertion)
pMakeNodesJunction: a=4WSM|1|1K|G|46 r=4WSM|1|1K|G|46 s=4WSM|1|1K|C|57 t=4WSM|1|1K|U|58 u=B=4WSM|1|1K|U|76
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WSM|1|1K|G|46 and 4WSM|1|1K|C|57 and between 4WSM|1|1K|U|58 and 4WSM|1|1K|U|76
pMakeNodesJunction: about to make a junction: a=4WSM|1|1K|G|46 s=4WSM|1|1K|C|57 t=4WSM|1|1K|U|58 B=4WSM|1|1K|U|76
pMakeNodesJunction: first branch starts at   4WSM|1|1K|G|46
pMakeNodesJunction: first branch ends around 4WSM|1|1K|C|57
pMakeNodesJunction: second branch starts at  4WSM|1|1K|U|58
pMakeNodesJunction: junction ends at         4WSM|1|1K|U|76
pMakeNodesJunction: first branch strand start goes up to  4WSM|1|1K|G|46
pMakeNodesJunction: first branch strand end goes down to  4WSM|1|1K|C|57
pMakeNodesJunction: second branch strand start goes up to 4WSM|1|1K|A|60
pMakeNodesJunction: last strand of junction goes down to  4WSM|1|1K|U|76

Junction with 2 loops, call it J9133
Actual Branch 1 of junction J9133 - Nucleotides 4WSM|1|1K|G|46 to 4WSM|1|1K|C|57, length   2
Actual Branch 2 of junction J9133 - Nucleotides 4WSM|1|1K|U|58 to 4WSM|1|1K|U|76, length   4
  9 Junction

2B Branch 1 of 2 of junction J9133 - Nucleotides    46 to    57, length   2
pMakeNodes starting loop:     a=4WSM|1|1K|G|46 B=4WSM|1|1K|C|57
 11 Basepair    46   57 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J9133 - Nucleotides    58 to    76, length   4
pMakeNodes starting loop:     a=4WSM|1|1K|U|58 B=4WSM|1|1K|U|76
    Insertion on left  4WSM|1|1K|U|58
    Insertion on left  4WSM|1|1K|U|59
pMakeNodesProbeForInsertions:  a 4WSM|1|1K|A|60 interacts with 4WSM|1|1K|U|76
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|76 interacts with 4WSM|1|1K|A|60
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|76 interacts with 4WSM|1|1K|A|60
 13 Initial     58 (2 insertion) and   76 (0 insertion)
 14 Basepair    60   76 AU cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 29
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 29
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 28
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 22
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 Right 22
pMakeMotifModelFromSSF:   6  Basepair Left 20 Right 21
pMakeMotifModelFromSSF:   7   Hairpin Left 21 Right 20
pMakeMotifModelFromSSF:   8   Initial Left 23 Right 28
pMakeMotifModelFromSSF:   9  Junction Left 23 Right 28
pMakeMotifModelFromSSF:  10   Initial Left 23 Right 24
pMakeMotifModelFromSSF:  11  Basepair Left 23 Right 24
pMakeMotifModelFromSSF:  12   Hairpin Left 24 Right 23
pMakeMotifModelFromSSF:  13   Initial Left 25 Right 28
pMakeMotifModelFromSSF:  14  Basepair Left 27 Right 28
pMakeMotifModelFromSSF:  15   Hairpin Left 28 Right 27
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WSM|1|1K|G|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WSM|1|1K|C|57
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: 29
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [29×29 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 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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: 29
             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 G7 - C77 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 2
            RightIndex: 28
             Insertion: []
                    id: 'J1269'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U8 - U76 ID J1269'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 22
             Insertion: []
                    id: 'J1269'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|U|8 - 4WSM|1|1K|U|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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 10 11 12 13 14 15 16 17 18 19]
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGUGGAAUGUAGACACG'
           RightLetter: 'U'
               Comment: ' // Cluster node 4WSM|1|1K|U|8:4WSM|1|1K|G|27 and 4WSM|1|1K|U|45:4WSM|1|1K|U|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×15 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 15 16 17 18]
                 Right: 1
      InsertionComment: []
                IBases: [15×2 double]
    InteractionComment: {1×15 cell}
      JunctionDeletion: []
          InterIndices: [15×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [3 6 8 9 10 11 12 14 15 17]
         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: 20
            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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 20
            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 C28 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 21
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 21
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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: 23
            RightIndex: 28
             Insertion: []
                    id: 'J1269'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|G|46 - 4WSM|1|1K|U|76 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 23
            RightIndex: 28
             Insertion: []
                    id: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G46 - U76 ID J9133'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 23
            RightIndex: 24
             Insertion: []
                    id: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 23
            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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G46 - C57 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 24
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 24
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 25
            RightIndex: 28
             Insertion: []
                    id: 'J9133'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|U|58 - 4WSM|1|1K|U|76 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 25
            RightIndex: 28
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WSM|1|1K|G|46'
              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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 26
            RightIndex: 28
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-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: 28
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 26
            RightIndex: 28
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WSM|1|1K|C|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 27
            RightIndex: 28
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 27
            RightIndex: 28
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 - U76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 28
            RightIndex: 27
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 28
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 29
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 29
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 28
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 22
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 Right 22
pMakeMotifModelFromSSF:   6   Initial Left 20 Right 21
pMakeMotifModelFromSSF:   7  Basepair Left 20 Right 21
pMakeMotifModelFromSSF:   8   Hairpin Left 21 Right 20
pMakeMotifModelFromSSF:   9   Initial Left 23 Right 28
pMakeMotifModelFromSSF:  10  Junction Left 23 Right 28
pMakeMotifModelFromSSF:  11   Initial Left 23 Right 24
pMakeMotifModelFromSSF:  12  Basepair Left 23 Right 24
pMakeMotifModelFromSSF:  13   Hairpin Left 24 Right 23
pMakeMotifModelFromSSF:  14   Initial Left 25 Right 28
pMakeMotifModelFromSSF:  15     Fixed Left 25 Right 28
pMakeMotifModelFromSSF:  16   Initial Left 26 Right 28
pMakeMotifModelFromSSF:  17     Fixed Left 26 Right 28
pMakeMotifModelFromSSF:  18   Initial Left 27 Right 28
pMakeMotifModelFromSSF:  19  Basepair Left 27 Right 28
pMakeMotifModelFromSSF:  20   Hairpin Left 28 Right 27
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 22
             Insertion: []
                    id: 'J1269'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|U|8 - 4WSM|1|1K|U|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 23
            RightIndex: 28
             Insertion: []
                    id: 'J1269'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|G|46 - 4WSM|1|1K|U|76 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_04237.1. Nodes 4 and 9 both model an insertion before position 23. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 23
            RightIndex: 24
             Insertion: []
                    id: 'J9133'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 25
            RightIndex: 28
             Insertion: []
                    id: 'J9133'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 4WSM|1|1K|U|58 - 4WSM|1|1K|U|76 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_04237.1. Nodes 11 and 14 both model an insertion before position 25. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_04237.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -21.1059

Timestamp 18-Jul-2025 00:12:43
pMakeSCFGModels: Making JAR3D model for motif group J4_04930.2, number 3 of 65
pMakeNodes starting loop:     a=4Y4O|1|2A|C|2285 B=4Y4O|1|2A|G|2383
  2 Basepair  2285 2383 CG cWW 
pMakeNodes probe for inserts:  a=4Y4O|1|2A|A|2286 B=4Y4O|1|2A|G|2382
    Insertion on left  4Y4O|1|2A|A|2286
    Insertion on right 4Y4O|1|2A|G|2382
pMakeNodes probed for insert:  a=4Y4O|1|2A|A|2287 B=4Y4O|1|2A|C|2381
pMakeNodesJunction: a=4Y4O|1|2A|A|2287 r=4Y4O|1|2A|A|2287 s=4Y4O|1|2A|U|2344 t=4Y4O|1|2A|G|2345 u=B=4Y4O|1|2A|C|2381
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|A|2287 and 4Y4O|1|2A|U|2344 and between 4Y4O|1|2A|G|2345 and 4Y4O|1|2A|C|2381
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|A|2287 s=4Y4O|1|2A|U|2344 t=4Y4O|1|2A|G|2345 B=4Y4O|1|2A|C|2381
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|A|2287
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|U|2344
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|G|2345
pMakeNodesJunction: junction ends at         4Y4O|1|2A|C|2381
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|G|2289
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|C|2343
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|C|2347
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|C|2381

Junction with 2 loops, call it J6323
Actual Branch 1 of junction J6323 - Nucleotides 4Y4O|1|2A|A|2287 to 4Y4O|1|2A|U|2344, length   4
Actual Branch 2 of junction J6323 - Nucleotides 4Y4O|1|2A|G|2345 to 4Y4O|1|2A|C|2381, length   7
  3 Junction

2B Branch 1 of 2 of junction J6323 - Nucleotides  2287 to  2344, length   4
pMakeNodes starting loop:     a=4Y4O|1|2A|A|2287 B=4Y4O|1|2A|U|2344
  5 Basepair  2287 2344 AU tWW 
No need to probe because of interaction between a=4Y4O|1|2A|G|2289 B=4Y4O|1|2A|C|2343
  6 Basepair  2289 2343 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J6323 - Nucleotides  2345 to  2381, length   7
pMakeNodes starting loop:     a=4Y4O|1|2A|G|2345 B=4Y4O|1|2A|C|2381
  8 Initial   2345 (0 insertion) and 2381 (0 insertion)
pMakeNodesJunction: a=4Y4O|1|2A|G|2345 r=4Y4O|1|2A|G|2345 s=4Y4O|1|2A|G|2371 t=4Y4O|1|2A|G|2372 u=B=4Y4O|1|2A|C|2381
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|G|2345 and 4Y4O|1|2A|G|2371 and between 4Y4O|1|2A|G|2372 and 4Y4O|1|2A|C|2381
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|G|2345 s=4Y4O|1|2A|G|2371 t=4Y4O|1|2A|G|2372 B=4Y4O|1|2A|C|2381
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|G|2345
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|G|2371
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|G|2372
pMakeNodesJunction: junction ends at         4Y4O|1|2A|C|2381
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|C|2347
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|G|2370
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|G|2372
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|C|2381

Junction with 2 loops, call it J975
Actual Branch 1 of junction J975 - Nucleotides 4Y4O|1|2A|G|2345 to 4Y4O|1|2A|G|2371, length   5
Actual Branch 2 of junction J975 - Nucleotides 4Y4O|1|2A|G|2372 to 4Y4O|1|2A|C|2381, length   2
  9 Junction

2B Branch 1 of 2 of junction J975 - Nucleotides  2345 to  2371, length   5
pMakeNodes starting loop:     a=4Y4O|1|2A|G|2345 B=4Y4O|1|2A|G|2371
 11 Basepair  2345 2371 GG cHW 
pMakeNodes probe for inserts:  a=4Y4O|1|2A|A|2346 B=4Y4O|1|2A|G|2370
    Insertion on left  4Y4O|1|2A|A|2346
pMakeNodesProbeForInsertions:  a 4Y4O|1|2A|C|2347 interacts with 4Y4O|1|2A|G|2370
pMakeNodesProbeForInsertions:  B 4Y4O|1|2A|G|2370 interacts with 4Y4O|1|2A|C|2347
pMakeNodesProbeForInsertions:  B 4Y4O|1|2A|G|2370 interacts with 4Y4O|1|2A|C|2347
pMakeNodes probed for insert:  a=4Y4O|1|2A|C|2347 B=4Y4O|1|2A|G|2370
 12 Basepair  2347 2370 CG cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J975 - Nucleotides  2372 to  2381, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|G|2372 B=4Y4O|1|2A|C|2381
 15 Basepair  2372 2381 GC cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 13
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
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 13
pMakeMotifModelFromSSF:   9  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  14   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  15  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  16   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 4Y4O|1|2A|A|2286
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|C|2381
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|G|2345
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: []
           numbranches: []
              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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'GG'
               Comment: ' // Basepair C2285 - G2383 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J6323'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y4O|1|2A|A|2286'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6323'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 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 4Y4O|1|2A|C|2381'
              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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             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: '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]
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: 'J6323'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2287 - C2381 ID J6323'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6323'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             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 A2287 - U2344 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]
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 G2289 - C2343 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

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: 'J6323'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|2345 - 4Y4O|1|2A|C|2381 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 14]
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J975'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2345 - C2381 ID J975'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J975'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 7
            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: 'GA'
           RightLetter: 'G'
               Comment: ' // Basepair G2345 - G2371 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]
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y4O|1|2A|G|2345'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             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 C2347 - G2370 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 19

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: []
           numbranches: []
              NormCons: 1

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J975'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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 G2372 - C2381 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  3 Right 13
pMakeMotifModelFromSSF:   7  Junction Left  3 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  13  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right 11
pMakeMotifModelFromSSF:  16     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  18  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  19   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  20   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  21  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  22   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J6323'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J6323'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|2345 - 4Y4O|1|2A|C|2381 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_04930.2. Nodes 8 and 12 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: 'J975'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J975'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_04930.2. Nodes 14 and 20 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_04930.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7931
   -8.4926
   -7.5389
   -7.5389
  -11.1306
  -10.7478

Timestamp 18-Jul-2025 00:12:44
pMakeSCFGModels: Making JAR3D model for motif group J4_07491.1, number 4 of 65
pMakeNodes starting loop:     a=4XNR|1|X|A|21 B=4XNR|1|X|U|75
  2 Basepair    21   75 AU cWW 
pMakeNodes probe for inserts:  a=4XNR|1|X|U|22 B=4XNR|1|X|U|74
    Insertion on left  4XNR|1|X|U|22
    Insertion on right 4XNR|1|X|U|74
    Insertion on right 4XNR|1|X|A|73
pMakeNodes probed for insert:  a=4XNR|1|X|A|23 B=4XNR|1|X|G|72
pMakeNodesJunction: a=4XNR|1|X|A|23 r=4XNR|1|X|A|23 s=4XNR|1|X|A|45 t=4XNR|1|X|G|46 u=B=4XNR|1|X|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4XNR|1|X|A|23 and 4XNR|1|X|A|45 and between 4XNR|1|X|G|46 and 4XNR|1|X|G|72
pMakeNodesJunction: about to make a junction: a=4XNR|1|X|A|23 s=4XNR|1|X|A|45 t=4XNR|1|X|G|46 B=4XNR|1|X|G|72
pMakeNodesJunction: first branch starts at   4XNR|1|X|A|23
pMakeNodesJunction: first branch ends around 4XNR|1|X|A|45
pMakeNodesJunction: second branch starts at  4XNR|1|X|G|46
pMakeNodesJunction: junction ends at         4XNR|1|X|G|72
pMakeNodesJunction: first branch strand start goes up to  4XNR|1|X|U|25
pMakeNodesJunction: first branch strand end goes down to  4XNR|1|X|A|45
pMakeNodesJunction: second branch strand start goes up to 4XNR|1|X|G|46
pMakeNodesJunction: last strand of junction goes down to  4XNR|1|X|G|72
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J2784
Actual Branch 1 of junction J2784 - Nucleotides 4XNR|1|X|A|23 to 4XNR|1|X|A|45, length   4
Actual Branch 2 of junction J2784 - Nucleotides 4XNR|1|X|G|46 to 4XNR|1|X|G|72, length   4
  3 Junction

2B Branch 1 of 2 of junction J2784 - Nucleotides    23 to    45, length   4
pMakeNodes starting loop:     a=4XNR|1|X|A|23 B=4XNR|1|X|A|45
    Insertion on left  4XNR|1|X|A|23
    Insertion on left  4XNR|1|X|A|24
pMakeNodesProbeForInsertions:  a 4XNR|1|X|U|25 interacts with 4XNR|1|X|A|45
pMakeNodesProbeForInsertions:  B 4XNR|1|X|A|45 interacts with 4XNR|1|X|U|25
pMakeNodesProbeForInsertions:  B 4XNR|1|X|A|45 interacts with 4XNR|1|X|U|25
  4 Initial     23 (2 insertion) and   45 (0 insertion)
  5 Basepair    25   45 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2784 - Nucleotides    46 to    72, length   4
pMakeNodes starting loop:     a=4XNR|1|X|G|46 B=4XNR|1|X|G|72
  7 Initial     46 (0 insertion) and   72 (0 insertion)
pMakeNodesJunction: a=4XNR|1|X|G|46 r=4XNR|1|X|G|46 s=4XNR|1|X|C|53 t=4XNR|1|X|C|54 u=B=4XNR|1|X|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4XNR|1|X|G|46 and 4XNR|1|X|C|53 and between 4XNR|1|X|C|54 and 4XNR|1|X|G|72
pMakeNodesJunction: about to make a junction: a=4XNR|1|X|G|46 s=4XNR|1|X|C|53 t=4XNR|1|X|C|54 B=4XNR|1|X|G|72
pMakeNodesJunction: first branch starts at   4XNR|1|X|G|46
pMakeNodesJunction: first branch ends around 4XNR|1|X|C|53
pMakeNodesJunction: second branch starts at  4XNR|1|X|C|54
pMakeNodesJunction: junction ends at         4XNR|1|X|G|72
pMakeNodesJunction: first branch strand start goes up to  4XNR|1|X|G|46
pMakeNodesJunction: first branch strand end goes down to  4XNR|1|X|C|53
pMakeNodesJunction: second branch strand start goes up to 4XNR|1|X|C|54
pMakeNodesJunction: last strand of junction goes down to  4XNR|1|X|G|72

Junction with 2 loops, call it J5468
Actual Branch 1 of junction J5468 - Nucleotides 4XNR|1|X|G|46 to 4XNR|1|X|C|53, length   2
Actual Branch 2 of junction J5468 - Nucleotides 4XNR|1|X|C|54 to 4XNR|1|X|G|72, length   2
  8 Junction

2B Branch 1 of 2 of junction J5468 - Nucleotides    46 to    53, length   2
pMakeNodes starting loop:     a=4XNR|1|X|G|46 B=4XNR|1|X|C|53
 10 Basepair    46   53 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J5468 - Nucleotides    54 to    72, length   2
pMakeNodes starting loop:     a=4XNR|1|X|C|54 B=4XNR|1|X|G|72
 13 Basepair    54   72 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  7 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XNR|1|X|U|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4XNR|1|X|U|74
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4XNR|1|X|A|73
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XNR|1|X|A|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XNR|1|X|A|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: 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: []
           numbranches: []
              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: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'AUU'
               Comment: ' // Basepair A21 - U75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J2784'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XNR|1|X|U|22'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2784'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4XNR|1|X|U|74'
              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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: 'J2784'
        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 4XNR|1|X|A|73'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J5468'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J2784'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A23 - G72 ID J2784'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J2784'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4XNR|1|X|A|23 - 4XNR|1|X|A|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             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 4XNR|1|X|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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: 'J5468'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             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 4XNR|1|X|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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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: 10
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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 U25 - 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]
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J2784'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4XNR|1|X|G|46 - 4XNR|1|X|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J5468'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G46 - G72 ID J5468'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J5468'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 G46 - 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]
           numbranches: []
              NormCons: []

Node 21

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: []
           numbranches: []
              NormCons: 1

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: 'J5468'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C54 - 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]
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 26
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   9  Junction Left  3 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  3 Right  6
pMakeMotifModelFromSSF:  11     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  4 Right  6
pMakeMotifModelFromSSF:  13     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:  14   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  15  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  16   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  17   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  18  Junction Left  7 Right 10
pMakeMotifModelFromSSF:  19   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  20  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  21   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  22   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  23  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  24   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J2784'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4XNR|1|X|A|23 - 4XNR|1|X|A|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J2784'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4XNR|1|X|G|46 - 4XNR|1|X|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_07491.1. Nodes 10 and 17 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J5468'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J5468'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_07491.1. Nodes 19 and 22 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWS  between 3 and 7
pConservedInteractionList: did not find a substitution probability matrix for tWS  between 3 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_07491.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9591
   -6.9591
   -5.8605
   -5.8605
   -6.4404
   -5.8605
   -6.4404
   -9.2938
   -9.2938

Timestamp 18-Jul-2025 00:12:44
pMakeSCFGModels: Making JAR3D model for motif group J4_10313.2, number 5 of 65
pMakeNodes starting loop:     a=4Y4O|1|2A|U|1313 B=4Y4O|1|2A|A|1603
  2 Basepair  1313 1603 UA cWW 
pMakeNodes probe for inserts:  a=4Y4O|1|2A|C|1314 B=4Y4O|1|2A|U|1602
    Insertion on right 4Y4O|1|2A|U|1602
    Insertion on right 4Y4O|1|2A|G|1601
    Insertion on right 4Y4O|1|2A|C|1600
    Insertion on right 4Y4O|1|2A|C|1599
    Insertion on right 4Y4O|1|2A|C|1598
pMakeNodes probed for insert:  a=4Y4O|1|2A|C|1314 B=4Y4O|1|2A|A|1597
pMakeNodesJunction: a=4Y4O|1|2A|C|1314 r=4Y4O|1|2A|C|1314 s=4Y4O|1|2A|G|1338 t=4Y4O|1|2A|G|1339 u=B=4Y4O|1|2A|A|1597
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|C|1314 and 4Y4O|1|2A|G|1338 and between 4Y4O|1|2A|G|1339 and 4Y4O|1|2A|A|1597
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|C|1314 s=4Y4O|1|2A|G|1338 t=4Y4O|1|2A|G|1339 B=4Y4O|1|2A|A|1597
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|C|1314
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|G|1338
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|G|1339
pMakeNodesJunction: junction ends at         4Y4O|1|2A|A|1597
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|C|1314
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|G|1338
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|G|1343
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|A|1597

Junction with 2 loops, call it J9575
Actual Branch 1 of junction J9575 - Nucleotides 4Y4O|1|2A|C|1314 to 4Y4O|1|2A|G|1338, length   2
Actual Branch 2 of junction J9575 - Nucleotides 4Y4O|1|2A|G|1339 to 4Y4O|1|2A|A|1597, length   7
  3 Junction

2B Branch 1 of 2 of junction J9575 - Nucleotides  1314 to  1338, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|C|1314 B=4Y4O|1|2A|G|1338
  5 Basepair  1314 1338 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9575 - Nucleotides  1339 to  1597, length   7
pMakeNodes starting loop:     a=4Y4O|1|2A|G|1339 B=4Y4O|1|2A|A|1597
    Insertion on left  4Y4O|1|2A|G|1339
    Insertion on left  4Y4O|1|2A|U|1340
    Insertion on left  4Y4O|1|2A|A|1342
  7 Initial   1339 (3 insertion) and 1597 (0 insertion)
pMakeNodesJunction: a=4Y4O|1|2A|G|1343 r=4Y4O|1|2A|G|1343 s=4Y4O|1|2A|C|1404 t=4Y4O|1|2A|U|1405 u=B=4Y4O|1|2A|A|1597
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|G|1343 and 4Y4O|1|2A|C|1404 and between 4Y4O|1|2A|U|1405 and 4Y4O|1|2A|A|1597
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|G|1343 s=4Y4O|1|2A|C|1404 t=4Y4O|1|2A|U|1405 B=4Y4O|1|2A|A|1597
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|G|1343
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|C|1404
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|U|1405
pMakeNodesJunction: junction ends at         4Y4O|1|2A|A|1597
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|G|1343
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|C|1404
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|U|1405
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|A|1597

Junction with 2 loops, call it J9648
Actual Branch 1 of junction J9648 - Nucleotides 4Y4O|1|2A|G|1343 to 4Y4O|1|2A|C|1404, length   2
Actual Branch 2 of junction J9648 - Nucleotides 4Y4O|1|2A|U|1405 to 4Y4O|1|2A|A|1597, length   2
  8 Junction

2B Branch 1 of 2 of junction J9648 - Nucleotides  1343 to  1404, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|G|1343 B=4Y4O|1|2A|C|1404
 10 Basepair  1343 1404 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9648 - Nucleotides  1405 to  1597, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|U|1405 B=4Y4O|1|2A|A|1597
 13 Basepair  1405 1597 UA cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  7 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|G|1601
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|C|1600
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|C|1599
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|C|1598
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|A|1597
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|G|1339
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|U|1340
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|U|1341
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 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: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
        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: 'U'
           RightLetter: 'CCCGUA'
               Comment: ' // Basepair U1313 - A1603 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J9575'
        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 4Y4O|1|2A|G|1601'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: 'J9575'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            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 4Y4O|1|2A|C|1600'
              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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            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: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: 'J9575'
        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 4Y4O|1|2A|C|1599'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: 'J9648'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: 'J9648'
        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 4Y4O|1|2A|C|1598'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 2
            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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 2
            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 4Y4O|1|2A|A|1597'
              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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              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: 'J9648'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: 'J9575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1314 - A1597 ID J9575'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J9575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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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: 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 C1314 - G1338 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J9575'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUA'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|1339 - 4Y4O|1|2A|A|1597 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 4Y4O|1|2A|G|1339'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 4Y4O|1|2A|U|1340'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 4Y4O|1|2A|U|1341'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             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: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J9648'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1343 - A1597 ID J9648'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J9648'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 27
             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 G1343 - C1404 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: []
           numbranches: []
              NormCons: 1

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9648'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 30
             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 U1405 - A1597 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 32
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  2 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  2 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  2 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  2 Right 10
pMakeMotifModelFromSSF:  13  Junction Left  2 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  2 Right  3
pMakeMotifModelFromSSF:  15  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:  16   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:  17   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  18     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:  19   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  20     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  21   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  22     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  23   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  24  Junction Left  7 Right 10
pMakeMotifModelFromSSF:  25   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  26  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  27   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  28   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  29  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  30   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 24
pNextNodeJunction: Found a junction child at node 25
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a junction child at node 28
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J9575'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J9575'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUA'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|1339 - 4Y4O|1|2A|A|1597 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10313.2. Nodes 14 and 17 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J9648'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9648'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10313.2. Nodes 25 and 28 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 24
pNextNodeJunction: Found a junction child at node 25
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a junction child at node 28
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 6 and 15
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 6 and 15
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_10313.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2549
   -8.2049
   -9.0522
  -10.1508
  -11.0481

Timestamp 18-Jul-2025 00:12:45
pMakeSCFGModels: Making JAR3D model for motif group J4_10408.3, number 6 of 65
pMakeNodes starting loop:     a=6OF1|1|1w|G|5 B=6OF1|1|1w|C|68
  2 Basepair     5   68 GC cWW 
pMakeNodes probe for inserts:  a=6OF1|1|1w|A|6 B=6OF1|1|1w|A|66
    Insertion on left  6OF1|1|1w|A|6
    Insertion on left  6OF1|1|1w|A|9
    Insertion on right 6OF1|1|1w|A|66
pMakeNodes probed for insert:  a=6OF1|1|1w|G|10 B=6OF1|1|1w|C|65
pMakeNodesJunction: a=6OF1|1|1w|G|10 r=6OF1|1|1w|G|10 s=6OF1|1|1w|C|25 t=6OF1|1|1w|A|26 u=B=6OF1|1|1w|C|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6OF1|1|1w|G|10 and 6OF1|1|1w|C|25 and between 6OF1|1|1w|A|26 and 6OF1|1|1w|C|65
pMakeNodesJunction: about to make a junction: a=6OF1|1|1w|G|10 s=6OF1|1|1w|C|25 t=6OF1|1|1w|A|26 B=6OF1|1|1w|C|65
pMakeNodesJunction: first branch starts at   6OF1|1|1w|G|10
pMakeNodesJunction: first branch ends around 6OF1|1|1w|C|25
pMakeNodesJunction: second branch starts at  6OF1|1|1w|A|26
pMakeNodesJunction: junction ends at         6OF1|1|1w|C|65
pMakeNodesJunction: first branch strand start goes up to  6OF1|1|1w|G|10
pMakeNodesJunction: first branch strand end goes down to  6OF1|1|1w|C|25
pMakeNodesJunction: second branch strand start goes up to 6OF1|1|1w|C|27
pMakeNodesJunction: last strand of junction goes down to  6OF1|1|1w|C|65

Junction with 2 loops, call it J1576
Actual Branch 1 of junction J1576 - Nucleotides 6OF1|1|1w|G|10 to 6OF1|1|1w|C|25, length   2
Actual Branch 2 of junction J1576 - Nucleotides 6OF1|1|1w|A|26 to 6OF1|1|1w|C|65, length   8
  3 Junction

2B Branch 1 of 2 of junction J1576 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=6OF1|1|1w|G|10 B=6OF1|1|1w|C|25
  5 Basepair    10   25 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1576 - Nucleotides    26 to    65, length   8
pMakeNodes starting loop:     a=6OF1|1|1w|A|26 B=6OF1|1|1w|C|65
  7 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=6OF1|1|1w|A|26 r=6OF1|1|1w|A|26 s=6OF1|1|1w|G|44 t=6OF1|1|1w|G|45 u=B=6OF1|1|1w|C|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6OF1|1|1w|A|26 and 6OF1|1|1w|G|44 and between 6OF1|1|1w|G|45 and 6OF1|1|1w|C|65
pMakeNodesJunction: about to make a junction: a=6OF1|1|1w|A|26 s=6OF1|1|1w|G|44 t=6OF1|1|1w|G|45 B=6OF1|1|1w|C|65
pMakeNodesJunction: first branch starts at   6OF1|1|1w|A|26
pMakeNodesJunction: first branch ends around 6OF1|1|1w|G|44
pMakeNodesJunction: second branch starts at  6OF1|1|1w|G|45
pMakeNodesJunction: junction ends at         6OF1|1|1w|C|65
pMakeNodesJunction: first branch strand start goes up to  6OF1|1|1w|C|27
pMakeNodesJunction: first branch strand end goes down to  6OF1|1|1w|G|43
pMakeNodesJunction: second branch strand start goes up to 6OF1|1|1w|G|49
pMakeNodesJunction: last strand of junction goes down to  6OF1|1|1w|C|65

Junction with 2 loops, call it J9705
Actual Branch 1 of junction J9705 - Nucleotides 6OF1|1|1w|A|26 to 6OF1|1|1w|G|44, length   4
Actual Branch 2 of junction J9705 - Nucleotides 6OF1|1|1w|G|45 to 6OF1|1|1w|C|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J9705 - Nucleotides    26 to    44, length   4
pMakeNodes starting loop:     a=6OF1|1|1w|A|26 B=6OF1|1|1w|G|44
 10 Basepair    26   44 AG cWW 
No need to probe because of interaction between a=6OF1|1|1w|C|27 B=6OF1|1|1w|G|43
 11 Basepair    27   43 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J9705 - Nucleotides    45 to    65, length   4
pMakeNodes starting loop:     a=6OF1|1|1w|G|45 B=6OF1|1|1w|C|65
    Insertion on left  6OF1|1|1w|G|45
    Insertion on left  6OF1|1|1w|7MG|46
pMakeNodesProbeForInsertions:  a 6OF1|1|1w|G|49 interacts with 6OF1|1|1w|C|65
pMakeNodesProbeForInsertions:  B 6OF1|1|1w|C|65 interacts with 6OF1|1|1w|G|49
pMakeNodesProbeForInsertions:  B 6OF1|1|1w|C|65 interacts with 6OF1|1|1w|G|49
 13 Initial     45 (2 insertion) and   65 (0 insertion)
 14 Basepair    49   65 GC cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 13
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
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  14  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  15   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OF1|1|1w|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OF1|1|1w|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6OF1|1|1w|U|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OF1|1|1w|G|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OF1|1|1w|G|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: 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: []
           numbranches: []
              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: [0.0082 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 G5 - 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]
           numbranches: []
              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: 'J1576'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OF1|1|1w|A|6'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1576'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 6OF1|1|1w|U|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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 14
             Insertion: []
                    id: 'J1576'
        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 6OF1|1|1w|U|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J9705'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J1576'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - C65 ID J1576'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J1576'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             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 - 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]
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             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: []
           numbranches: []
              NormCons: 1

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: 'J1576'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6OF1|1|1w|A|26 - 6OF1|1|1w|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J9705'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A26 - C65 ID J9705'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J9705'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A26 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: '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]
           numbranches: []
              NormCons: []

Node 18

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: []
           numbranches: []
              NormCons: 1

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: 'J9705'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 6OF1|1|1w|G|45 - 6OF1|1|1w|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OF1|1|1w|G|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 6OF1|1|1w|G|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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 G49 - C65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  4 Right 13
pMakeMotifModelFromSSF:   9  Junction Left  4 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  12   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  13   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  14  Junction Left  6 Right 13
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
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  20     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  23   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J1576'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J1576'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6OF1|1|1w|A|26 - 6OF1|1|1w|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10408.3. Nodes 10 and 13 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J9705'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J9705'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 6OF1|1|1w|G|45 - 6OF1|1|1w|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10408.3. Nodes 15 and 19 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 4 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 4 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_10408.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.5459
  -15.1894

Timestamp 18-Jul-2025 00:12:45
pMakeSCFGModels: Making JAR3D model for motif group J4_10571.1, number 7 of 65
pMakeNodes starting loop:     a=2ZNI|1|C|U|7 B=2ZNI|1|C|A|66
  2 Basepair     7   66 UA cWW 
pMakeNodes probe for inserts:  a=2ZNI|1|C|G|10 B=2ZNI|1|C|U|65
pMakeNodes probed for insert:  a=2ZNI|1|C|G|10 B=2ZNI|1|C|U|65
pMakeNodesJunction: a=2ZNI|1|C|G|10 r=2ZNI|1|C|G|10 s=2ZNI|1|C|C|24 t=2ZNI|1|C|A|25 u=B=2ZNI|1|C|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 2ZNI|1|C|G|10 and 2ZNI|1|C|C|24 and between 2ZNI|1|C|A|25 and 2ZNI|1|C|U|65
pMakeNodesJunction: about to make a junction: a=2ZNI|1|C|G|10 s=2ZNI|1|C|C|24 t=2ZNI|1|C|A|25 B=2ZNI|1|C|U|65
pMakeNodesJunction: first branch starts at   2ZNI|1|C|G|10
pMakeNodesJunction: first branch ends around 2ZNI|1|C|C|24
pMakeNodesJunction: second branch starts at  2ZNI|1|C|A|25
pMakeNodesJunction: junction ends at         2ZNI|1|C|U|65
pMakeNodesJunction: first branch strand start goes up to  2ZNI|1|C|G|10
pMakeNodesJunction: first branch strand end goes down to  2ZNI|1|C|C|24
pMakeNodesJunction: second branch strand start goes up to 2ZNI|1|C|C|26
pMakeNodesJunction: last strand of junction goes down to  2ZNI|1|C|U|65

Junction with 2 loops, call it J9571
Actual Branch 1 of junction J9571 - Nucleotides 2ZNI|1|C|G|10 to 2ZNI|1|C|C|24, length   2
Actual Branch 2 of junction J9571 - Nucleotides 2ZNI|1|C|A|25 to 2ZNI|1|C|U|65, length   8
  3 Junction

2B Branch 1 of 2 of junction J9571 - Nucleotides    10 to    24, length   2
pMakeNodes starting loop:     a=2ZNI|1|C|G|10 B=2ZNI|1|C|C|24
  5 Basepair    10   24 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9571 - Nucleotides    25 to    65, length   8
pMakeNodes starting loop:     a=2ZNI|1|C|A|25 B=2ZNI|1|C|U|65
  7 Initial     25 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=2ZNI|1|C|A|25 r=2ZNI|1|C|A|25 s=2ZNI|1|C|C|45 t=2ZNI|1|C|A|46 u=B=2ZNI|1|C|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2ZNI|1|C|A|25 and 2ZNI|1|C|C|45 and between 2ZNI|1|C|A|46 and 2ZNI|1|C|U|65
pMakeNodesJunction: about to make a junction: a=2ZNI|1|C|A|25 s=2ZNI|1|C|C|45 t=2ZNI|1|C|A|46 B=2ZNI|1|C|U|65
pMakeNodesJunction: first branch starts at   2ZNI|1|C|A|25
pMakeNodesJunction: first branch ends around 2ZNI|1|C|C|45
pMakeNodesJunction: second branch starts at  2ZNI|1|C|A|46
pMakeNodesJunction: junction ends at         2ZNI|1|C|U|65
pMakeNodesJunction: first branch strand start goes up to  2ZNI|1|C|C|26
pMakeNodesJunction: first branch strand end goes down to  2ZNI|1|C|G|44
pMakeNodesJunction: second branch strand start goes up to 2ZNI|1|C|G|49
pMakeNodesJunction: last strand of junction goes down to  2ZNI|1|C|U|65

Junction with 2 loops, call it J4853
Actual Branch 1 of junction J4853 - Nucleotides 2ZNI|1|C|A|25 to 2ZNI|1|C|C|45, length   4
Actual Branch 2 of junction J4853 - Nucleotides 2ZNI|1|C|A|46 to 2ZNI|1|C|U|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J4853 - Nucleotides    25 to    45, length   4
pMakeNodes starting loop:     a=2ZNI|1|C|A|25 B=2ZNI|1|C|C|45
 10 Basepair    25   45 AC cWW 
No need to probe because of interaction between a=2ZNI|1|C|C|26 B=2ZNI|1|C|G|44
 11 Basepair    26   44 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J4853 - Nucleotides    46 to    65, length   4
pMakeNodes starting loop:     a=2ZNI|1|C|A|46 B=2ZNI|1|C|U|65
    Insertion on left  2ZNI|1|C|A|46
    Insertion on left  2ZNI|1|C|G|47
pMakeNodesProbeForInsertions:  a 2ZNI|1|C|G|49 interacts with 2ZNI|1|C|U|65
pMakeNodesProbeForInsertions:  B 2ZNI|1|C|U|65 interacts with 2ZNI|1|C|G|49
pMakeNodesProbeForInsertions:  B 2ZNI|1|C|U|65 interacts with 2ZNI|1|C|G|49
 13 Initial     46 (2 insertion) and   65 (0 insertion)
 14 Basepair    49   65 GU cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ZNI|1|C|C|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ZNI|1|C|A|46
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: 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: []
           numbranches: []
              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: 'A'
               Comment: ' // Basepair U7 - A66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: 'J9571'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - U65 ID J9571'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J9571'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G10 - 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 11
             Insertion: []
                    id: 'J9571'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2ZNI|1|C|A|25 - 2ZNI|1|C|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J4853'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A25 - U65 ID J4853'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J4853'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 A25 - 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]
           numbranches: []
              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 C26 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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: 'J4853'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 2ZNI|1|C|A|46 - 2ZNI|1|C|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 2ZNI|1|C|C|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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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 2ZNI|1|C|A|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G49 - U65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 19

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
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 junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J9571'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J9571'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2ZNI|1|C|A|25 - 2ZNI|1|C|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10571.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J4853'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J4853'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 2ZNI|1|C|A|46 - 2ZNI|1|C|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_10571.1. Nodes 9 and 13 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_10571.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.1255

Timestamp 18-Jul-2025 00:12:45
pMakeSCFGModels: Making JAR3D model for motif group J4_11418.1, number 8 of 65
pMakeNodes starting loop:     a=4V9F|1|0|A|302 B=4V9F|1|0|U|349
  2 Basepair   302  349 AU cWW 
No need to probe because of interaction between a=4V9F|1|0|C|303 B=4V9F|1|0|C|348
  3 Basepair   303  348 CC bif 
No need to probe because of interaction between a=4V9F|1|0|G|304 B=4V9F|1|0|A|347
  4 Basepair   304  347 GA tSH 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|305 B=4V9F|1|0|U|346
    Insertion on right 4V9F|1|0|U|346
pMakeNodes probed for insert:  a=4V9F|1|0|A|305 B=4V9F|1|0|G|345
pMakeNodes making a cluster near strand break a=4V9F|1|0|A|305 B=4V9F|1|0|G|345
pMakeNodesCluster: amax is 5 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 15 to 15
aa is 5 bb is 15
  5 Cluster   4V9F|1|0|A|305:4V9F|1|0|A|306 4V9F|1|0|G|345:4V9F|1|0|G|345
    LR Inter  4V9F|1|0|A|305 4V9F|1|0|G|345 cHH 
    LR Inter  4V9F|1|0|A|306 4V9F|1|0|G|345 wat 
pMakeNodesCluster a=6 B=14 at the end
pMakeNodesCluster a=6 B=14 at the end
pMakeNodes probe for inserts:  a=4V9F|1|0|G|307 B=4V9F|1|0|C|344
  6 Initial    307 (0 insertion) and  344 (0 insertion)
pMakeNodes probed for insert:  a=4V9F|1|0|G|307 B=4V9F|1|0|C|344
pMakeNodesJunction: a=4V9F|1|0|G|307 r=4V9F|1|0|G|307 s=4V9F|1|0|C|323 t=4V9F|1|0|G|324 u=B=4V9F|1|0|C|344
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|307 and 4V9F|1|0|C|323 and between 4V9F|1|0|G|324 and 4V9F|1|0|C|344
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|307 s=4V9F|1|0|C|323 t=4V9F|1|0|G|324 B=4V9F|1|0|C|344
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|307
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|323
pMakeNodesJunction: second branch starts at  4V9F|1|0|G|324
pMakeNodesJunction: junction ends at         4V9F|1|0|C|344
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|307
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|323
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|326
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|344

Junction with 2 loops, call it J8002
Actual Branch 1 of junction J8002 - Nucleotides 4V9F|1|0|G|307 to 4V9F|1|0|C|323, length   2
Actual Branch 2 of junction J8002 - Nucleotides 4V9F|1|0|G|324 to 4V9F|1|0|C|344, length   7
  7 Junction

2B Branch 1 of 2 of junction J8002 - Nucleotides   307 to   323, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|307 B=4V9F|1|0|C|323
  9 Basepair   307  323 GC cWW 
 10 Hairpin type *

2B Branch 2 of 2 of junction J8002 - Nucleotides   324 to   344, length   7
pMakeNodes starting loop:     a=4V9F|1|0|G|324 B=4V9F|1|0|C|344
    Insertion on left  4V9F|1|0|G|324
    Insertion on left  4V9F|1|0|U|325
 11 Initial    324 (2 insertion) and  344 (0 insertion)
pMakeNodesJunction: a=4V9F|1|0|G|326 r=4V9F|1|0|G|326 s=4V9F|1|0|C|330 t=4V9F|1|0|A|331 u=B=4V9F|1|0|C|344
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|326 and 4V9F|1|0|C|330 and between 4V9F|1|0|A|331 and 4V9F|1|0|C|344
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|326 s=4V9F|1|0|C|330 t=4V9F|1|0|A|331 B=4V9F|1|0|C|344
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|326
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|330
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|331
pMakeNodesJunction: junction ends at         4V9F|1|0|C|344
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|326
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|330
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|332
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|344

Junction with 2 loops, call it J1418
Actual Branch 1 of junction J1418 - Nucleotides 4V9F|1|0|G|326 to 4V9F|1|0|C|330, length   2
Actual Branch 2 of junction J1418 - Nucleotides 4V9F|1|0|A|331 to 4V9F|1|0|C|344, length   3
 12 Junction

2B Branch 1 of 2 of junction J1418 - Nucleotides   326 to   330, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|326 B=4V9F|1|0|C|330
 14 Basepair   326  330 GC cWW 
 15 Hairpin type *

2B Branch 2 of 2 of junction J1418 - Nucleotides   331 to   344, length   3
pMakeNodes starting loop:     a=4V9F|1|0|A|331 B=4V9F|1|0|C|344
    Insertion on left  4V9F|1|0|A|331
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|332 interacts with 4V9F|1|0|C|344
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|344 interacts with 4V9F|1|0|G|332
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|344 interacts with 4V9F|1|0|G|332
 16 Initial    331 (1 insertion) and  344 (0 insertion)
 17 Basepair   332  344 GC cWW 
 18 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 18
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 17
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   7  Junction Left  6 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  11   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  12  Junction Left 10 Right 14
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  16   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  17  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  18   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|U|346
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|324
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|325
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|331
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: 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: []
           numbranches: []

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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 A302 - U349 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            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: 'C'
               Comment: ' // Basepair C303 - C348 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: []
           numbranches: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             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: 'UA'
               Comment: ' // Basepair G304 - A347 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: []
           numbranches: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            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|U|346'
              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: 0.7799
           numbranches: []

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5]
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'G'
               Comment: ' // Cluster node 4V9F|1|0|A|305:4V9F|1|0|A|306 and 4V9F|1|0|G|345:4V9F|1|0|G|345'
              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: 0.7799
           numbranches: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 14
             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|0|G|307 - 4V9F|1|0|C|344 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [8 11]
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J8002'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G307 - C344 ID J8002'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

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: 'J8002'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 G307 - C323 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 12

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
           numbranches: []

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: 'J8002'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|324 - 4V9F|1|0|C|344 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 4V9F|1|0|G|324'
              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: []
           numbranches: []

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: [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
           numbranches: []

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: 'J1418'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|325'
              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: []
           numbranches: []

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: '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: []
           numbranches: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [13 16]
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: 'J1418'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G326 - C344 ID J1418'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J1418'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 G326 - C330 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 21

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: 'J1418'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|331 - 4V9F|1|0|C|344 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 12
            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 4V9F|1|0|A|331'
              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: []
           numbranches: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             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 G332 - C344 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 18
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   7   Cluster Left  4  5 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   9  Junction Left  6 Right 14
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
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  Junction Left 10 Right 14
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  20  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  21   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  23     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  24   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  25  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  26   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J8002'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J8002'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|324 - 4V9F|1|0|C|344 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_11418.1. Nodes 10 and 13 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J1418'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: 'J1418'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|331 - 4V9F|1|0|C|344 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_11418.1. Nodes 19 and 22 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHS  between 12 and 15
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 12 and 15
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_11418.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9234

Timestamp 18-Jul-2025 00:12:46
pMakeSCFGModels: Making JAR3D model for motif group J4_12209.1, number 9 of 65
pMakeNodes starting loop:     a=1U9S|1|A|C|119 B=1U9S|1|A|G|222
  2 Basepair   119  222 CG cWW 
pMakeNodes probe for inserts:  a=1U9S|1|A|A|120 B=1U9S|1|A|C|221
    Insertion on right 1U9S|1|A|C|221
pMakeNodes probed for insert:  a=1U9S|1|A|A|120 B=1U9S|1|A|C|219
pMakeNodesJunction: a=1U9S|1|A|A|120 r=1U9S|1|A|A|120 s=1U9S|1|A|A|174 t=1U9S|1|A|C|175 u=B=1U9S|1|A|C|219
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 1U9S|1|A|A|120 and 1U9S|1|A|A|174 and between 1U9S|1|A|C|175 and 1U9S|1|A|C|219
pMakeNodesJunction: about to make a junction: a=1U9S|1|A|A|120 s=1U9S|1|A|A|174 t=1U9S|1|A|C|175 B=1U9S|1|A|C|219
pMakeNodesJunction: first branch starts at   1U9S|1|A|A|120
pMakeNodesJunction: first branch ends around 1U9S|1|A|A|174
pMakeNodesJunction: second branch starts at  1U9S|1|A|C|175
pMakeNodesJunction: junction ends at         1U9S|1|A|C|219
pMakeNodesJunction: first branch strand start goes up to  1U9S|1|A|G|125
pMakeNodesJunction: first branch strand end goes down to  1U9S|1|A|G|169
pMakeNodesJunction: second branch strand start goes up to 1U9S|1|A|G|176
pMakeNodesJunction: last strand of junction goes down to  1U9S|1|A|C|219

Junction with 2 loops, call it J4217
Actual Branch 1 of junction J4217 - Nucleotides 1U9S|1|A|A|120 to 1U9S|1|A|A|174, length  19
Actual Branch 2 of junction J4217 - Nucleotides 1U9S|1|A|C|175 to 1U9S|1|A|C|219, length   5
  3 Junction

2B Branch 1 of 2 of junction J4217 - Nucleotides   120 to   174, length  19
pMakeNodes starting loop:     a=1U9S|1|A|A|120 B=1U9S|1|A|A|174
pMakeNodesProbeForInsertions:  a 1U9S|1|A|A|120 interacts with 1U9S|1|A|A|172
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|174 interacts with 1U9S|1|A|G|123
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|174 interacts with 1U9S|1|A|U|170
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial    120 (0 insertion) and  174 (0 insertion)
pMakeNodes making a cluster near strand break a=1U9S|1|A|A|120 B=1U9S|1|A|A|174
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 10 and then 16 to 20
aa is 10 bb is 16
  5 Cluster   1U9S|1|A|A|120:1U9S|1|A|A|129 1U9S|1|A|U|170:1U9S|1|A|A|174
    LR Inter  1U9S|1|A|A|122 1U9S|1|A|U|170 cSS 
    LR Inter  1U9S|1|A|A|126 1U9S|1|A|G|171 tWS 
    LR Inter  1U9S|1|A|A|120 1U9S|1|A|A|172 tHH 
    LR Inter  1U9S|1|A|G|123 1U9S|1|A|A|174 tSW 
    LR Inter  1U9S|1|A|A|129 1U9S|1|A|A|174 tSS 
    LL Inter  1U9S|1|A|A|122 1U9S|1|A|A|126 tWH 
    LL Inter  1U9S|1|A|G|125 1U9S|1|A|A|129 cSS 
    RR Inter  1U9S|1|A|U|170 1U9S|1|A|A|174 tWH 
    Left  strand conserved insertion 1U9S|1|A|C|121 at position 2
    Left  strand conserved insertion 1U9S|1|A|A|124 at position 5
    Left  strand conserved insertion 1U9S|1|A|A|127 at position 8
    Right strand conserved insertion 1U9S|1|A|A|173 at position 4
pMakeNodesCluster a=11 B=15 at the end
pMakeNodesCluster a=11 B=15 at the end
pMakeNodes probe for inserts:  a=1U9S|1|A|G|130 B=1U9S|1|A|G|169
    Insertion on left  1U9S|1|A|G|130
    Insertion on right 1U9S|1|A|G|169
pMakeNodesProbeForInsertions:  a 1U9S|1|A|A|131 interacts with 1U9S|1|A|C|132
pMakeNodesProbeForInsertions:  B 1U9S|1|A|G|168 interacts with 1U9S|1|A|C|132
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1U9S|1|A|G|168 interacts with 1U9S|1|A|C|132
  6 Initial    130 (1 insertion) and  169 (1 insertion)
pMakeNodes probed for insert:  a=1U9S|1|A|A|131 B=1U9S|1|A|G|168
pMakeNodes making a cluster near strand break a=1U9S|1|A|A|131 B=1U9S|1|A|G|168
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 12 to 13 and then 14 to 14
aa is 13 bb is 14
  7 Cluster   1U9S|1|A|A|131:1U9S|1|A|C|132 1U9S|1|A|G|168:1U9S|1|A|G|168
    LR Inter  1U9S|1|A|C|132 1U9S|1|A|G|168 cWW 
    LL Inter  1U9S|1|A|A|131 1U9S|1|A|C|132 cSH 
pMakeNodesCluster a=14 B=13 at the end
pMakeNodesCluster a=14 B=13 at the end
  8 Hairpin type *

2B Branch 2 of 2 of junction J4217 - Nucleotides   175 to   219, length   5
pMakeNodes starting loop:     a=1U9S|1|A|C|175 B=1U9S|1|A|C|219
    Insertion on left  1U9S|1|A|C|175
  9 Initial    175 (1 insertion) and  219 (0 insertion)
pMakeNodesJunction: a=1U9S|1|A|G|176 r=1U9S|1|A|G|176 s=1U9S|1|A|C|194 t=1U9S|1|A|G|195 u=B=1U9S|1|A|C|219
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1U9S|1|A|G|176 and 1U9S|1|A|C|194 and between 1U9S|1|A|G|195 and 1U9S|1|A|C|219
pMakeNodesJunction: about to make a junction: a=1U9S|1|A|G|176 s=1U9S|1|A|C|194 t=1U9S|1|A|G|195 B=1U9S|1|A|C|219
pMakeNodesJunction: first branch starts at   1U9S|1|A|G|176
pMakeNodesJunction: first branch ends around 1U9S|1|A|C|194
pMakeNodesJunction: second branch starts at  1U9S|1|A|G|195
pMakeNodesJunction: junction ends at         1U9S|1|A|C|219
pMakeNodesJunction: first branch strand start goes up to  1U9S|1|A|G|176
pMakeNodesJunction: first branch strand end goes down to  1U9S|1|A|C|194
pMakeNodesJunction: second branch strand start goes up to 1U9S|1|A|G|195
pMakeNodesJunction: last strand of junction goes down to  1U9S|1|A|C|219

Junction with 2 loops, call it J9157
Actual Branch 1 of junction J9157 - Nucleotides 1U9S|1|A|G|176 to 1U9S|1|A|C|194, length   2
Actual Branch 2 of junction J9157 - Nucleotides 1U9S|1|A|G|195 to 1U9S|1|A|C|219, length   2
 10 Junction

2B Branch 1 of 2 of junction J9157 - Nucleotides   176 to   194, length   2
pMakeNodes starting loop:     a=1U9S|1|A|G|176 B=1U9S|1|A|C|194
 12 Basepair   176  194 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J9157 - Nucleotides   195 to   219, length   2
pMakeNodes starting loop:     a=1U9S|1|A|G|195 B=1U9S|1|A|C|219
 15 Basepair   195  219 GC cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 27
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 27
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 25
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 20
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8  9 10 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   6   Initial Left 11 Right 15
pMakeMotifModelFromSSF:   7   Cluster Left 12 13 Right 14
pMakeMotifModelFromSSF:   8   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:   9   Initial Left 21 Right 25
pMakeMotifModelFromSSF:  10  Junction Left 22 Right 25
pMakeMotifModelFromSSF:  11   Initial Left 22 Right 23
pMakeMotifModelFromSSF:  12  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:  13   Hairpin Left 23 Right 22
pMakeMotifModelFromSSF:  14   Initial Left 24 Right 25
pMakeMotifModelFromSSF:  15  Basepair Left 24 Right 25
pMakeMotifModelFromSSF:  16   Hairpin Left 25 Right 24
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U9S|1|A|C|219
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U9S|1|A|A|129
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U9S|1|A|G|168
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U9S|1|A|A|174
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: 27
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [27×27 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 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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: 27
             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: 'CG'
               Comment: ' // Basepair C119 - G222 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          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: 26
             Insertion: []
                    id: 'J4217'
        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 1U9S|1|A|C|219'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 25
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 9]
             LeftIndex: 2
            RightIndex: 25
             Insertion: []
                    id: 'J4217'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A120 - C219 ID J4217'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [2 3 4 5 6 7 8 9 10]
            RightIndex: [16 17 18 19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACAGAGAAA'
           RightLetter: 'UGAAA'
               Comment: ' // Cluster node 1U9S|1|A|A|120:1U9S|1|A|A|129 and 1U9S|1|A|U|170:1U9S|1|A|A|174'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×12 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 4 5]
      InsertionComment: []
                IBases: [12×2 double]
    InteractionComment: {1×12 cell}
      JunctionDeletion: []
          InterIndices: [12×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [2 5 8]
         RightNotInter: 4
              NormCons: 8.7174e-04

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Initial node 1U9S|1|A|G|130 - 1U9S|1|A|G|169 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 11
            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 1U9S|1|A|A|129'
              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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: 'J9157'
        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 1U9S|1|A|G|168'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: 'J9157'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 14
             LeftIndex: [12 13]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 1U9S|1|A|A|131:1U9S|1|A|C|132 and 1U9S|1|A|G|168:1U9S|1|A|G|168'
              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: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2506

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 21
            RightIndex: 25
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|C|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 21
            RightIndex: 25
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U9S|1|A|A|174'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 25
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 22
            RightIndex: 25
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 22
            RightIndex: 25
             Insertion: []
                    id: 'J9157'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G176 - C219 ID J9157'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: 'J9157'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G176 - C194 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 24
            RightIndex: 25
             Insertion: []
                    id: 'J9157'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             LeftIndex: 24
            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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G195 - C219 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             LeftIndex: 25
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 25
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 27
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 27
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 26
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 25
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 25
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 20
pMakeMotifModelFromSSF:   7   Cluster Left  2  3  4  5  6  7  8  9 10 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left 12 Right 15
pMakeMotifModelFromSSF:  12   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  13   Cluster Left 12 13 Right 14
pMakeMotifModelFromSSF:  14   Initial Left 14 Right 13
pMakeMotifModelFromSSF:  15   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  16   Initial Left 21 Right 25
pMakeMotifModelFromSSF:  17     Fixed Left 21 Right 25
pMakeMotifModelFromSSF:  18   Initial Left 22 Right 25
pMakeMotifModelFromSSF:  19  Junction Left 22 Right 25
pMakeMotifModelFromSSF:  20   Initial Left 22 Right 23
pMakeMotifModelFromSSF:  21  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:  22   Hairpin Left 23 Right 22
pMakeMotifModelFromSSF:  23   Initial Left 24 Right 25
pMakeMotifModelFromSSF:  24  Basepair Left 24 Right 25
pMakeMotifModelFromSSF:  25   Hairpin Left 25 Right 24
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: 'J4217'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 21
            RightIndex: 25
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|C|219 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_12209.1. Nodes 6 and 16 both model an insertion before position 21. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: 'J9157'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 24
            RightIndex: 25
             Insertion: []
                    id: 'J9157'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_12209.1. Nodes 20 and 23 both model an insertion before position 24. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 19
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 19
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_12209.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.3146

Timestamp 18-Jul-2025 00:12:46
pMakeSCFGModels: Making JAR3D model for motif group J4_16596.1, number 10 of 65
pMakeNodes starting loop:     a=4FRG|1|B|G|18 B=4FRG|1|B|C|73
  2 Basepair    18   73 GC cWW 
pMakeNodes probe for inserts:  a=4FRG|1|B|G|19 B=4FRG|1|B|A|70
    Insertion on left  4FRG|1|B|G|19
    Insertion on left  4FRG|1|B|A|20
    Insertion on right 4FRG|1|B|A|70
pMakeNodes probed for insert:  a=4FRG|1|B|A|21 B=4FRG|1|B|A|69
pMakeNodesJunction: a=4FRG|1|B|A|21 r=4FRG|1|B|A|21 s=4FRG|1|B|C|40 t=4FRG|1|B|A|41 u=B=4FRG|1|B|A|69
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4FRG|1|B|A|21 and 4FRG|1|B|C|40 and between 4FRG|1|B|A|41 and 4FRG|1|B|A|69
pMakeNodesJunction: about to make a junction: a=4FRG|1|B|A|21 s=4FRG|1|B|C|40 t=4FRG|1|B|A|41 B=4FRG|1|B|A|69
pMakeNodesJunction: first branch starts at   4FRG|1|B|A|21
pMakeNodesJunction: first branch ends around 4FRG|1|B|C|40
pMakeNodesJunction: second branch starts at  4FRG|1|B|A|41
pMakeNodesJunction: junction ends at         4FRG|1|B|A|69
pMakeNodesJunction: first branch strand start goes up to  4FRG|1|B|G|23
pMakeNodesJunction: first branch strand end goes down to  4FRG|1|B|C|40
pMakeNodesJunction: second branch strand start goes up to 4FRG|1|B|A|43
pMakeNodesJunction: last strand of junction goes down to  4FRG|1|B|G|68
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J7922
Actual Branch 1 of junction J7922 - Nucleotides 4FRG|1|B|A|21 to 4FRG|1|B|C|40, length   4
Actual Branch 2 of junction J7922 - Nucleotides 4FRG|1|B|A|41 to 4FRG|1|B|A|69, length   8
  3 Junction

2B Branch 1 of 2 of junction J7922 - Nucleotides    21 to    40, length   4
pMakeNodes starting loop:     a=4FRG|1|B|A|21 B=4FRG|1|B|C|40
    Insertion on left  4FRG|1|B|A|21
    Insertion on left  4FRG|1|B|A|22
pMakeNodesProbeForInsertions:  a 4FRG|1|B|G|23 interacts with 4FRG|1|B|C|40
pMakeNodesProbeForInsertions:  B 4FRG|1|B|C|40 interacts with 4FRG|1|B|G|23
pMakeNodesProbeForInsertions:  B 4FRG|1|B|C|40 interacts with 4FRG|1|B|G|23
  4 Initial     21 (2 insertion) and   40 (0 insertion)
  5 Basepair    23   40 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7922 - Nucleotides    41 to    69, length   8
pMakeNodes starting loop:     a=4FRG|1|B|A|41 B=4FRG|1|B|A|69
    Insertion on left  4FRG|1|B|A|41
    Insertion on left  4FRG|1|B|G|42
  7 Initial     41 (2 insertion) and   69 (0 insertion)
pMakeNodesJunction: a=4FRG|1|B|A|43 r=4FRG|1|B|A|43 s=4FRG|1|B|U|54 t=4FRG|1|B|A|55 u=B=4FRG|1|B|A|69
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4FRG|1|B|A|43 and 4FRG|1|B|U|54 and between 4FRG|1|B|A|55 and 4FRG|1|B|A|69
pMakeNodesJunction: about to make a junction: a=4FRG|1|B|A|43 s=4FRG|1|B|U|54 t=4FRG|1|B|A|55 B=4FRG|1|B|A|69
pMakeNodesJunction: first branch starts at   4FRG|1|B|A|43
pMakeNodesJunction: first branch ends around 4FRG|1|B|U|54
pMakeNodesJunction: second branch starts at  4FRG|1|B|A|55
pMakeNodesJunction: junction ends at         4FRG|1|B|A|69
pMakeNodesJunction: first branch strand start goes up to  4FRG|1|B|A|43
pMakeNodesJunction: first branch strand end goes down to  4FRG|1|B|U|54
pMakeNodesJunction: second branch strand start goes up to 4FRG|1|B|C|56
pMakeNodesJunction: last strand of junction goes down to  4FRG|1|B|G|68

Junction with 2 loops, call it J9594
Actual Branch 1 of junction J9594 - Nucleotides 4FRG|1|B|A|43 to 4FRG|1|B|U|54, length   2
Actual Branch 2 of junction J9594 - Nucleotides 4FRG|1|B|A|55 to 4FRG|1|B|A|69, length   4
  8 Junction

2B Branch 1 of 2 of junction J9594 - Nucleotides    43 to    54, length   2
pMakeNodes starting loop:     a=4FRG|1|B|A|43 B=4FRG|1|B|U|54
 10 Basepair    43   54 AU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9594 - Nucleotides    55 to    69, length   4
pMakeNodes starting loop:     a=4FRG|1|B|A|55 B=4FRG|1|B|A|69
 13 Basepair    55   69 AA cWW 
No need to probe because of interaction between a=4FRG|1|B|C|56 B=4FRG|1|B|G|68
 14 Basepair    56   68 CG cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  8 Right 15
pMakeMotifModelFromSSF:   8  Junction Left 10 Right 15
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  12   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  13  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  14  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  15   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|G|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4FRG|1|B|A|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|G|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: 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: []
           numbranches: []
              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: [0.0082 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: 'AC'
               Comment: ' // Basepair G18 - C73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J7922'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|G|19'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7922'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4FRG|1|B|A|20'
              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]
           numbranches: []
              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: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J7922'
        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 4FRG|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: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: 'J9594'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: 'J7922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A21 - A69 ID J7922'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7922'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4FRG|1|B|A|21 - 4FRG|1|B|C|40 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             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 4FRG|1|B|A|21'
              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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: 'J9594'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             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 4FRG|1|B|A|22'
              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]
           numbranches: []
              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: '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]
           numbranches: []
              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 G23 - 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]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: 'J7922'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 4FRG|1|B|A|41 - 4FRG|1|B|A|69 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 4FRG|1|B|A|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 4FRG|1|B|G|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: 'J9594'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A43 - A69 ID J9594'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9594'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A43 - U54 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 26
             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: []
           numbranches: []
              NormCons: 1

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: 'J9594'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
               Comment: ' // Basepair A55 - A69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 C56 - G68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  4 Right 15
pMakeMotifModelFromSSF:   9  Junction Left  4 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  11     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  17   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  18     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  20     Fixed Left  9 Right 15
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  22  Junction Left 10 Right 15
pMakeMotifModelFromSSF:  23   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  24  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  25   Hairpin Left 11 Right 10
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 junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a junction child at node 26
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Finished at node 29 out of 29, type Hairpin
pNextNodeJunction: Finished at node 29 out of 29, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J7922'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4FRG|1|B|A|21 - 4FRG|1|B|C|40 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: 'J7922'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 4FRG|1|B|A|41 - 4FRG|1|B|A|69 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_16596.1. Nodes 10 and 17 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J9594'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: 'J9594'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_16596.1. Nodes 23 and 26 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a junction child at node 26
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Finished at node 29 out of 29, type Hairpin
pNextNodeJunction: Finished at node 29 out of 29, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 10
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_16596.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.5452
  -13.0343
  -17.0267

Timestamp 18-Jul-2025 00:12:47
pMakeSCFGModels: Making JAR3D model for motif group J4_19572.1, number 11 of 65
pMakeNodes starting loop:     a=1U9S|1|A|C|119 B=1U9S|1|A|G|222
  2 Basepair   119  222 CG cWW 
pMakeNodes probe for inserts:  a=1U9S|1|A|A|120 B=1U9S|1|A|C|221
    Insertion on right 1U9S|1|A|C|221
pMakeNodes probed for insert:  a=1U9S|1|A|A|120 B=1U9S|1|A|A|220
pMakeNodesJunction: a=1U9S|1|A|A|120 r=1U9S|1|A|A|120 s=1U9S|1|A|A|174 t=1U9S|1|A|C|175 u=B=1U9S|1|A|A|220
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 6
pMakeNodesJunction: Found nested interactions between 1U9S|1|A|A|120 and 1U9S|1|A|A|174 and between 1U9S|1|A|C|175 and 1U9S|1|A|A|220
pMakeNodesJunction: about to make a junction: a=1U9S|1|A|A|120 s=1U9S|1|A|A|174 t=1U9S|1|A|C|175 B=1U9S|1|A|A|220
pMakeNodesJunction: first branch starts at   1U9S|1|A|A|120
pMakeNodesJunction: first branch ends around 1U9S|1|A|A|174
pMakeNodesJunction: second branch starts at  1U9S|1|A|C|175
pMakeNodesJunction: junction ends at         1U9S|1|A|A|220
pMakeNodesJunction: first branch strand start goes up to  1U9S|1|A|G|125
pMakeNodesJunction: first branch strand end goes down to  1U9S|1|A|G|169
pMakeNodesJunction: second branch strand start goes up to 1U9S|1|A|G|176
pMakeNodesJunction: last strand of junction goes down to  1U9S|1|A|G|217

Junction with 2 loops, call it J6557
Actual Branch 1 of junction J6557 - Nucleotides 1U9S|1|A|A|120 to 1U9S|1|A|A|174, length  19
Actual Branch 2 of junction J6557 - Nucleotides 1U9S|1|A|C|175 to 1U9S|1|A|A|220, length   9
  3 Junction

2B Branch 1 of 2 of junction J6557 - Nucleotides   120 to   174, length  19
pMakeNodes starting loop:     a=1U9S|1|A|A|120 B=1U9S|1|A|A|174
pMakeNodesProbeForInsertions:  a 1U9S|1|A|A|120 interacts with 1U9S|1|A|A|172
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|174 interacts with 1U9S|1|A|G|123
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|174 interacts with 1U9S|1|A|U|170
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial    120 (0 insertion) and  174 (0 insertion)
pMakeNodes making a cluster near strand break a=1U9S|1|A|A|120 B=1U9S|1|A|A|174
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 10 and then 16 to 20
aa is 10 bb is 16
  5 Cluster   1U9S|1|A|A|120:1U9S|1|A|A|129 1U9S|1|A|U|170:1U9S|1|A|A|174
    LR Inter  1U9S|1|A|A|122 1U9S|1|A|U|170 cSS 
    LR Inter  1U9S|1|A|A|126 1U9S|1|A|G|171 tWS 
    LR Inter  1U9S|1|A|A|120 1U9S|1|A|A|172 tHH 
    LR Inter  1U9S|1|A|G|123 1U9S|1|A|A|174 tSW 
    LR Inter  1U9S|1|A|A|129 1U9S|1|A|A|174 tSS 
    LL Inter  1U9S|1|A|A|122 1U9S|1|A|A|126 tWH 
    LL Inter  1U9S|1|A|G|125 1U9S|1|A|A|129 cSS 
    RR Inter  1U9S|1|A|U|170 1U9S|1|A|A|174 tWH 
    Left  strand conserved insertion 1U9S|1|A|C|121 at position 2
    Left  strand conserved insertion 1U9S|1|A|A|124 at position 5
    Left  strand conserved insertion 1U9S|1|A|A|127 at position 8
    Right strand conserved insertion 1U9S|1|A|A|173 at position 4
pMakeNodesCluster a=11 B=15 at the end
pMakeNodesCluster a=11 B=15 at the end
pMakeNodes probe for inserts:  a=1U9S|1|A|G|130 B=1U9S|1|A|G|169
    Insertion on left  1U9S|1|A|G|130
    Insertion on right 1U9S|1|A|G|169
pMakeNodesProbeForInsertions:  a 1U9S|1|A|A|131 interacts with 1U9S|1|A|C|132
pMakeNodesProbeForInsertions:  B 1U9S|1|A|G|168 interacts with 1U9S|1|A|C|132
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1U9S|1|A|G|168 interacts with 1U9S|1|A|C|132
  6 Initial    130 (1 insertion) and  169 (1 insertion)
pMakeNodes probed for insert:  a=1U9S|1|A|A|131 B=1U9S|1|A|G|168
pMakeNodes making a cluster near strand break a=1U9S|1|A|A|131 B=1U9S|1|A|G|168
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 12 to 13 and then 14 to 14
aa is 13 bb is 14
  7 Cluster   1U9S|1|A|A|131:1U9S|1|A|C|132 1U9S|1|A|G|168:1U9S|1|A|G|168
    LR Inter  1U9S|1|A|C|132 1U9S|1|A|G|168 cWW 
    LL Inter  1U9S|1|A|A|131 1U9S|1|A|C|132 cSH 
pMakeNodesCluster a=14 B=13 at the end
pMakeNodesCluster a=14 B=13 at the end
  8 Hairpin type *

2B Branch 2 of 2 of junction J6557 - Nucleotides   175 to   220, length   9
pMakeNodes starting loop:     a=1U9S|1|A|C|175 B=1U9S|1|A|A|220
    Insertion on left  1U9S|1|A|C|175
  9 Initial    175 (1 insertion) and  220 (0 insertion)
pMakeNodesJunction: a=1U9S|1|A|G|176 r=1U9S|1|A|G|176 s=1U9S|1|A|C|194 t=1U9S|1|A|G|195 u=B=1U9S|1|A|A|220
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 1U9S|1|A|G|176 and 1U9S|1|A|C|194 and between 1U9S|1|A|G|195 and 1U9S|1|A|A|220
pMakeNodesJunction: about to make a junction: a=1U9S|1|A|G|176 s=1U9S|1|A|C|194 t=1U9S|1|A|G|195 B=1U9S|1|A|A|220
pMakeNodesJunction: first branch starts at   1U9S|1|A|G|176
pMakeNodesJunction: first branch ends around 1U9S|1|A|C|194
pMakeNodesJunction: second branch starts at  1U9S|1|A|G|195
pMakeNodesJunction: junction ends at         1U9S|1|A|A|220
pMakeNodesJunction: first branch strand start goes up to  1U9S|1|A|G|176
pMakeNodesJunction: first branch strand end goes down to  1U9S|1|A|C|194
pMakeNodesJunction: second branch strand start goes up to 1U9S|1|A|C|196
pMakeNodesJunction: last strand of junction goes down to  1U9S|1|A|G|217
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     0


Junction with 2 loops, call it J357
Actual Branch 1 of junction J357 - Nucleotides 1U9S|1|A|G|176 to 1U9S|1|A|C|194, length   2
Actual Branch 2 of junction J357 - Nucleotides 1U9S|1|A|G|195 to 1U9S|1|A|A|220, length   6
 10 Junction

2B Branch 1 of 2 of junction J357 - Nucleotides   176 to   194, length   2
pMakeNodes starting loop:     a=1U9S|1|A|G|176 B=1U9S|1|A|C|194
 12 Basepair   176  194 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J357 - Nucleotides   195 to   220, length   6
pMakeNodes starting loop:     a=1U9S|1|A|G|195 B=1U9S|1|A|A|220
pMakeNodesProbeForInsertions:  a 1U9S|1|A|G|195 interacts with 1U9S|1|A|C|219
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|220 interacts with 1U9S|1|A|G|217
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1U9S|1|A|A|220 interacts with 1U9S|1|A|G|217
 14 Initial    195 (0 insertion) and  220 (0 insertion)
pMakeNodes making a cluster near strand break a=1U9S|1|A|G|195 B=1U9S|1|A|A|220
pMakeNodesCluster: amax is 25 bmin is 26, use_amax is 1
pMakeNodesCluster: Cluster goes from 24 to 25 and then 26 to 29
aa is 25 bb is 26
 15 Cluster   1U9S|1|A|G|195:1U9S|1|A|C|196 1U9S|1|A|G|217:1U9S|1|A|A|220
    LR Inter  1U9S|1|A|C|196 1U9S|1|A|G|217 cWW 
    LR Inter  1U9S|1|A|G|195 1U9S|1|A|C|219 cWW 
    RR Inter  1U9S|1|A|G|217 1U9S|1|A|A|220 cSW 
    Right strand conserved insertion 1U9S|1|A|G|218 at position 2
pMakeNodesCluster a=26 B=25 at the end
pMakeNodesCluster a=26 B=25 at the end
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 31
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 31
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 29
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 20
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8  9 10 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   6   Initial Left 11 Right 15
pMakeMotifModelFromSSF:   7   Cluster Left 12 13 Right 14
pMakeMotifModelFromSSF:   8   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:   9   Initial Left 21 Right 29
pMakeMotifModelFromSSF:  10  Junction Left 22 Right 29
pMakeMotifModelFromSSF:  11   Initial Left 22 Right 23
pMakeMotifModelFromSSF:  12  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:  13   Hairpin Left 23 Right 22
pMakeMotifModelFromSSF:  14   Initial Left 24 Right 29
pMakeMotifModelFromSSF:  15   Cluster Left 24 25 Right 26 27 28 29
pMakeMotifModelFromSSF:  16   Hairpin Left 26 Right 25
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 1U9S|1|A|A|220
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U9S|1|A|A|129
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U9S|1|A|G|168
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U9S|1|A|A|174
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: 31
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [31×31 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 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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: 31
             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: 'CG'
               Comment: ' // Basepair C119 - G222 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          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: 30
             Insertion: []
                    id: 'J6557'
        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 1U9S|1|A|A|220'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 29
             Insertion: []
                    id: 'J6557'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 9]
             LeftIndex: 2
            RightIndex: 29
             Insertion: []
                    id: 'J6557'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A120 - A220 ID J6557'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: 'J6557'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [2 3 4 5 6 7 8 9 10]
            RightIndex: [16 17 18 19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACAGAGAAA'
           RightLetter: 'UGAAA'
               Comment: ' // Cluster node 1U9S|1|A|A|120:1U9S|1|A|A|129 and 1U9S|1|A|U|170:1U9S|1|A|A|174'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×12 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 4 5]
      InsertionComment: []
                IBases: [12×2 double]
    InteractionComment: {1×12 cell}
      JunctionDeletion: []
          InterIndices: [12×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [2 5 8]
         RightNotInter: 4
              NormCons: 8.7174e-04

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Initial node 1U9S|1|A|G|130 - 1U9S|1|A|G|169 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 11
            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 1U9S|1|A|A|129'
              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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: 'J6557'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: 'J357'
        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 1U9S|1|A|G|168'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: 'J357'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 14
             LeftIndex: [12 13]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 1U9S|1|A|A|131:1U9S|1|A|C|132 and 1U9S|1|A|G|168:1U9S|1|A|G|168'
              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: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2506

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 21
            RightIndex: 29
             Insertion: []
                    id: 'J6557'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|A|220 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 21
            RightIndex: 29
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U9S|1|A|A|174'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 22
            RightIndex: 29
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-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: 26
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 22
            RightIndex: 29
             Insertion: []
                    id: 'J357'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G176 - A220 ID J357'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: 'J357'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G176 - C194 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 24
            RightIndex: 29
             Insertion: []
                    id: 'J357'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|G|195 - 1U9S|1|A|A|220 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 25
             LeftIndex: [24 25]
            RightIndex: [26 27 28 29]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GC'
           RightLetter: 'GGCA'
               Comment: ' // Cluster node 1U9S|1|A|G|195:1U9S|1|A|C|196 and 1U9S|1|A|G|217:1U9S|1|A|A|220'
              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 4]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2500

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 26
            RightIndex: 25
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             LeftIndex: 26
            RightIndex: 25
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 26
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 31
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 31
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 30
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 29
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 29
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 20
pMakeMotifModelFromSSF:   7   Cluster Left  2  3  4  5  6  7  8  9 10 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left 12 Right 15
pMakeMotifModelFromSSF:  12   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  13   Cluster Left 12 13 Right 14
pMakeMotifModelFromSSF:  14   Initial Left 14 Right 13
pMakeMotifModelFromSSF:  15   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  16   Initial Left 21 Right 29
pMakeMotifModelFromSSF:  17     Fixed Left 21 Right 29
pMakeMotifModelFromSSF:  18   Initial Left 22 Right 29
pMakeMotifModelFromSSF:  19  Junction Left 22 Right 29
pMakeMotifModelFromSSF:  20   Initial Left 22 Right 23
pMakeMotifModelFromSSF:  21  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:  22   Hairpin Left 23 Right 22
pMakeMotifModelFromSSF:  23   Initial Left 24 Right 29
pMakeMotifModelFromSSF:  24   Cluster Left 24 25 Right 26 27 28 29
pMakeMotifModelFromSSF:  25   Initial Left 26 Right 25
pMakeMotifModelFromSSF:  26   Hairpin Left 26 Right 25
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pUpdateModelWithSSF: J4_19572.1 allow insertions from initial node 25?
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


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: 'J6557'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|A|120 - 1U9S|1|A|A|174 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 21
            RightIndex: 29
             Insertion: []
                    id: 'J6557'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|C|175 - 1U9S|1|A|A|220 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_19572.1. Nodes 6 and 16 both model an insertion before position 21. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: 'J357'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 24
            RightIndex: 29
             Insertion: []
                    id: 'J357'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1U9S|1|A|G|195 - 1U9S|1|A|A|220 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_19572.1. Nodes 20 and 23 both model an insertion before position 24. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 19
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 22 and 27
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 19
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 22 and 27
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_19572.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.7420

Timestamp 18-Jul-2025 00:12:48
pMakeSCFGModels: Making JAR3D model for motif group J4_22413.2, number 12 of 65
pMakeNodes starting loop:     a=1U0B|1|A|U|7 B=1U0B|1|A|A|66
  2 Basepair     7   66 UA cWW 
pMakeNodes probe for inserts:  a=1U0B|1|A|U|8 B=1U0B|1|A|A|65
    Insertion on left  1U0B|1|A|U|8
    Insertion on left  1U0B|1|A|A|9
pMakeNodes probed for insert:  a=1U0B|1|A|A|10 B=1U0B|1|A|A|65
pMakeNodesJunction: a=1U0B|1|A|A|10 r=1U0B|1|A|A|10 s=1U0B|1|A|U|25 t=1U0B|1|A|A|26 u=B=1U0B|1|A|A|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 1U0B|1|A|A|10 and 1U0B|1|A|U|25 and between 1U0B|1|A|A|26 and 1U0B|1|A|A|65
pMakeNodesJunction: about to make a junction: a=1U0B|1|A|A|10 s=1U0B|1|A|U|25 t=1U0B|1|A|A|26 B=1U0B|1|A|A|65
pMakeNodesJunction: first branch starts at   1U0B|1|A|A|10
pMakeNodesJunction: first branch ends around 1U0B|1|A|U|25
pMakeNodesJunction: second branch starts at  1U0B|1|A|A|26
pMakeNodesJunction: junction ends at         1U0B|1|A|A|65
pMakeNodesJunction: first branch strand start goes up to  1U0B|1|A|A|10
pMakeNodesJunction: first branch strand end goes down to  1U0B|1|A|U|25
pMakeNodesJunction: second branch strand start goes up to 1U0B|1|A|G|27
pMakeNodesJunction: last strand of junction goes down to  1U0B|1|A|A|65

Junction with 2 loops, call it J8491
Actual Branch 1 of junction J8491 - Nucleotides 1U0B|1|A|A|10 to 1U0B|1|A|U|25, length   2
Actual Branch 2 of junction J8491 - Nucleotides 1U0B|1|A|A|26 to 1U0B|1|A|A|65, length   9
  3 Junction

2B Branch 1 of 2 of junction J8491 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=1U0B|1|A|A|10 B=1U0B|1|A|U|25
  5 Basepair    10   25 AU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J8491 - Nucleotides    26 to    65, length   9
pMakeNodes starting loop:     a=1U0B|1|A|A|26 B=1U0B|1|A|A|65
    Insertion on left  1U0B|1|A|A|26
  7 Initial     26 (1 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=1U0B|1|A|G|27 r=1U0B|1|A|G|27 s=1U0B|1|A|U|43 t=1U0B|1|A|C|44 u=B=1U0B|1|A|A|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1U0B|1|A|G|27 and 1U0B|1|A|U|43 and between 1U0B|1|A|C|44 and 1U0B|1|A|A|65
pMakeNodesJunction: about to make a junction: a=1U0B|1|A|G|27 s=1U0B|1|A|U|43 t=1U0B|1|A|C|44 B=1U0B|1|A|A|65
pMakeNodesJunction: first branch starts at   1U0B|1|A|G|27
pMakeNodesJunction: first branch ends around 1U0B|1|A|U|43
pMakeNodesJunction: second branch starts at  1U0B|1|A|C|44
pMakeNodesJunction: junction ends at         1U0B|1|A|A|65
pMakeNodesJunction: first branch strand start goes up to  1U0B|1|A|G|27
pMakeNodesJunction: first branch strand end goes down to  1U0B|1|A|U|43
pMakeNodesJunction: second branch strand start goes up to 1U0B|1|A|U|49
pMakeNodesJunction: last strand of junction goes down to  1U0B|1|A|A|65

Junction with 2 loops, call it J9339
Actual Branch 1 of junction J9339 - Nucleotides 1U0B|1|A|G|27 to 1U0B|1|A|U|43, length   2
Actual Branch 2 of junction J9339 - Nucleotides 1U0B|1|A|C|44 to 1U0B|1|A|A|65, length   6
  8 Junction

2B Branch 1 of 2 of junction J9339 - Nucleotides    27 to    43, length   2
pMakeNodes starting loop:     a=1U0B|1|A|G|27 B=1U0B|1|A|U|43
 10 Basepair    27   43 GU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9339 - Nucleotides    44 to    65, length   6
pMakeNodes starting loop:     a=1U0B|1|A|C|44 B=1U0B|1|A|A|65
    Insertion on left  1U0B|1|A|C|44
    Insertion on left  1U0B|1|A|U|45
    Insertion on left  1U0B|1|A|A|46
    Insertion on left  1U0B|1|A|G|48
pMakeNodesProbeForInsertions:  a 1U0B|1|A|U|49 interacts with 1U0B|1|A|A|65
pMakeNodesProbeForInsertions:  B 1U0B|1|A|A|65 interacts with 1U0B|1|A|U|49
pMakeNodesProbeForInsertions:  B 1U0B|1|A|A|65 interacts with 1U0B|1|A|U|49
 12 Initial     44 (4 insertion) and   65 (0 insertion)
 13 Basepair    49   65 UA cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  7 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  14   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|A|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|C|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|U|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|A|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U0B|1|A|G|48
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: []
           numbranches: []
              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: [0.0082 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: 'A'
               Comment: ' // Basepair U7 - A66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J8491'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U0B|1|A|U|8'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8491'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 1U0B|1|A|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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J8491'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A10 - A65 ID J8491'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8491'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 A10 - 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]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

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: 'J8491'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 1U0B|1|A|A|26 - 1U0B|1|A|A|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J9339'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U0B|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: []
           numbranches: []
              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: '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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: 'J9339'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G27 - A65 ID J9339'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9339'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'U'
               Comment: ' // Basepair G27 - U43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 17

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: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J9339'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUAG'
           RightLetter: []
               Comment: ' // Initial node 1U0B|1|A|C|44 - 1U0B|1|A|A|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             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 1U0B|1|A|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U0B|1|A|U|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             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: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 1U0B|1|A|A|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 12
            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 1U0B|1|A|G|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             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 U49 - A65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 28

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  14  Junction Left  7 Right 14
pMakeMotifModelFromSSF:  15   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  23     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  26   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  27  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  28   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J8491'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J8491'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 1U0B|1|A|A|26 - 1U0B|1|A|A|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_22413.2. Nodes 8 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J9339'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J9339'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUAG'
           RightLetter: []
               Comment: ' // Initial node 1U0B|1|A|C|44 - 1U0B|1|A|A|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_22413.2. Nodes 15 and 18 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHW  between 4 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 4 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_22413.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.9220
  -10.7533
  -10.7573

Timestamp 18-Jul-2025 00:12:48
pMakeSCFGModels: Making JAR3D model for motif group J4_24220.1, number 13 of 65
pMakeNodes starting loop:     a=4FEN|1|B|A|21 B=4FEN|1|B|U|75
  2 Basepair    21   75 AU cWW 
pMakeNodes probe for inserts:  a=4FEN|1|B|U|22 B=4FEN|1|B|C|74
    Insertion on left  4FEN|1|B|U|22
    Insertion on right 4FEN|1|B|C|74
    Insertion on right 4FEN|1|B|A|73
pMakeNodes probed for insert:  a=4FEN|1|B|A|23 B=4FEN|1|B|G|72
pMakeNodesJunction: a=4FEN|1|B|A|23 r=4FEN|1|B|A|23 s=4FEN|1|B|A|45 t=4FEN|1|B|G|46 u=B=4FEN|1|B|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4FEN|1|B|A|23 and 4FEN|1|B|A|45 and between 4FEN|1|B|G|46 and 4FEN|1|B|G|72
pMakeNodesJunction: about to make a junction: a=4FEN|1|B|A|23 s=4FEN|1|B|A|45 t=4FEN|1|B|G|46 B=4FEN|1|B|G|72
pMakeNodesJunction: first branch starts at   4FEN|1|B|A|23
pMakeNodesJunction: first branch ends around 4FEN|1|B|A|45
pMakeNodesJunction: second branch starts at  4FEN|1|B|G|46
pMakeNodesJunction: junction ends at         4FEN|1|B|G|72
pMakeNodesJunction: first branch strand start goes up to  4FEN|1|B|C|26
pMakeNodesJunction: first branch strand end goes down to  4FEN|1|B|G|44
pMakeNodesJunction: second branch strand start goes up to 4FEN|1|B|G|46
pMakeNodesJunction: last strand of junction goes down to  4FEN|1|B|G|72
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J6787
Actual Branch 1 of junction J6787 - Nucleotides 4FEN|1|B|A|23 to 4FEN|1|B|A|45, length   6
Actual Branch 2 of junction J6787 - Nucleotides 4FEN|1|B|G|46 to 4FEN|1|B|G|72, length   4
  3 Junction

2B Branch 1 of 2 of junction J6787 - Nucleotides    23 to    45, length   6
pMakeNodes starting loop:     a=4FEN|1|B|A|23 B=4FEN|1|B|A|45
    Insertion on left  4FEN|1|B|A|23
    Insertion on left  4FEN|1|B|U|24
pMakeNodesProbeForInsertions:  a 4FEN|1|B|A|25 interacts with 4FEN|1|B|A|45
pMakeNodesProbeForInsertions:  B 4FEN|1|B|A|45 interacts with 4FEN|1|B|A|25
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4FEN|1|B|A|45 interacts with 4FEN|1|B|A|25
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial     23 (2 insertion) and   45 (0 insertion)
  5 Basepair    25   45 AA tHS 
No need to probe because of interaction between a=4FEN|1|B|C|26 B=4FEN|1|B|G|44
  6 Basepair    26   44 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J6787 - Nucleotides    46 to    72, length   4
pMakeNodes starting loop:     a=4FEN|1|B|G|46 B=4FEN|1|B|G|72
  8 Initial     46 (0 insertion) and   72 (0 insertion)
pMakeNodesJunction: a=4FEN|1|B|G|46 r=4FEN|1|B|G|46 s=4FEN|1|B|C|53 t=4FEN|1|B|C|54 u=B=4FEN|1|B|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4FEN|1|B|G|46 and 4FEN|1|B|C|53 and between 4FEN|1|B|C|54 and 4FEN|1|B|G|72
pMakeNodesJunction: about to make a junction: a=4FEN|1|B|G|46 s=4FEN|1|B|C|53 t=4FEN|1|B|C|54 B=4FEN|1|B|G|72
pMakeNodesJunction: first branch starts at   4FEN|1|B|G|46
pMakeNodesJunction: first branch ends around 4FEN|1|B|C|53
pMakeNodesJunction: second branch starts at  4FEN|1|B|C|54
pMakeNodesJunction: junction ends at         4FEN|1|B|G|72
pMakeNodesJunction: first branch strand start goes up to  4FEN|1|B|G|46
pMakeNodesJunction: first branch strand end goes down to  4FEN|1|B|C|53
pMakeNodesJunction: second branch strand start goes up to 4FEN|1|B|C|54
pMakeNodesJunction: last strand of junction goes down to  4FEN|1|B|G|72

Junction with 2 loops, call it J7577
Actual Branch 1 of junction J7577 - Nucleotides 4FEN|1|B|G|46 to 4FEN|1|B|C|53, length   2
Actual Branch 2 of junction J7577 - Nucleotides 4FEN|1|B|C|54 to 4FEN|1|B|G|72, length   2
  9 Junction

2B Branch 1 of 2 of junction J7577 - Nucleotides    46 to    53, length   2
pMakeNodes starting loop:     a=4FEN|1|B|G|46 B=4FEN|1|B|C|53
 11 Basepair    46   53 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J7577 - Nucleotides    54 to    72, length   2
pMakeNodes starting loop:     a=4FEN|1|B|C|54 B=4FEN|1|B|G|72
 14 Basepair    54   72 CG cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  9 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  13   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  15   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FEN|1|B|U|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4FEN|1|B|C|74
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4FEN|1|B|A|73
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FEN|1|B|A|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FEN|1|B|U|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: 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: []
           numbranches: []
              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: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'ACU'
               Comment: ' // Basepair A21 - U75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J6787'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4FEN|1|B|U|22'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6787'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'AU'
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 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 4FEN|1|B|C|74'
              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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             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: '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]
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             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 4FEN|1|B|A|73'
              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: []
           numbranches: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J6787'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J6787'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A23 - G72 ID J6787'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J6787'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: []
               Comment: ' // Initial node 4FEN|1|B|A|23 - 4FEN|1|B|A|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             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 4FEN|1|B|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]
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             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: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J7577'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4FEN|1|B|U|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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]
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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 A25 - A45 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]
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             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 C26 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 17

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: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J6787'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4FEN|1|B|G|46 - 4FEN|1|B|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J7577'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G46 - G72 ID J7577'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J7577'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G46 - 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]
           numbranches: []
              NormCons: []

Node 22

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: []
           numbranches: []
              NormCons: 1

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: 'J7577'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C54 - 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]
           numbranches: []
              NormCons: []

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  3 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  3 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  3 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  4 Right  8
pMakeMotifModelFromSSF:  13     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  14   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  17   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  19  Junction Left  9 Right 12
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  23   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  24  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  25   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J6787'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'AU'
           RightLetter: []
               Comment: ' // Initial node 4FEN|1|B|A|23 - 4FEN|1|B|A|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J6787'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4FEN|1|B|G|46 - 4FEN|1|B|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_24220.1. Nodes 10 and 18 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J7577'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: 'J7577'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_24220.1. Nodes 20 and 23 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWS  between 3 and 9
pConservedInteractionList: did not find a substitution probability matrix for tWS  between 3 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_24220.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9590

Timestamp 18-Jul-2025 00:12:48
pMakeSCFGModels: Making JAR3D model for motif group J4_26776.1, number 14 of 65
pMakeNodes starting loop:     a=4RUM|1|A|C|16 B=4RUM|1|A|G|88
  2 Basepair    16   88 CG cWW 
pMakeNodes probe for inserts:  a=4RUM|1|A|A|17 B=4RUM|1|A|G|87
    Insertion on right 4RUM|1|A|G|87
pMakeNodes probed for insert:  a=4RUM|1|A|A|17 B=4RUM|1|A|G|86
pMakeNodesJunction: a=4RUM|1|A|A|17 r=4RUM|1|A|A|17 s=4RUM|1|A|G|45 t=4RUM|1|A|G|46 u=B=4RUM|1|A|G|86
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4RUM|1|A|A|17 and 4RUM|1|A|G|45 and between 4RUM|1|A|G|46 and 4RUM|1|A|G|86
pMakeNodesJunction: about to make a junction: a=4RUM|1|A|A|17 s=4RUM|1|A|G|45 t=4RUM|1|A|G|46 B=4RUM|1|A|G|86
pMakeNodesJunction: first branch starts at   4RUM|1|A|A|17
pMakeNodesJunction: first branch ends around 4RUM|1|A|G|45
pMakeNodesJunction: second branch starts at  4RUM|1|A|G|46
pMakeNodesJunction: junction ends at         4RUM|1|A|G|86
pMakeNodesJunction: first branch strand start goes up to  4RUM|1|A|G|18
pMakeNodesJunction: first branch strand end goes down to  4RUM|1|A|C|44
pMakeNodesJunction: second branch strand start goes up to 4RUM|1|A|G|47
pMakeNodesJunction: last strand of junction goes down to  4RUM|1|A|U|85

Junction with 2 loops, call it J7431
Actual Branch 1 of junction J7431 - Nucleotides 4RUM|1|A|A|17 to 4RUM|1|A|G|45, length   4
Actual Branch 2 of junction J7431 - Nucleotides 4RUM|1|A|G|46 to 4RUM|1|A|G|86, length   7
  3 Junction

2B Branch 1 of 2 of junction J7431 - Nucleotides    17 to    45, length   4
pMakeNodes starting loop:     a=4RUM|1|A|A|17 B=4RUM|1|A|G|45
  5 Basepair    17   45 AG tHS 
No need to probe because of interaction between a=4RUM|1|A|G|18 B=4RUM|1|A|C|44
  6 Basepair    18   44 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7431 - Nucleotides    46 to    86, length   7
pMakeNodes starting loop:     a=4RUM|1|A|G|46 B=4RUM|1|A|G|86
    Insertion on left  4RUM|1|A|G|46
  8 Initial     46 (1 insertion) and   86 (0 insertion)
pMakeNodesJunction: a=4RUM|1|A|G|47 r=4RUM|1|A|G|47 s=4RUM|1|A|C|60 t=4RUM|1|A|A|61 u=B=4RUM|1|A|G|86
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4RUM|1|A|G|47 and 4RUM|1|A|C|60 and between 4RUM|1|A|A|61 and 4RUM|1|A|G|86
pMakeNodesJunction: about to make a junction: a=4RUM|1|A|G|47 s=4RUM|1|A|C|60 t=4RUM|1|A|A|61 B=4RUM|1|A|G|86
pMakeNodesJunction: first branch starts at   4RUM|1|A|G|47
pMakeNodesJunction: first branch ends around 4RUM|1|A|C|60
pMakeNodesJunction: second branch starts at  4RUM|1|A|A|61
pMakeNodesJunction: junction ends at         4RUM|1|A|G|86
pMakeNodesJunction: first branch strand start goes up to  4RUM|1|A|G|47
pMakeNodesJunction: first branch strand end goes down to  4RUM|1|A|C|60
pMakeNodesJunction: second branch strand start goes up to 4RUM|1|A|A|62
pMakeNodesJunction: last strand of junction goes down to  4RUM|1|A|U|85

Junction with 2 loops, call it J3922
Actual Branch 1 of junction J3922 - Nucleotides 4RUM|1|A|G|47 to 4RUM|1|A|C|60, length   2
Actual Branch 2 of junction J3922 - Nucleotides 4RUM|1|A|A|61 to 4RUM|1|A|G|86, length   4
  9 Junction

2B Branch 1 of 2 of junction J3922 - Nucleotides    47 to    60, length   2
pMakeNodes starting loop:     a=4RUM|1|A|G|47 B=4RUM|1|A|C|60
 11 Basepair    47   60 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J3922 - Nucleotides    61 to    86, length   4
pMakeNodes starting loop:     a=4RUM|1|A|A|61 B=4RUM|1|A|G|86
 14 Basepair    61   86 AG tHS 
No need to probe because of interaction between a=4RUM|1|A|A|62 B=4RUM|1|A|U|85
 15 Basepair    62   85 AU cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  7 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
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
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4RUM|1|A|G|87
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4RUM|1|A|G|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: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 1 1 0 0 0 0 0 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
           RightLetter: 'GG'
               Comment: ' // Basepair C16 - G88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J7431'
        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 4RUM|1|A|G|87'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J7431'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: 'J7431'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A17 - G86 ID J7431'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: 'J7431'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             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 A17 - G45 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]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             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 - 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]
           numbranches: []
              NormCons: []

Node 9

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: []
           numbranches: []
              NormCons: 1

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: 'J7431'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4RUM|1|A|G|46 - 4RUM|1|A|G|86 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4RUM|1|A|G|46'
              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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: 'J3922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G47 - G86 ID J3922'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G47 - 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]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J3922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             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 A61 - G86 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]
           numbranches: []
              NormCons: []

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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A62 - U85 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   9   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13  Junction Left  7 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  18  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  20   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: 'J7431'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J7431'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4RUM|1|A|G|46 - 4RUM|1|A|G|86 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_26776.1. Nodes 6 and 10 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J3922'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J3922'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_26776.1. Nodes 14 and 17 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_26776.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5062

Timestamp 18-Jul-2025 00:12:49
pMakeSCFGModels: Making JAR3D model for motif group J4_26796.1, number 15 of 65
pMakeNodes starting loop:     a=4V88|1|A6|C|99 B=4V88|1|A6|G|384
pMakeNodes making a cluster near strand break a=4V88|1|A6|C|99 B=4V88|1|A6|G|384
pMakeNodesCluster: amax is 8 bmin is 18, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 18 to 18
aa is 2 bb is 18
  2 Cluster   4V88|1|A6|C|99:4V88|1|A6|A|100 4V88|1|A6|G|384:4V88|1|A6|G|384
    LR Inter  4V88|1|A6|C|99 4V88|1|A6|G|384 cWW 
    LL Inter  4V88|1|A6|C|99 4V88|1|A6|A|100 cSH 
pMakeNodesCluster a=3 B=17 at the end
pMakeNodesCluster a=3 B=17 at the end
pMakeNodes probe for inserts:  a=4V88|1|A6|U|101 B=4V88|1|A6|G|383
    Insertion on left  4V88|1|A6|U|101
    Insertion on left  4V88|1|A6|U|102
    Insertion on left  4V88|1|A6|A|103
    Insertion on left  4V88|1|A6|A|104
  3 Initial    101 (4 insertion) and  383 (0 insertion)
pMakeNodes probed for insert:  a=4V88|1|A6|A|105 B=4V88|1|A6|G|383
pMakeNodesJunction: a=4V88|1|A6|A|105 r=4V88|1|A6|A|105 s=4V88|1|A6|C|308 t=4V88|1|A6|C|309 u=B=4V88|1|A6|G|383
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|A|105 and 4V88|1|A6|C|308 and between 4V88|1|A6|C|309 and 4V88|1|A6|G|383
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|A|105 s=4V88|1|A6|C|308 t=4V88|1|A6|C|309 B=4V88|1|A6|G|383
pMakeNodesJunction: first branch starts at   4V88|1|A6|A|105
pMakeNodesJunction: first branch ends around 4V88|1|A6|C|308
pMakeNodesJunction: second branch starts at  4V88|1|A6|C|309
pMakeNodesJunction: junction ends at         4V88|1|A6|G|383
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|C|107
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|G|307
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|C|309
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|G|383

Junction with 2 loops, call it J6554
Actual Branch 1 of junction J6554 - Nucleotides 4V88|1|A6|A|105 to 4V88|1|A6|C|308, length   5
Actual Branch 2 of junction J6554 - Nucleotides 4V88|1|A6|C|309 to 4V88|1|A6|G|383, length   6
  4 Junction

2B Branch 1 of 2 of junction J6554 - Nucleotides   105 to   308, length   5
pMakeNodes starting loop:     a=4V88|1|A6|A|105 B=4V88|1|A6|C|308
  6 Basepair   105  308 AC tHW 
pMakeNodes probe for inserts:  a=4V88|1|A6|U|106 B=4V88|1|A6|G|307
    Insertion on left  4V88|1|A6|U|106
pMakeNodesProbeForInsertions:  a 4V88|1|A6|C|107 interacts with 4V88|1|A6|G|307
pMakeNodesProbeForInsertions:  B 4V88|1|A6|G|307 interacts with 4V88|1|A6|C|107
pMakeNodesProbeForInsertions:  B 4V88|1|A6|G|307 interacts with 4V88|1|A6|C|107
pMakeNodes probed for insert:  a=4V88|1|A6|C|107 B=4V88|1|A6|G|307
  7 Basepair   107  307 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6554 - Nucleotides   309 to   383, length   6
pMakeNodes starting loop:     a=4V88|1|A6|C|309 B=4V88|1|A6|G|383
  9 Initial    309 (0 insertion) and  383 (0 insertion)
pMakeNodesJunction: a=4V88|1|A6|C|309 r=4V88|1|A6|C|309 s=4V88|1|A6|G|357 t=4V88|1|A6|U|358 u=B=4V88|1|A6|G|383
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|C|309 and 4V88|1|A6|G|357 and between 4V88|1|A6|U|358 and 4V88|1|A6|G|383
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|C|309 s=4V88|1|A6|G|357 t=4V88|1|A6|U|358 B=4V88|1|A6|G|383
pMakeNodesJunction: first branch starts at   4V88|1|A6|C|309
pMakeNodesJunction: first branch ends around 4V88|1|A6|G|357
pMakeNodesJunction: second branch starts at  4V88|1|A6|U|358
pMakeNodesJunction: junction ends at         4V88|1|A6|G|383
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|C|309
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|G|357
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|C|361
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|G|383

Junction with 2 loops, call it J1711
Actual Branch 1 of junction J1711 - Nucleotides 4V88|1|A6|C|309 to 4V88|1|A6|G|357, length   2
Actual Branch 2 of junction J1711 - Nucleotides 4V88|1|A6|U|358 to 4V88|1|A6|G|383, length   4
 10 Junction

2B Branch 1 of 2 of junction J1711 - Nucleotides   309 to   357, length   2
pMakeNodes starting loop:     a=4V88|1|A6|C|309 B=4V88|1|A6|G|357
 12 Basepair   309  357 CG cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J1711 - Nucleotides   358 to   383, length   4
pMakeNodes starting loop:     a=4V88|1|A6|U|358 B=4V88|1|A6|G|383
    Insertion on left  4V88|1|A6|U|358
    Insertion on left  4V88|1|A6|A|360
pMakeNodesProbeForInsertions:  a 4V88|1|A6|C|361 interacts with 4V88|1|A6|G|383
pMakeNodesProbeForInsertions:  B 4V88|1|A6|G|383 interacts with 4V88|1|A6|C|361
pMakeNodesProbeForInsertions:  B 4V88|1|A6|G|383 interacts with 4V88|1|A6|C|361
 14 Initial    358 (2 insertion) and  383 (0 insertion)
 15 Basepair   361  383 CG cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 18
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   4  Junction Left  7 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   8   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:   9   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  10  Junction Left 12 Right 17
pMakeMotifModelFromSSF:  11   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  13   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  14   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  15  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  16   Hairpin Left 17 Right 16
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|101
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|102
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|103
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|104
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|106
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|358
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|359
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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 18
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Cluster node 4V88|1|A6|C|99:4V88|1|A6|A|100 and 4V88|1|A6|G|384:4V88|1|A6|G|384'
              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: 0.2506
           numbranches: []
                  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: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUAA'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|U|101 - 4V88|1|A6|G|383 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 17
             Insertion: []
                    id: 'J6554'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V88|1|A6|U|101'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

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: 'J6554'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: []
           numbranches: []
                  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: 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 4V88|1|A6|U|102'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 'Fixed'
              nextnode: 9
             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 4V88|1|A6|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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 'Initial'
              nextnode: 10
             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: [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
           numbranches: []
                  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: 17
             Insertion: []
                    id: 'J6554'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V88|1|A6|A|104'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 17
             Insertion: []
                    id: 'J1711'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 7
            RightIndex: 17
             Insertion: []
                    id: 'J6554'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A105 - G383 ID J6554'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: 'J6554'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            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: 'AU'
           RightLetter: 'C'
               Comment: ' // Basepair A105 - C308 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

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 4V88|1|A6|U|106'
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

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: [5×5 double]
                     Z: []
           MiddleIndex: 17
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

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 C107 - G307 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 18

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: 'J6554'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|C|309 - 4V88|1|A6|G|383 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: 'J1711'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C309 - G383 ID J1711'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

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: 'J1711'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C309 - G357 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 14
            RightIndex: 17
             Insertion: []
                    id: 'J1711'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|U|358 - 4V88|1|A6|G|383 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 14
            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 4V88|1|A6|U|358'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 15
            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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 28
             LeftIndex: 15
            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 4V88|1|A6|A|359'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 30
             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 C361 - G383 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 32
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 18
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 17
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 17
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  12  Junction Left  7 Right 17
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right 11
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
pMakeMotifModelFromSSF:  19   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  20  Junction Left 12 Right 17
pMakeMotifModelFromSSF:  21   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  22  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  23   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  24   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  25     Fixed Left 14 Right 17
pMakeMotifModelFromSSF:  26   Initial Left 15 Right 17
pMakeMotifModelFromSSF:  27     Fixed Left 15 Right 17
pMakeMotifModelFromSSF:  28   Initial Left 16 Right 17
pMakeMotifModelFromSSF:  29  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  30   Hairpin Left 17 Right 16
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a junction at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: 'J6554'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: 'J6554'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|C|309 - 4V88|1|A6|G|383 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_26796.1. Nodes 13 and 19 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J1711'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 14
            RightIndex: 17
             Insertion: []
                    id: 'J1711'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|U|358 - 4V88|1|A6|G|383 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_26796.1. Nodes 21 and 24 both model an insertion before position 14. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a junction at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 5 and 14
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 5 and 14
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_26796.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.8726

Timestamp 18-Jul-2025 00:12:49
pMakeSCFGModels: Making JAR3D model for motif group J4_28426.1, number 16 of 65
pMakeNodes starting loop:     a=4OQU|1|A|C|5 B=4OQU|1|A|G|67
  2 Basepair     5   67 CG cWW 
pMakeNodes probe for inserts:  a=4OQU|1|A|A|6 B=4OQU|1|A|G|66
    Insertion on left  4OQU|1|A|A|6
    Insertion on left  4OQU|1|A|C|7
    Insertion on left  4OQU|1|A|G|8
    Insertion on left  4OQU|1|A|A|9
pMakeNodes probed for insert:  a=4OQU|1|A|G|10 B=4OQU|1|A|G|66
pMakeNodesJunction: a=4OQU|1|A|G|10 r=4OQU|1|A|G|10 s=4OQU|1|A|C|21 t=4OQU|1|A|G|22 u=B=4OQU|1|A|G|66
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4OQU|1|A|G|10 and 4OQU|1|A|C|21 and between 4OQU|1|A|G|22 and 4OQU|1|A|G|66
pMakeNodesJunction: about to make a junction: a=4OQU|1|A|G|10 s=4OQU|1|A|C|21 t=4OQU|1|A|G|22 B=4OQU|1|A|G|66
pMakeNodesJunction: first branch starts at   4OQU|1|A|G|10
pMakeNodesJunction: first branch ends around 4OQU|1|A|C|21
pMakeNodesJunction: second branch starts at  4OQU|1|A|G|22
pMakeNodesJunction: junction ends at         4OQU|1|A|G|66
pMakeNodesJunction: first branch strand start goes up to  4OQU|1|A|G|10
pMakeNodesJunction: first branch strand end goes down to  4OQU|1|A|C|21
pMakeNodesJunction: second branch strand start goes up to 4OQU|1|A|G|22
pMakeNodesJunction: last strand of junction goes down to  4OQU|1|A|G|66

Junction with 2 loops, call it J7060
Actual Branch 1 of junction J7060 - Nucleotides 4OQU|1|A|G|10 to 4OQU|1|A|C|21, length   2
Actual Branch 2 of junction J7060 - Nucleotides 4OQU|1|A|G|22 to 4OQU|1|A|G|66, length   6
  3 Junction

2B Branch 1 of 2 of junction J7060 - Nucleotides    10 to    21, length   2
pMakeNodes starting loop:     a=4OQU|1|A|G|10 B=4OQU|1|A|C|21
  5 Basepair    10   21 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7060 - Nucleotides    22 to    66, length   6
pMakeNodes starting loop:     a=4OQU|1|A|G|22 B=4OQU|1|A|G|66
  7 Initial     22 (0 insertion) and   66 (0 insertion)
pMakeNodesJunction: a=4OQU|1|A|G|22 r=4OQU|1|A|G|22 s=4OQU|1|A|U|50 t=4OQU|1|A|C|51 u=B=4OQU|1|A|G|66
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4OQU|1|A|G|22 and 4OQU|1|A|U|50 and between 4OQU|1|A|C|51 and 4OQU|1|A|G|66
pMakeNodesJunction: about to make a junction: a=4OQU|1|A|G|22 s=4OQU|1|A|U|50 t=4OQU|1|A|C|51 B=4OQU|1|A|G|66
pMakeNodesJunction: first branch starts at   4OQU|1|A|G|22
pMakeNodesJunction: first branch ends around 4OQU|1|A|U|50
pMakeNodesJunction: second branch starts at  4OQU|1|A|C|51
pMakeNodesJunction: junction ends at         4OQU|1|A|G|66
pMakeNodesJunction: first branch strand start goes up to  4OQU|1|A|G|22
pMakeNodesJunction: first branch strand end goes down to  4OQU|1|A|U|50
pMakeNodesJunction: second branch strand start goes up to 4OQU|1|A|C|53
pMakeNodesJunction: last strand of junction goes down to  4OQU|1|A|G|66

Junction with 2 loops, call it J318
Actual Branch 1 of junction J318 - Nucleotides 4OQU|1|A|G|22 to 4OQU|1|A|U|50, length   2
Actual Branch 2 of junction J318 - Nucleotides 4OQU|1|A|C|51 to 4OQU|1|A|G|66, length   4
  8 Junction

2B Branch 1 of 2 of junction J318 - Nucleotides    22 to    50, length   2
pMakeNodes starting loop:     a=4OQU|1|A|G|22 B=4OQU|1|A|U|50
 10 Basepair    22   50 GU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J318 - Nucleotides    51 to    66, length   4
pMakeNodes starting loop:     a=4OQU|1|A|C|51 B=4OQU|1|A|G|66
    Insertion on left  4OQU|1|A|C|51
    Insertion on left  4OQU|1|A|A|52
pMakeNodesProbeForInsertions:  a 4OQU|1|A|C|53 interacts with 4OQU|1|A|G|66
pMakeNodesProbeForInsertions:  B 4OQU|1|A|G|66 interacts with 4OQU|1|A|C|53
pMakeNodesProbeForInsertions:  B 4OQU|1|A|G|66 interacts with 4OQU|1|A|C|53
 12 Initial     51 (2 insertion) and   66 (0 insertion)
 13 Basepair    53   66 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  8 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  8 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  12   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  13  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  14   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|C|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OQU|1|A|A|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: 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: []
           numbranches: []
              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-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: 'CACGA'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G67 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J7060'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4OQU|1|A|A|6'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7060'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4OQU|1|A|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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: '*'
           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: []
           numbranches: []
              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: 13
             Insertion: []
                    id: 'J7060'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4OQU|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: []
           numbranches: []
              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: 'J318'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J318'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4OQU|1|A|A|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: '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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J7060'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - G66 ID J7060'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7060'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G10 - 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]
           numbranches: []
              NormCons: []

Node 14

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: []
           numbranches: []
              NormCons: 1

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J7060'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4OQU|1|A|G|22 - 4OQU|1|A|G|66 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J318'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G22 - G66 ID J318'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J318'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G22 - 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]
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: 1

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J318'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: []
               Comment: ' // Initial node 4OQU|1|A|C|51 - 4OQU|1|A|G|66 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             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 4OQU|1|A|C|51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             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: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 4OQU|1|A|A|52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             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 - G66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  6 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  15   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  16  Junction Left  8 Right 13
pMakeMotifModelFromSSF:  17   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  23     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  25  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  26   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J7060'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J7060'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4OQU|1|A|G|22 - 4OQU|1|A|G|66 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_28426.1. Nodes 12 and 15 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: 'J318'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J318'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: []
               Comment: ' // Initial node 4OQU|1|A|C|51 - 4OQU|1|A|G|66 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_28426.1. Nodes 17 and 20 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_28426.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9665

Timestamp 18-Jul-2025 00:12:49
pMakeSCFGModels: Making JAR3D model for motif group J4_28473.1, number 17 of 65
pMakeNodes starting loop:     a=4V9F|1|0|G|2679 B=4V9F|1|0|C|2806
  2 Basepair  2679 2806 GC cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|2680 B=4V9F|1|0|A|2805
    Insertion on left  4V9F|1|0|A|2680
    Insertion on left  4V9F|1|0|A|2681
pMakeNodes probed for insert:  a=4V9F|1|0|C|2682 B=4V9F|1|0|A|2805
pMakeNodesJunction: a=4V9F|1|0|C|2682 r=4V9F|1|0|C|2682 s=4V9F|1|0|G|2712 t=4V9F|1|0|G|2713 u=B=4V9F|1|0|A|2805
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|C|2682 and 4V9F|1|0|G|2712 and between 4V9F|1|0|G|2713 and 4V9F|1|0|A|2805
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|C|2682 s=4V9F|1|0|G|2712 t=4V9F|1|0|G|2713 B=4V9F|1|0|A|2805
pMakeNodesJunction: first branch starts at   4V9F|1|0|C|2682
pMakeNodesJunction: first branch ends around 4V9F|1|0|G|2712
pMakeNodesJunction: second branch starts at  4V9F|1|0|G|2713
pMakeNodesJunction: junction ends at         4V9F|1|0|A|2805
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|C|2682
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|G|2712
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|2713
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|2804

Junction with 2 loops, call it J2769
Actual Branch 1 of junction J2769 - Nucleotides 4V9F|1|0|C|2682 to 4V9F|1|0|G|2712, length   2
Actual Branch 2 of junction J2769 - Nucleotides 4V9F|1|0|G|2713 to 4V9F|1|0|A|2805, length   7
  3 Junction

2B Branch 1 of 2 of junction J2769 - Nucleotides  2682 to  2712, length   2
pMakeNodes starting loop:     a=4V9F|1|0|C|2682 B=4V9F|1|0|G|2712
  5 Basepair  2682 2712 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2769 - Nucleotides  2713 to  2805, length   7
pMakeNodes starting loop:     a=4V9F|1|0|G|2713 B=4V9F|1|0|A|2805
  7 Initial   2713 (0 insertion) and 2805 (0 insertion)
pMakeNodesJunction: a=4V9F|1|0|G|2713 r=4V9F|1|0|G|2713 s=4V9F|1|0|C|2767 t=4V9F|1|0|A|2768 u=B=4V9F|1|0|A|2805
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|2713 and 4V9F|1|0|C|2767 and between 4V9F|1|0|A|2768 and 4V9F|1|0|A|2805
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|2713 s=4V9F|1|0|C|2767 t=4V9F|1|0|A|2768 B=4V9F|1|0|A|2805
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|2713
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|2767
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|2768
pMakeNodesJunction: junction ends at         4V9F|1|0|A|2805
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|2713
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|2767
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|2770
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|2804

Junction with 2 loops, call it J461
Actual Branch 1 of junction J461 - Nucleotides 4V9F|1|0|G|2713 to 4V9F|1|0|C|2767, length   2
Actual Branch 2 of junction J461 - Nucleotides 4V9F|1|0|A|2768 to 4V9F|1|0|A|2805, length   5
  8 Junction

2B Branch 1 of 2 of junction J461 - Nucleotides  2713 to  2767, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|2713 B=4V9F|1|0|C|2767
 10 Basepair  2713 2767 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J461 - Nucleotides  2768 to  2805, length   5
pMakeNodes starting loop:     a=4V9F|1|0|A|2768 B=4V9F|1|0|A|2805
    Insertion on left  4V9F|1|0|A|2768
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|2769 interacts with 4V9F|1|0|A|2805
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2805 interacts with 4V9F|1|0|C|2769
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2805 interacts with 4V9F|1|0|C|2769
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 12 Initial   2768 (1 insertion) and 2805 (0 insertion)
 13 Basepair  2769 2805 CA tHS 
No need to probe because of interaction between a=4V9F|1|0|G|2770 B=4V9F|1|0|C|2804
 14 Basepair  2770 2804 GC cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 12
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 12
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|2680
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|2681
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|2768
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: []
           numbranches: []
              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: 'GAA'
           RightLetter: 'C'
               Comment: ' // Basepair G2679 - C2806 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J2769'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2680'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2769'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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|A|2681'
              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]
           numbranches: []
              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: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J2769'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C2682 - A2805 ID J2769'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2769'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C2682 - G2712 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J2769'
        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|0|G|2713 - 4V9F|1|0|A|2805 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J461'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2713 - A2805 ID J461'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J461'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
               Comment: ' // Basepair G2713 - C2767 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

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: 'J461'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|2768 - 4V9F|1|0|A|2805 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2768'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             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: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C2769 - A2805 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]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 G2770 - C2804 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 12
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  20  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  21   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J2769'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J2769'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|2713 - 4V9F|1|0|A|2805 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_28473.1. Nodes 8 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J461'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: 'J461'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|2768 - 4V9F|1|0|A|2805 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_28473.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_28473.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8578

Timestamp 18-Jul-2025 00:12:50
pMakeSCFGModels: Making JAR3D model for motif group J4_34476.1, number 18 of 65
pMakeNodes starting loop:     a=4V9F|1|0|G|1828 B=4V9F|1|0|C|2020
  2 Basepair  1828 2020 GC cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1829 B=4V9F|1|0|A|2019
    Insertion on right 4V9F|1|0|A|2019
pMakeNodes probed for insert:  a=4V9F|1|0|A|1829 B=4V9F|1|0|A|2018
  3 Basepair  1829 2018 AA tSW 
pMakeNodes probe for inserts:  a=4V9F|1|0|C|1830 B=4V9F|1|0|U|2017
pMakeNodes probed for insert:  a=4V9F|1|0|C|1830 B=4V9F|1|0|U|2017
pMakeNodesJunction: a=4V9F|1|0|C|1830 r=4V9F|1|0|C|1830 s=4V9F|1|0|U|1846 t=4V9F|1|0|A|1847 u=B=4V9F|1|0|U|2017
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|C|1830 and 4V9F|1|0|U|1846 and between 4V9F|1|0|A|1847 and 4V9F|1|0|U|2017
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|C|1830 s=4V9F|1|0|U|1846 t=4V9F|1|0|A|1847 B=4V9F|1|0|U|2017
pMakeNodesJunction: first branch starts at   4V9F|1|0|C|1830
pMakeNodesJunction: first branch ends around 4V9F|1|0|U|1846
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|1847
pMakeNodesJunction: junction ends at         4V9F|1|0|U|2017
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|1832
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|1844
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|1848
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|A|2015

Junction with 2 loops, call it J971
Actual Branch 1 of junction J971 - Nucleotides 4V9F|1|0|C|1830 to 4V9F|1|0|U|1846, length   6
Actual Branch 2 of junction J971 - Nucleotides 4V9F|1|0|A|1847 to 4V9F|1|0|U|2017, length  10
  4 Junction

2B Branch 1 of 2 of junction J971 - Nucleotides  1830 to  1846, length   6
pMakeNodes starting loop:     a=4V9F|1|0|C|1830 B=4V9F|1|0|U|1846
  6 Basepair  1830 1846 CU tHS 
No need to probe because of interaction between a=4V9F|1|0|U|1831 B=4V9F|1|0|A|1845
  7 Basepair  1831 1845 UA tHS 
No need to probe because of interaction between a=4V9F|1|0|G|1832 B=4V9F|1|0|C|1844
  8 Basepair  1832 1844 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J971 - Nucleotides  1847 to  2017, length  10
pMakeNodes starting loop:     a=4V9F|1|0|A|1847 B=4V9F|1|0|U|2017
 10 Initial   1847 (0 insertion) and 2017 (0 insertion)
pMakeNodesJunction: a=4V9F|1|0|A|1847 r=4V9F|1|0|A|1847 s=4V9F|1|0|G|1884 t=4V9F|1|0|A|1885 u=B=4V9F|1|0|U|2017
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|A|1847 and 4V9F|1|0|G|1884 and between 4V9F|1|0|A|1885 and 4V9F|1|0|U|2017
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|A|1847 s=4V9F|1|0|G|1884 t=4V9F|1|0|A|1885 B=4V9F|1|0|U|2017
pMakeNodesJunction: first branch starts at   4V9F|1|0|A|1847
pMakeNodesJunction: first branch ends around 4V9F|1|0|G|1884
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|1885
pMakeNodesJunction: junction ends at         4V9F|1|0|U|2017
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|1848
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|U|1883
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|U|1887
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|A|2015

Junction with 2 loops, call it J8234
Actual Branch 1 of junction J8234 - Nucleotides 4V9F|1|0|A|1847 to 4V9F|1|0|G|1884, length   4
Actual Branch 2 of junction J8234 - Nucleotides 4V9F|1|0|A|1885 to 4V9F|1|0|U|2017, length   6
 11 Junction

2B Branch 1 of 2 of junction J8234 - Nucleotides  1847 to  1884, length   4
pMakeNodes starting loop:     a=4V9F|1|0|A|1847 B=4V9F|1|0|G|1884
 13 Basepair  1847 1884 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|G|1848 B=4V9F|1|0|U|1883
 14 Basepair  1848 1883 GU cWW 
 15 Hairpin type *

2B Branch 2 of 2 of junction J8234 - Nucleotides  1885 to  2017, length   6
pMakeNodes starting loop:     a=4V9F|1|0|A|1885 B=4V9F|1|0|U|2017
 17 Basepair  1885 2017 AU tHS 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1886 B=4V9F|1|0|U|2016
    Insertion on left  4V9F|1|0|A|1886
    Insertion on right 4V9F|1|0|U|2016
pMakeNodesProbeForInsertions:  a 4V9F|1|0|U|1887 interacts with 4V9F|1|0|A|2015
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2015 interacts with 4V9F|1|0|U|1887
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2015 interacts with 4V9F|1|0|U|1887
pMakeNodes probed for insert:  a=4V9F|1|0|U|1887 B=4V9F|1|0|A|2015
 18 Basepair  1887 2015 UA cWW 
 19 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 19
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 18
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 18
pMakeMotifModelFromSSF:  11  Junction Left  9 Right 18
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  16   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  17  Basepair Left 13 Right 18
pMakeMotifModelFromSSF:  18  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  19   Hairpin Left 16 Right 15
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 4V9F|1|0|A|2019
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|1886
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|U|2016
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: 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: []
           numbranches: []
              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: [0.9950 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: 'AC'
               Comment: ' // Basepair G1828 - C2020 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 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|2019'
              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]
           numbranches: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: 'J971'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            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: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1829 - A2018 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 10]
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: 'J971'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1830 - U2017 ID J971'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J971'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             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 C1830 - U1846 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]
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             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 U1831 - A1845 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]
           numbranches: []
              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 G1832 - C1844 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: 'J971'
        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|0|A|1847 - 4V9F|1|0|U|2017 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [12 16]
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: 'J8234'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1847 - U2017 ID J8234'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J8234'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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 A1847 - 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]
           numbranches: []
              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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1848 - 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]
           numbranches: []
              NormCons: []

Node 17

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: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
                    id: 'J8234'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 13
            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: 'AA'
           RightLetter: 'UU'
               Comment: ' // Basepair A1885 - U2017 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]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 14
            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 4V9F|1|0|A|1886'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 15
            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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 15
            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|U|2016'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1887 - A2015 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  2 Right 19
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right 19
pMakeMotifModelFromSSF:   6  Junction Left  3 Right 18
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 18
pMakeMotifModelFromSSF:  13  Junction Left  9 Right 18
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  16  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  18   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  19  Basepair Left 13 Right 18
pMakeMotifModelFromSSF:  20     Fixed Left 14 Right 17
pMakeMotifModelFromSSF:  21   Initial Left 15 Right 17
pMakeMotifModelFromSSF:  22     Fixed Left 15 Right 17
pMakeMotifModelFromSSF:  23   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  24  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  25   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J971'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: 'J971'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|1847 - 4V9F|1|0|U|2017 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_34476.1. Nodes 7 and 12 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J8234'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
                    id: 'J8234'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_34476.1. Nodes 14 and 18 both model an insertion before position 13. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHS  between 2 and 9
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 2 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_34476.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.1340
  -13.1340

Timestamp 18-Jul-2025 00:12:50
pMakeSCFGModels: Making JAR3D model for motif group J4_35578.2, number 19 of 65
pMakeNodes starting loop:     a=4LFB|1|A|G|115 B=4LFB|1|A|C|312
  2 Basepair   115  312 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|116 B=4LFB|1|A|C|311
    Insertion on left  4LFB|1|A|A|116
    Insertion on left  4LFB|1|A|G|117
    Insertion on left  4LFB|1|A|U|118
    Insertion on left  4LFB|1|A|A|119
    Insertion on left  4LFB|1|A|A|120
pMakeNodes probed for insert:  a=4LFB|1|A|G|122 B=4LFB|1|A|C|311
pMakeNodesJunction: a=4LFB|1|A|G|122 r=4LFB|1|A|G|122 s=4LFB|1|A|U|239 t=4LFB|1|A|C|240 u=B=4LFB|1|A|C|311
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|G|122 and 4LFB|1|A|U|239 and between 4LFB|1|A|C|240 and 4LFB|1|A|C|311
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|G|122 s=4LFB|1|A|U|239 t=4LFB|1|A|C|240 B=4LFB|1|A|C|311
pMakeNodesJunction: first branch starts at   4LFB|1|A|G|122
pMakeNodesJunction: first branch ends around 4LFB|1|A|U|239
pMakeNodesJunction: second branch starts at  4LFB|1|A|C|240
pMakeNodesJunction: junction ends at         4LFB|1|A|C|311
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|G|122
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|U|239
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|C|240
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|311

Junction with 2 loops, call it J6948
Actual Branch 1 of junction J6948 - Nucleotides 4LFB|1|A|G|122 to 4LFB|1|A|U|239, length   2
Actual Branch 2 of junction J6948 - Nucleotides 4LFB|1|A|C|240 to 4LFB|1|A|C|311, length   6
  3 Junction

2B Branch 1 of 2 of junction J6948 - Nucleotides   122 to   239, length   2
pMakeNodes starting loop:     a=4LFB|1|A|G|122 B=4LFB|1|A|U|239
  5 Basepair   122  239 GU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J6948 - Nucleotides   240 to   311, length   6
pMakeNodes starting loop:     a=4LFB|1|A|C|240 B=4LFB|1|A|C|311
  7 Initial    240 (0 insertion) and  311 (0 insertion)
pMakeNodesJunction: a=4LFB|1|A|C|240 r=4LFB|1|A|C|240 s=4LFB|1|A|G|286 t=4LFB|1|A|U|287 u=B=4LFB|1|A|C|311
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|C|240 and 4LFB|1|A|G|286 and between 4LFB|1|A|U|287 and 4LFB|1|A|C|311
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|C|240 s=4LFB|1|A|G|286 t=4LFB|1|A|U|287 B=4LFB|1|A|C|311
pMakeNodesJunction: first branch starts at   4LFB|1|A|C|240
pMakeNodesJunction: first branch ends around 4LFB|1|A|G|286
pMakeNodesJunction: second branch starts at  4LFB|1|A|U|287
pMakeNodesJunction: junction ends at         4LFB|1|A|C|311
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|C|240
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|G|286
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|G|289
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|311

Junction with 2 loops, call it J3170
Actual Branch 1 of junction J3170 - Nucleotides 4LFB|1|A|C|240 to 4LFB|1|A|G|286, length   2
Actual Branch 2 of junction J3170 - Nucleotides 4LFB|1|A|U|287 to 4LFB|1|A|C|311, length   4
  8 Junction

2B Branch 1 of 2 of junction J3170 - Nucleotides   240 to   286, length   2
pMakeNodes starting loop:     a=4LFB|1|A|C|240 B=4LFB|1|A|G|286
 10 Basepair   240  286 CG cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J3170 - Nucleotides   287 to   311, length   4
pMakeNodes starting loop:     a=4LFB|1|A|U|287 B=4LFB|1|A|C|311
    Insertion on left  4LFB|1|A|U|287
    Insertion on left  4LFB|1|A|A|288
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|289 interacts with 4LFB|1|A|C|311
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|311 interacts with 4LFB|1|A|G|289
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|311 interacts with 4LFB|1|A|G|289
 12 Initial    287 (2 insertion) and  311 (0 insertion)
 13 Basepair   289  311 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  7 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  9 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  12   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  14   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|116
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|117
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|118
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|119
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|120
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|286
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|287
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: []
           numbranches: []
              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-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: 'GAGUAA'
           RightLetter: 'C'
               Comment: ' // Basepair G115 - C312 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J6948'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|116'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6948'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 4LFB|1|A|G|117'
              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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 14
             Insertion: []
                    id: 'J6948'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|118'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'J3170'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J3170'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|119'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: '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]
           numbranches: []
              NormCons: []

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 4LFB|1|A|A|120'
              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: []
           numbranches: []
              NormCons: 1

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: 'J3170'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: 'J6948'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G122 - C311 ID J6948'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6948'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G122 - U239 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J6948'
        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|C|240 - 4LFB|1|A|C|311 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J3170'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C240 - C311 ID J3170'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J3170'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C240 - G286 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

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: []
           numbranches: []
              NormCons: 1

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J3170'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|U|287 - 4LFB|1|A|C|311 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 4LFB|1|A|G|286'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 12
            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 4LFB|1|A|U|287'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             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 G289 - C311 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 28

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  7 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  18  Junction Left  9 Right 14
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  20  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  21   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  23     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  26   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  27  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  28   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J6948'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J6948'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|240 - 4LFB|1|A|C|311 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_35578.2. Nodes 14 and 17 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J3170'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J3170'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|U|287 - 4LFB|1|A|C|311 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_35578.2. Nodes 19 and 22 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 5 and 11
pConservedInteractionList: did not find a substitution probability matrix for rib  between 7 and 13
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 5 and 11
pConservedInteractionList: did not find a substitution probability matrix for rib  between 7 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_35578.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2564
   -8.8206
   -8.2564

Timestamp 18-Jul-2025 00:12:50
pMakeSCFGModels: Making JAR3D model for motif group J4_36296.1, number 20 of 65
pMakeNodes starting loop:     a=2CSX|1|C|G|7 B=2CSX|1|C|C|66
  2 Basepair     7   66 GC cWW 
pMakeNodes probe for inserts:  a=2CSX|1|C|A|9 B=2CSX|1|C|C|65
    Insertion on left  2CSX|1|C|A|9
pMakeNodes probed for insert:  a=2CSX|1|C|G|10 B=2CSX|1|C|C|65
pMakeNodesJunction: a=2CSX|1|C|G|10 r=2CSX|1|C|G|10 s=2CSX|1|C|C|25 t=2CSX|1|C|G|26 u=B=2CSX|1|C|C|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 2CSX|1|C|G|10 and 2CSX|1|C|C|25 and between 2CSX|1|C|G|26 and 2CSX|1|C|C|65
pMakeNodesJunction: about to make a junction: a=2CSX|1|C|G|10 s=2CSX|1|C|C|25 t=2CSX|1|C|G|26 B=2CSX|1|C|C|65
pMakeNodesJunction: first branch starts at   2CSX|1|C|G|10
pMakeNodesJunction: first branch ends around 2CSX|1|C|C|25
pMakeNodesJunction: second branch starts at  2CSX|1|C|G|26
pMakeNodesJunction: junction ends at         2CSX|1|C|C|65
pMakeNodesJunction: first branch strand start goes up to  2CSX|1|C|G|10
pMakeNodesJunction: first branch strand end goes down to  2CSX|1|C|C|25
pMakeNodesJunction: second branch strand start goes up to 2CSX|1|C|G|27
pMakeNodesJunction: last strand of junction goes down to  2CSX|1|C|C|65

Junction with 2 loops, call it J9502
Actual Branch 1 of junction J9502 - Nucleotides 2CSX|1|C|G|10 to 2CSX|1|C|C|25, length   2
Actual Branch 2 of junction J9502 - Nucleotides 2CSX|1|C|G|26 to 2CSX|1|C|C|65, length   7
  3 Junction

2B Branch 1 of 2 of junction J9502 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=2CSX|1|C|G|10 B=2CSX|1|C|C|25
  5 Basepair    10   25 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9502 - Nucleotides    26 to    65, length   7
pMakeNodes starting loop:     a=2CSX|1|C|G|26 B=2CSX|1|C|C|65
    Insertion on left  2CSX|1|C|G|26
  7 Initial     26 (1 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=2CSX|1|C|G|27 r=2CSX|1|C|G|27 s=2CSX|1|C|C|43 t=2CSX|1|C|A|44 u=B=2CSX|1|C|C|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2CSX|1|C|G|27 and 2CSX|1|C|C|43 and between 2CSX|1|C|A|44 and 2CSX|1|C|C|65
pMakeNodesJunction: about to make a junction: a=2CSX|1|C|G|27 s=2CSX|1|C|C|43 t=2CSX|1|C|A|44 B=2CSX|1|C|C|65
pMakeNodesJunction: first branch starts at   2CSX|1|C|G|27
pMakeNodesJunction: first branch ends around 2CSX|1|C|C|43
pMakeNodesJunction: second branch starts at  2CSX|1|C|A|44
pMakeNodesJunction: junction ends at         2CSX|1|C|C|65
pMakeNodesJunction: first branch strand start goes up to  2CSX|1|C|G|27
pMakeNodesJunction: first branch strand end goes down to  2CSX|1|C|C|43
pMakeNodesJunction: second branch strand start goes up to 2CSX|1|C|G|49
pMakeNodesJunction: last strand of junction goes down to  2CSX|1|C|C|65

Junction with 2 loops, call it J344
Actual Branch 1 of junction J344 - Nucleotides 2CSX|1|C|G|27 to 2CSX|1|C|C|43, length   2
Actual Branch 2 of junction J344 - Nucleotides 2CSX|1|C|A|44 to 2CSX|1|C|C|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J344 - Nucleotides    27 to    43, length   2
pMakeNodes starting loop:     a=2CSX|1|C|G|27 B=2CSX|1|C|C|43
 10 Basepair    27   43 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J344 - Nucleotides    44 to    65, length   4
pMakeNodes starting loop:     a=2CSX|1|C|A|44 B=2CSX|1|C|C|65
    Insertion on left  2CSX|1|C|A|44
    Insertion on left  2CSX|1|C|G|46
pMakeNodesProbeForInsertions:  a 2CSX|1|C|G|49 interacts with 2CSX|1|C|C|65
pMakeNodesProbeForInsertions:  B 2CSX|1|C|C|65 interacts with 2CSX|1|C|G|49
pMakeNodesProbeForInsertions:  B 2CSX|1|C|C|65 interacts with 2CSX|1|C|G|49
 12 Initial     44 (2 insertion) and   65 (0 insertion)
 13 Basepair    49   65 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  14   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2CSX|1|C|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2CSX|1|C|C|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2CSX|1|C|C|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2CSX|1|C|A|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: 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: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - 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]
           numbranches: []
              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: 'J9502'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2CSX|1|C|U|8'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9502'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: 'J9502'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - C65 ID J9502'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9502'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G10 - 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]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: 'J9502'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 2CSX|1|C|G|26 - 2CSX|1|C|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 2CSX|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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J344'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G27 - C65 ID J344'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J344'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
               Comment: ' // Basepair G27 - 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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J344'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 2CSX|1|C|A|44 - 2CSX|1|C|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             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 2CSX|1|C|C|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2CSX|1|C|A|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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 G49 - C65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 11
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  21  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  22   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J9502'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: 'J9502'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 2CSX|1|C|G|26 - 2CSX|1|C|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_36296.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J344'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J344'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 2CSX|1|C|A|44 - 2CSX|1|C|C|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_36296.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_36296.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.6546
  -12.2032
  -12.1942
  -16.3006
  -14.9016

Timestamp 18-Jul-2025 00:12:51
pMakeSCFGModels: Making JAR3D model for motif group J4_36540.1, number 21 of 65
pMakeNodes starting loop:     a=3F2X|1|X|G|32 B=3F2X|1|X|C|83
  2 Basepair    32   83 GC cWW 
pMakeNodes probe for inserts:  a=3F2X|1|X|G|33 B=3F2X|1|X|C|82
pMakeNodes probed for insert:  a=3F2X|1|X|G|33 B=3F2X|1|X|C|82
pMakeNodesJunction: a=3F2X|1|X|G|33 r=3F2X|1|X|G|33 s=3F2X|1|X|C|46 t=3F2X|1|X|G|47 u=B=3F2X|1|X|C|82
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3F2X|1|X|G|33 and 3F2X|1|X|C|46 and between 3F2X|1|X|G|47 and 3F2X|1|X|C|82
pMakeNodesJunction: about to make a junction: a=3F2X|1|X|G|33 s=3F2X|1|X|C|46 t=3F2X|1|X|G|47 B=3F2X|1|X|C|82
pMakeNodesJunction: first branch starts at   3F2X|1|X|G|33
pMakeNodesJunction: first branch ends around 3F2X|1|X|C|46
pMakeNodesJunction: second branch starts at  3F2X|1|X|G|47
pMakeNodesJunction: junction ends at         3F2X|1|X|C|82
pMakeNodesJunction: first branch strand start goes up to  3F2X|1|X|G|33
pMakeNodesJunction: first branch strand end goes down to  3F2X|1|X|C|46
pMakeNodesJunction: second branch strand start goes up to 3F2X|1|X|A|49
pMakeNodesJunction: last strand of junction goes down to  3F2X|1|X|A|80

Junction with 2 loops, call it J4387
Actual Branch 1 of junction J4387 - Nucleotides 3F2X|1|X|G|33 to 3F2X|1|X|C|46, length   2
Actual Branch 2 of junction J4387 - Nucleotides 3F2X|1|X|G|47 to 3F2X|1|X|C|82, length  10
  3 Junction

2B Branch 1 of 2 of junction J4387 - Nucleotides    33 to    46, length   2
pMakeNodes starting loop:     a=3F2X|1|X|G|33 B=3F2X|1|X|C|46
  5 Basepair    33   46 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J4387 - Nucleotides    47 to    82, length  10
pMakeNodes starting loop:     a=3F2X|1|X|G|47 B=3F2X|1|X|C|82
    Insertion on left  3F2X|1|X|G|47
    Insertion on left  3F2X|1|X|A|48
  7 Initial     47 (2 insertion) and   82 (0 insertion)
pMakeNodesJunction: a=3F2X|1|X|A|49 r=3F2X|1|X|A|49 s=3F2X|1|X|U|60 t=3F2X|1|X|G|62 u=B=3F2X|1|X|C|82
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3F2X|1|X|A|49 and 3F2X|1|X|U|60 and between 3F2X|1|X|G|62 and 3F2X|1|X|C|82
pMakeNodesJunction: about to make a junction: a=3F2X|1|X|A|49 s=3F2X|1|X|U|60 t=3F2X|1|X|G|62 B=3F2X|1|X|C|82
pMakeNodesJunction: first branch starts at   3F2X|1|X|A|49
pMakeNodesJunction: first branch ends around 3F2X|1|X|U|60
pMakeNodesJunction: second branch starts at  3F2X|1|X|G|62
pMakeNodesJunction: junction ends at         3F2X|1|X|C|82
pMakeNodesJunction: first branch strand start goes up to  3F2X|1|X|A|49
pMakeNodesJunction: first branch strand end goes down to  3F2X|1|X|U|60
pMakeNodesJunction: second branch strand start goes up to 3F2X|1|X|U|64
pMakeNodesJunction: last strand of junction goes down to  3F2X|1|X|A|80

Junction with 2 loops, call it J3815
Actual Branch 1 of junction J3815 - Nucleotides 3F2X|1|X|A|49 to 3F2X|1|X|U|60, length   2
Actual Branch 2 of junction J3815 - Nucleotides 3F2X|1|X|G|62 to 3F2X|1|X|C|82, length   6
  8 Junction

2B Branch 1 of 2 of junction J3815 - Nucleotides    49 to    60, length   2
pMakeNodes starting loop:     a=3F2X|1|X|A|49 B=3F2X|1|X|U|60
 10 Basepair    49   60 AU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J3815 - Nucleotides    62 to    82, length   6
pMakeNodes starting loop:     a=3F2X|1|X|G|62 B=3F2X|1|X|C|82
    Insertion on left  3F2X|1|X|G|62
pMakeNodesProbeForInsertions:  a 3F2X|1|X|A|63 interacts with 3F2X|1|X|C|82
pMakeNodesProbeForInsertions:  B 3F2X|1|X|C|82 interacts with 3F2X|1|X|A|63
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3F2X|1|X|C|82 interacts with 3F2X|1|X|A|63
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 12 Initial     62 (1 insertion) and   82 (0 insertion)
 13 Basepair    63   82 AC cSS 
pMakeNodes probe for inserts:  a=3F2X|1|X|U|64 B=3F2X|1|X|A|81
    Insertion on right 3F2X|1|X|A|81
pMakeNodesProbeForInsertions:  a 3F2X|1|X|U|64 interacts with 3F2X|1|X|A|80
pMakeNodesProbeForInsertions:  B 3F2X|1|X|A|80 interacts with 3F2X|1|X|U|64
pMakeNodesProbeForInsertions:  B 3F2X|1|X|A|80 interacts with 3F2X|1|X|U|64
pMakeNodes probed for insert:  a=3F2X|1|X|U|64 B=3F2X|1|X|A|80
 14 Basepair    64   80 UA cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 13
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3F2X|1|X|G|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3F2X|1|X|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3F2X|1|X|U|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3F2X|1|X|A|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: 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: []
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G32 - C83 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: 'J4387'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G33 - C82 ID J4387'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J4387'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G33 - 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 13
             Insertion: []
                    id: 'J4387'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 3F2X|1|X|G|47 - 3F2X|1|X|C|82 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J3815'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3F2X|1|X|G|47'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: 'J3815'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             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 3F2X|1|X|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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             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: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J3815'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A49 - C82 ID J3815'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3815'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A49 - U60 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

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: 'J3815'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 3F2X|1|X|G|62 - 3F2X|1|X|C|82 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3F2X|1|X|U|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 13
             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: 'AC'
               Comment: ' // Basepair A63 - C82 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]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 3F2X|1|X|A|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 23
             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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U64 - 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]
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 13
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 13
pMakeMotifModelFromSSF:  20     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  22  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  23   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J4387'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J4387'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 3F2X|1|X|G|47 - 3F2X|1|X|C|82 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_36540.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J3815'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.0238 0.9512 0.0238 0.0012]
       rightLetterDist: [0.1250 0.1250 0.1250 0.6250 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J3815'
        leftLengthDist: [0.0238 0.9512 0.0238 0.0012]
        leftLetterDist: [0.1250 0.1250 0.1250 0.6250 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 3F2X|1|X|G|62 - 3F2X|1|X|C|82 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_36540.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_36540.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1653
  -10.1653

Timestamp 18-Jul-2025 00:12:51
pMakeSCFGModels: Making JAR3D model for motif group J4_36568.1, number 22 of 65
pMakeNodes starting loop:     a=6CZR|1|1a|G|137 B=6CZR|1|1a|C|217
  2 Basepair   137  217 GC cWW 
No need to probe because of interaction between a=6CZR|1|1a|A|138 B=6CZR|1|1a|G|216
  3 Basepair   138  216 AG cWW 
pMakeNodes probe for inserts:  a=6CZR|1|1a|G|139 B=6CZR|1|1a|C|215
pMakeNodes probed for insert:  a=6CZR|1|1a|G|139 B=6CZR|1|1a|C|215
pMakeNodesJunction: a=6CZR|1|1a|G|139 r=6CZR|1|1a|G|139 s=6CZR|1|1a|C|173 t=6CZR|1|1a|A|174 u=B=6CZR|1|1a|C|215
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6CZR|1|1a|G|139 and 6CZR|1|1a|C|173 and between 6CZR|1|1a|A|174 and 6CZR|1|1a|C|215
pMakeNodesJunction: about to make a junction: a=6CZR|1|1a|G|139 s=6CZR|1|1a|C|173 t=6CZR|1|1a|A|174 B=6CZR|1|1a|C|215
pMakeNodesJunction: first branch starts at   6CZR|1|1a|G|139
pMakeNodesJunction: first branch ends around 6CZR|1|1a|C|173
pMakeNodesJunction: second branch starts at  6CZR|1|1a|A|174
pMakeNodesJunction: junction ends at         6CZR|1|1a|C|215
pMakeNodesJunction: first branch strand start goes up to  6CZR|1|1a|G|139
pMakeNodesJunction: first branch strand end goes down to  6CZR|1|1a|C|173
pMakeNodesJunction: second branch strand start goes up to 6CZR|1|1a|G|178
pMakeNodesJunction: last strand of junction goes down to  6CZR|1|1a|C|215

Junction with 2 loops, call it J7655
Actual Branch 1 of junction J7655 - Nucleotides 6CZR|1|1a|G|139 to 6CZR|1|1a|C|173, length   2
Actual Branch 2 of junction J7655 - Nucleotides 6CZR|1|1a|A|174 to 6CZR|1|1a|C|215, length  11
  4 Junction

2B Branch 1 of 2 of junction J7655 - Nucleotides   139 to   173, length   2
pMakeNodes starting loop:     a=6CZR|1|1a|G|139 B=6CZR|1|1a|C|173
  6 Basepair   139  173 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7655 - Nucleotides   174 to   215, length  11
pMakeNodes starting loop:     a=6CZR|1|1a|A|174 B=6CZR|1|1a|C|215
  8 Initial    174 (0 insertion) and  215 (0 insertion)
pMakeNodesJunction: a=6CZR|1|1a|A|174 r=6CZR|1|1a|A|174 s=6CZR|1|1a|A|203 t=6CZR|1|1a|A|204 u=B=6CZR|1|1a|C|215
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6CZR|1|1a|A|174 and 6CZR|1|1a|A|203 and between 6CZR|1|1a|A|204 and 6CZR|1|1a|C|215
pMakeNodesJunction: about to make a junction: a=6CZR|1|1a|A|174 s=6CZR|1|1a|A|203 t=6CZR|1|1a|A|204 B=6CZR|1|1a|C|215
pMakeNodesJunction: first branch starts at   6CZR|1|1a|A|174
pMakeNodesJunction: first branch ends around 6CZR|1|1a|A|203
pMakeNodesJunction: second branch starts at  6CZR|1|1a|A|204
pMakeNodesJunction: junction ends at         6CZR|1|1a|C|215
pMakeNodesJunction: first branch strand start goes up to  6CZR|1|1a|G|178
pMakeNodesJunction: first branch strand end goes down to  6CZR|1|1a|C|201
pMakeNodesJunction: second branch strand start goes up to 6CZR|1|1a|G|205
pMakeNodesJunction: last strand of junction goes down to  6CZR|1|1a|C|215

Junction with 2 loops, call it J7951
Actual Branch 1 of junction J7951 - Nucleotides 6CZR|1|1a|A|174 to 6CZR|1|1a|A|203, length   8
Actual Branch 2 of junction J7951 - Nucleotides 6CZR|1|1a|A|204 to 6CZR|1|1a|C|215, length   3
  9 Junction

2B Branch 1 of 2 of junction J7951 - Nucleotides   174 to   203, length   8
pMakeNodes starting loop:     a=6CZR|1|1a|A|174 B=6CZR|1|1a|A|203
 11 Basepair   174  203 AA tWH 
No need to probe because of interaction between a=6CZR|1|1a|U|175 B=6CZR|1|1a|A|202
 12 Basepair   175  202 UA tWH 
pMakeNodes probe for inserts:  a=6CZR|1|1a|G|176 B=6CZR|1|1a|C|201
pMakeNodesProbeForInsertions:  a 6CZR|1|1a|G|176 interacts with 6CZR|1|1a|U|177
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|C|201 interacts with 6CZR|1|1a|G|178
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|C|201 interacts with 6CZR|1|1a|G|178
pMakeNodes probed for insert:  a=6CZR|1|1a|G|176 B=6CZR|1|1a|C|201
pMakeNodes making a cluster near strand break a=6CZR|1|1a|G|176 B=6CZR|1|1a|C|201
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 9 and then 10 to 10
aa is 9 bb is 10
 13 Cluster   6CZR|1|1a|G|176:6CZR|1|1a|G|178 6CZR|1|1a|C|201:6CZR|1|1a|C|201
    LR Inter  6CZR|1|1a|G|178 6CZR|1|1a|C|201 cWW 
    LL Inter  6CZR|1|1a|G|176 6CZR|1|1a|U|177 cSH 
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
 14 Hairpin type *

2B Branch 2 of 2 of junction J7951 - Nucleotides   204 to   215, length   3
pMakeNodes starting loop:     a=6CZR|1|1a|A|204 B=6CZR|1|1a|C|215
    Insertion on left  6CZR|1|1a|A|204
pMakeNodesProbeForInsertions:  a 6CZR|1|1a|G|205 interacts with 6CZR|1|1a|C|215
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|C|215 interacts with 6CZR|1|1a|G|205
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|C|215 interacts with 6CZR|1|1a|G|205
 15 Initial    204 (1 insertion) and  215 (0 insertion)
 16 Basepair   205  215 GC cWW 
 17 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  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  13   Cluster Left  7  8  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  15   Initial Left 13 Right 15
pMakeMotifModelFromSSF:  16  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  17   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|A|204
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: 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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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 G137 - C217 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A138 - 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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J7655'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G139 - C215 ID J7655'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J7655'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             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 G139 - C173 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 7

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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

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: 'J7655'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|A|174 - 6CZR|1|1a|C|215 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 15]
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J7951'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A174 - C215 ID J7951'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J7951'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             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 A174 - A203 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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: [0.9950 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 U175 - A202 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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 14
             LeftIndex: [7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 6CZR|1|1a|G|176:6CZR|1|1a|G|178 and 6CZR|1|1a|C|201:6CZR|1|1a|C|201'
              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: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 13
            RightIndex: 15
             Insertion: []
                    id: 'J7951'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|A|204 - 6CZR|1|1a|C|215 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 13
            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 6CZR|1|1a|A|204'
              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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 15
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G205 - C215 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

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  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  13   Cluster Left  7  8  9 Right 10
pMakeMotifModelFromSSF:  14   Initial Left 10 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  16   Initial Left 13 Right 15
pMakeMotifModelFromSSF:  17     Fixed Left 13 Right 15
pMakeMotifModelFromSSF:  18   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  19  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  20   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J7655'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J7655'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|A|174 - 6CZR|1|1a|C|215 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_36568.1. Nodes 5 and 8 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J7951'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 13
            RightIndex: 15
             Insertion: []
                    id: 'J7951'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|A|204 - 6CZR|1|1a|C|215 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_36568.1. Nodes 10 and 16 both model an insertion before position 13. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 12
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 12 and 17
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 13 and 16
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 1 and 12
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 12 and 17
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 13 and 16
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_36568.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0468
  -10.0468

Timestamp 18-Jul-2025 00:12:51
pMakeSCFGModels: Making JAR3D model for motif group J4_40439.2, number 23 of 65
pMakeNodes starting loop:     a=4KQY|1|A|C|8 B=4KQY|1|A|G|110
  2 Basepair     8  110 CG cWW 
pMakeNodes probe for inserts:  a=4KQY|1|A|A|9 B=4KQY|1|A|A|109
    Insertion on left  4KQY|1|A|A|9
    Insertion on left  4KQY|1|A|A|10
    Insertion on left  4KQY|1|A|G|11
    Insertion on left  4KQY|1|A|A|12
pMakeNodes probed for insert:  a=4KQY|1|A|G|13 B=4KQY|1|A|A|109
pMakeNodesJunction: a=4KQY|1|A|G|13 r=4KQY|1|A|G|13 s=4KQY|1|A|C|42 t=4KQY|1|A|A|43 u=B=4KQY|1|A|A|109
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4KQY|1|A|G|13 and 4KQY|1|A|C|42 and between 4KQY|1|A|A|43 and 4KQY|1|A|A|109
pMakeNodesJunction: about to make a junction: a=4KQY|1|A|G|13 s=4KQY|1|A|C|42 t=4KQY|1|A|A|43 B=4KQY|1|A|A|109
pMakeNodesJunction: first branch starts at   4KQY|1|A|G|13
pMakeNodesJunction: first branch ends around 4KQY|1|A|C|42
pMakeNodesJunction: second branch starts at  4KQY|1|A|A|43
pMakeNodesJunction: junction ends at         4KQY|1|A|A|109
pMakeNodesJunction: first branch strand start goes up to  4KQY|1|A|G|13
pMakeNodesJunction: first branch strand end goes down to  4KQY|1|A|C|42
pMakeNodesJunction: second branch strand start goes up to 4KQY|1|A|A|43
pMakeNodesJunction: last strand of junction goes down to  4KQY|1|A|A|109

Junction with 2 loops, call it J1868
Actual Branch 1 of junction J1868 - Nucleotides 4KQY|1|A|G|13 to 4KQY|1|A|C|42, length   2
Actual Branch 2 of junction J1868 - Nucleotides 4KQY|1|A|A|43 to 4KQY|1|A|A|109, length   7
  3 Junction

2B Branch 1 of 2 of junction J1868 - Nucleotides    13 to    42, length   2
pMakeNodes starting loop:     a=4KQY|1|A|G|13 B=4KQY|1|A|C|42
  5 Basepair    13   42 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1868 - Nucleotides    43 to   109, length   7
pMakeNodes starting loop:     a=4KQY|1|A|A|43 B=4KQY|1|A|A|109
  7 Initial     43 (0 insertion) and  109 (0 insertion)
pMakeNodesJunction: a=4KQY|1|A|A|43 r=4KQY|1|A|A|43 s=4KQY|1|A|U|81 t=4KQY|1|A|A|82 u=B=4KQY|1|A|A|109
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4KQY|1|A|A|43 and 4KQY|1|A|U|81 and between 4KQY|1|A|A|82 and 4KQY|1|A|A|109
pMakeNodesJunction: about to make a junction: a=4KQY|1|A|A|43 s=4KQY|1|A|U|81 t=4KQY|1|A|A|82 B=4KQY|1|A|A|109
pMakeNodesJunction: first branch starts at   4KQY|1|A|A|43
pMakeNodesJunction: first branch ends around 4KQY|1|A|U|81
pMakeNodesJunction: second branch starts at  4KQY|1|A|A|82
pMakeNodesJunction: junction ends at         4KQY|1|A|A|109
pMakeNodesJunction: first branch strand start goes up to  4KQY|1|A|A|43
pMakeNodesJunction: first branch strand end goes down to  4KQY|1|A|U|81
pMakeNodesJunction: second branch strand start goes up to 4KQY|1|A|U|85
pMakeNodesJunction: last strand of junction goes down to  4KQY|1|A|A|109

Junction with 2 loops, call it J4897
Actual Branch 1 of junction J4897 - Nucleotides 4KQY|1|A|A|43 to 4KQY|1|A|U|81, length   2
Actual Branch 2 of junction J4897 - Nucleotides 4KQY|1|A|A|82 to 4KQY|1|A|A|109, length   5
  8 Junction

2B Branch 1 of 2 of junction J4897 - Nucleotides    43 to    81, length   2
pMakeNodes starting loop:     a=4KQY|1|A|A|43 B=4KQY|1|A|U|81
 10 Basepair    43   81 AU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J4897 - Nucleotides    82 to   109, length   5
pMakeNodes starting loop:     a=4KQY|1|A|A|82 B=4KQY|1|A|A|109
    Insertion on left  4KQY|1|A|A|82
    Insertion on left  4KQY|1|A|A|83
    Insertion on left  4KQY|1|A|A|84
pMakeNodesProbeForInsertions:  a 4KQY|1|A|U|85 interacts with 4KQY|1|A|A|109
pMakeNodesProbeForInsertions:  B 4KQY|1|A|A|109 interacts with 4KQY|1|A|U|85
pMakeNodesProbeForInsertions:  B 4KQY|1|A|A|109 interacts with 4KQY|1|A|U|85
 12 Initial     82 (3 insertion) and  109 (0 insertion)
 13 Basepair    85  109 UA cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  8 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  8 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  12   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  14   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|A|82
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|A|83
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|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: 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: []
           numbranches: []
              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-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: 'CAAGA'
           RightLetter: 'G'
               Comment: ' // Basepair C8 - 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]
           numbranches: []
              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: 'J1868'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|A|9'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1868'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 4KQY|1|A|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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 14
             Insertion: []
                    id: 'J1868'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'J4897'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J4897'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|A|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: '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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J1868'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G13 - A109 ID J1868'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1868'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G13 - C42 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 14

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: []
           numbranches: []
              NormCons: 1

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J1868'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4KQY|1|A|A|43 - 4KQY|1|A|A|109 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J4897'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A43 - A109 ID J4897'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J4897'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 A43 - 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]
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: 1

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: 'J4897'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: []
               Comment: ' // Initial node 4KQY|1|A|A|82 - 4KQY|1|A|A|109 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 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|A|82'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             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: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 4KQY|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: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 12
            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 4KQY|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: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             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 U85 - A109 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 28

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  6 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  15   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  16  Junction Left  8 Right 14
pMakeMotifModelFromSSF:  17   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  23     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  26   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  27  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  28   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J1868'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J1868'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4KQY|1|A|A|43 - 4KQY|1|A|A|109 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_40439.2. Nodes 12 and 15 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: 'J4897'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: 'J4897'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: []
               Comment: ' // Initial node 4KQY|1|A|A|82 - 4KQY|1|A|A|109 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_40439.2. Nodes 17 and 20 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_40439.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4169
   -8.8493
   -8.8493

Timestamp 18-Jul-2025 00:12:52
pMakeSCFGModels: Making JAR3D model for motif group J4_43687.1, number 24 of 65
pMakeNodes starting loop:     a=7KKV|1|B|U|526 B=7KKV|1|B|A|513
  2 Basepair   526  513 UA cWW 
pMakeNodes probe for inserts:  a=7KKV|1|B|G|527 B=7KKV|1|B|A|512
pMakeNodes probed for insert:  a=7KKV|1|B|G|527 B=7KKV|1|B|A|512
pMakeNodesJunction: a=7KKV|1|B|G|527 r=7KKV|1|B|G|527 s=7KKV|1|B|C|535 t=7KKV|1|B|U|536 u=B=7KKV|1|B|A|512
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 7KKV|1|B|G|527 and 7KKV|1|B|C|535 and between 7KKV|1|B|U|536 and 7KKV|1|B|A|512
pMakeNodesJunction: about to make a junction: a=7KKV|1|B|G|527 s=7KKV|1|B|C|535 t=7KKV|1|B|U|536 B=7KKV|1|B|A|512
pMakeNodesJunction: first branch starts at   7KKV|1|B|G|527
pMakeNodesJunction: first branch ends around 7KKV|1|B|C|535
pMakeNodesJunction: second branch starts at  7KKV|1|B|U|536
pMakeNodesJunction: junction ends at         7KKV|1|B|A|512
pMakeNodesJunction: first branch strand start goes up to  7KKV|1|B|G|527
pMakeNodesJunction: first branch strand end goes down to  7KKV|1|B|C|535
pMakeNodesJunction: second branch strand start goes up to 7KKV|1|B|A|537
pMakeNodesJunction: last strand of junction goes down to  7KKV|1|B|A|512

Junction with 2 loops, call it J4455
Actual Branch 1 of junction J4455 - Nucleotides 7KKV|1|B|G|527 to 7KKV|1|B|C|535, length   2
Actual Branch 2 of junction J4455 - Nucleotides 7KKV|1|B|U|536 to 7KKV|1|B|A|512, length   6
  3 Junction

2B Branch 1 of 2 of junction J4455 - Nucleotides   527 to   535, length   2
pMakeNodes starting loop:     a=7KKV|1|B|G|527 B=7KKV|1|B|C|535
  5 Basepair   527  535 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J4455 - Nucleotides   536 to   512, length   6
pMakeNodes starting loop:     a=7KKV|1|B|U|536 B=7KKV|1|B|A|512
  7 Initial    536 (0 insertion) and  512 (0 insertion)
pMakeNodesJunction: a=7KKV|1|B|U|536 r=7KKV|1|B|U|536 s=7KKV|1|B|C|491 t=7KKV|1|B|U|492 u=B=7KKV|1|B|A|512
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7KKV|1|B|U|536 and 7KKV|1|B|C|491 and between 7KKV|1|B|U|492 and 7KKV|1|B|A|512
pMakeNodesJunction: about to make a junction: a=7KKV|1|B|U|536 s=7KKV|1|B|C|491 t=7KKV|1|B|U|492 B=7KKV|1|B|A|512
pMakeNodesJunction: first branch starts at   7KKV|1|B|U|536
pMakeNodesJunction: first branch ends around 7KKV|1|B|C|491
pMakeNodesJunction: second branch starts at  7KKV|1|B|U|492
pMakeNodesJunction: junction ends at         7KKV|1|B|A|512
pMakeNodesJunction: first branch strand start goes up to  7KKV|1|B|A|537
pMakeNodesJunction: first branch strand end goes down to  7KKV|1|B|U|490
pMakeNodesJunction: second branch strand start goes up to 7KKV|1|B|U|492
pMakeNodesJunction: last strand of junction goes down to  7KKV|1|B|A|512

Junction with 2 loops, call it J6463
Actual Branch 1 of junction J6463 - Nucleotides 7KKV|1|B|U|536 to 7KKV|1|B|C|491, length   4
Actual Branch 2 of junction J6463 - Nucleotides 7KKV|1|B|U|492 to 7KKV|1|B|A|512, length   2
  8 Junction

2B Branch 1 of 2 of junction J6463 - Nucleotides   536 to   491, length   4
pMakeNodes starting loop:     a=7KKV|1|B|U|536 B=7KKV|1|B|C|491
 10 Basepair   536  491 UC cWW 
No need to probe because of interaction between a=7KKV|1|B|A|537 B=7KKV|1|B|U|490
 11 Basepair   537  490 AU cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J6463 - Nucleotides   492 to   512, length   2
pMakeNodes starting loop:     a=7KKV|1|B|U|492 B=7KKV|1|B|A|512
 14 Basepair   492  512 UA cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   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: 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: []
           numbranches: []
              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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U526 - A513 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G527 - A512 ID J4455'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J4455'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G527 - C535 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7KKV|1|B|U|536 - 7KKV|1|B|A|512 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: 'J6463'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U536 - A512 ID J6463'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J6463'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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: 'C'
               Comment: ' // Basepair U536 - 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]
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A537 - U490 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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: 'J6463'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U492 - A512 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J4455'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7KKV|1|B|U|536 - 7KKV|1|B|A|512 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_43687.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J6463'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: 'J6463'
        leftLengthDist: [0.4934 0.4934 0.0126 6.0168e-04]
        leftLetterDist: [0.5000 0.1667 0.1667 0.1667 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_43687.1. Nodes 9 and 13 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_43687.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5986
   -9.7620

Timestamp 18-Jul-2025 00:12:52
pMakeSCFGModels: Making JAR3D model for motif group J4_44058.1, number 25 of 65
pMakeNodes starting loop:     a=6VMY|1|A|G|245 B=6VMY|1|A|C|309
  2 Basepair   245  309 GC cWW 
No need to probe because of interaction between a=6VMY|1|A|G|246 B=6VMY|1|A|A|308
  3 Basepair   246  308 GA cWW 
pMakeNodes probe for inserts:  a=6VMY|1|A|A|247 B=6VMY|1|A|A|306
    Insertion on left  6VMY|1|A|A|247
pMakeNodes probed for insert:  a=6VMY|1|A|A|248 B=6VMY|1|A|A|306
pMakeNodesJunction: a=6VMY|1|A|A|248 r=6VMY|1|A|A|248 s=6VMY|1|A|C|266 t=6VMY|1|A|G|267 u=B=6VMY|1|A|A|306
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6VMY|1|A|A|248 and 6VMY|1|A|C|266 and between 6VMY|1|A|G|267 and 6VMY|1|A|A|306
pMakeNodesJunction: about to make a junction: a=6VMY|1|A|A|248 s=6VMY|1|A|C|266 t=6VMY|1|A|G|267 B=6VMY|1|A|A|306
pMakeNodesJunction: first branch starts at   6VMY|1|A|A|248
pMakeNodesJunction: first branch ends around 6VMY|1|A|C|266
pMakeNodesJunction: second branch starts at  6VMY|1|A|G|267
pMakeNodesJunction: junction ends at         6VMY|1|A|A|306
pMakeNodesJunction: first branch strand start goes up to  6VMY|1|A|A|249
pMakeNodesJunction: first branch strand end goes down to  6VMY|1|A|U|264
pMakeNodesJunction: second branch strand start goes up to 6VMY|1|A|G|267
pMakeNodesJunction: last strand of junction goes down to  6VMY|1|A|G|304

Junction with 2 loops, call it J7093
Actual Branch 1 of junction J7093 - Nucleotides 6VMY|1|A|A|248 to 6VMY|1|A|C|266, length   5
Actual Branch 2 of junction J7093 - Nucleotides 6VMY|1|A|G|267 to 6VMY|1|A|A|306, length   6
  4 Junction

2B Branch 1 of 2 of junction J7093 - Nucleotides   248 to   266, length   5
pMakeNodes starting loop:     a=6VMY|1|A|A|248 B=6VMY|1|A|C|266
  6 Basepair   248  266 AC cSS 
pMakeNodes probe for inserts:  a=6VMY|1|A|A|249 B=6VMY|1|A|G|265
    Insertion on right 6VMY|1|A|G|265
pMakeNodesProbeForInsertions:  a 6VMY|1|A|A|249 interacts with 6VMY|1|A|U|264
pMakeNodesProbeForInsertions:  B 6VMY|1|A|U|264 interacts with 6VMY|1|A|A|249
pMakeNodesProbeForInsertions:  B 6VMY|1|A|U|264 interacts with 6VMY|1|A|A|249
pMakeNodes probed for insert:  a=6VMY|1|A|A|249 B=6VMY|1|A|U|264
  7 Basepair   249  264 AU cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J7093 - Nucleotides   267 to   306, length   6
pMakeNodes starting loop:     a=6VMY|1|A|G|267 B=6VMY|1|A|A|306
  9 Initial    267 (0 insertion) and  306 (0 insertion)
pMakeNodesJunction: a=6VMY|1|A|G|267 r=6VMY|1|A|G|267 s=6VMY|1|A|C|275 t=6VMY|1|A|A|276 u=B=6VMY|1|A|A|306
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6VMY|1|A|G|267 and 6VMY|1|A|C|275 and between 6VMY|1|A|A|276 and 6VMY|1|A|A|306
pMakeNodesJunction: about to make a junction: a=6VMY|1|A|G|267 s=6VMY|1|A|C|275 t=6VMY|1|A|A|276 B=6VMY|1|A|A|306
pMakeNodesJunction: first branch starts at   6VMY|1|A|G|267
pMakeNodesJunction: first branch ends around 6VMY|1|A|C|275
pMakeNodesJunction: second branch starts at  6VMY|1|A|A|276
pMakeNodesJunction: junction ends at         6VMY|1|A|A|306
pMakeNodesJunction: first branch strand start goes up to  6VMY|1|A|G|267
pMakeNodesJunction: first branch strand end goes down to  6VMY|1|A|C|275
pMakeNodesJunction: second branch strand start goes up to 6VMY|1|A|C|277
pMakeNodesJunction: last strand of junction goes down to  6VMY|1|A|G|304

Junction with 2 loops, call it J7546
Actual Branch 1 of junction J7546 - Nucleotides 6VMY|1|A|G|267 to 6VMY|1|A|C|275, length   2
Actual Branch 2 of junction J7546 - Nucleotides 6VMY|1|A|A|276 to 6VMY|1|A|A|306, length   4
 10 Junction

2B Branch 1 of 2 of junction J7546 - Nucleotides   267 to   275, length   2
pMakeNodes starting loop:     a=6VMY|1|A|G|267 B=6VMY|1|A|C|275
 12 Basepair   267  275 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J7546 - Nucleotides   276 to   306, length   4
pMakeNodes starting loop:     a=6VMY|1|A|A|276 B=6VMY|1|A|A|306
 15 Basepair   276  306 AA cWW 
No need to probe because of interaction between a=6VMY|1|A|C|277 B=6VMY|1|A|G|304
 16 Basepair   277  304 CG cWW 
 17 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  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  10  Junction Left  9 Right 14
pMakeMotifModelFromSSF:  11   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  14   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  15  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:  16  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  17   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 6VMY|1|A|A|247
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6VMY|1|A|G|265
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: []
           numbranches: []
              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 G245 - C309 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [0.0826 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 G246 - A308 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J7093'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|247'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7093'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J7093'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A248 - A306 ID J7093'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J7093'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             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: 'GC'
               Comment: ' // Basepair A248 - C266 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]
           numbranches: []
              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: 'J7093'
        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 6VMY|1|A|G|265'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J7546'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A249 - U264 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J7093'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6VMY|1|A|G|267 - 6VMY|1|A|A|306 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J7546'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G267 - A306 ID J7546'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J7546'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G267 - C275 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J7546'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             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: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A276 - A306 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 C277 - G304 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  8
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
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  14  Junction Left  9 Right 14
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:  20  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  21   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J7093'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J7093'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6VMY|1|A|G|267 - 6VMY|1|A|A|306 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_44058.1. Nodes 7 and 13 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J7546'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J7546'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_44058.1. Nodes 15 and 18 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_44058.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.0406

Timestamp 18-Jul-2025 00:12:52
pMakeSCFGModels: Making JAR3D model for motif group J4_45582.1, number 26 of 65
pMakeNodes starting loop:     a=4Y1M|1|B|C|17 B=4Y1M|1|B|G|94
  2 Basepair    17   94 CG cWW 
pMakeNodes probe for inserts:  a=4Y1M|1|B|G|18 B=4Y1M|1|B|A|93
    Insertion on left  4Y1M|1|B|G|18
pMakeNodes probed for insert:  a=4Y1M|1|B|A|19 B=4Y1M|1|B|A|93
pMakeNodesJunction: a=4Y1M|1|B|A|19 r=4Y1M|1|B|A|19 s=4Y1M|1|B|U|34 t=4Y1M|1|B|G|35 u=B=4Y1M|1|B|A|93
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4Y1M|1|B|A|19 and 4Y1M|1|B|U|34 and between 4Y1M|1|B|G|35 and 4Y1M|1|B|A|93
pMakeNodesJunction: about to make a junction: a=4Y1M|1|B|A|19 s=4Y1M|1|B|U|34 t=4Y1M|1|B|G|35 B=4Y1M|1|B|A|93
pMakeNodesJunction: first branch starts at   4Y1M|1|B|A|19
pMakeNodesJunction: first branch ends around 4Y1M|1|B|U|34
pMakeNodesJunction: second branch starts at  4Y1M|1|B|G|35
pMakeNodesJunction: junction ends at         4Y1M|1|B|A|93
pMakeNodesJunction: first branch strand start goes up to  4Y1M|1|B|A|19
pMakeNodesJunction: first branch strand end goes down to  4Y1M|1|B|U|34
pMakeNodesJunction: second branch strand start goes up to 4Y1M|1|B|G|35
pMakeNodesJunction: last strand of junction goes down to  4Y1M|1|B|C|92

Junction with 2 loops, call it J2760
Actual Branch 1 of junction J2760 - Nucleotides 4Y1M|1|B|A|19 to 4Y1M|1|B|U|34, length   2
Actual Branch 2 of junction J2760 - Nucleotides 4Y1M|1|B|G|35 to 4Y1M|1|B|A|93, length   6
  3 Junction

2B Branch 1 of 2 of junction J2760 - Nucleotides    19 to    34, length   2
pMakeNodes starting loop:     a=4Y1M|1|B|A|19 B=4Y1M|1|B|U|34
  5 Basepair    19   34 AU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2760 - Nucleotides    35 to    93, length   6
pMakeNodes starting loop:     a=4Y1M|1|B|G|35 B=4Y1M|1|B|A|93
  7 Initial     35 (0 insertion) and   93 (0 insertion)
pMakeNodesJunction: a=4Y1M|1|B|G|35 r=4Y1M|1|B|G|35 s=4Y1M|1|B|C|73 t=4Y1M|1|B|G|74 u=B=4Y1M|1|B|A|93
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4Y1M|1|B|G|35 and 4Y1M|1|B|C|73 and between 4Y1M|1|B|G|74 and 4Y1M|1|B|A|93
pMakeNodesJunction: about to make a junction: a=4Y1M|1|B|G|35 s=4Y1M|1|B|C|73 t=4Y1M|1|B|G|74 B=4Y1M|1|B|A|93
pMakeNodesJunction: first branch starts at   4Y1M|1|B|G|35
pMakeNodesJunction: first branch ends around 4Y1M|1|B|C|73
pMakeNodesJunction: second branch starts at  4Y1M|1|B|G|74
pMakeNodesJunction: junction ends at         4Y1M|1|B|A|93
pMakeNodesJunction: first branch strand start goes up to  4Y1M|1|B|G|35
pMakeNodesJunction: first branch strand end goes down to  4Y1M|1|B|C|73
pMakeNodesJunction: second branch strand start goes up to 4Y1M|1|B|G|75
pMakeNodesJunction: last strand of junction goes down to  4Y1M|1|B|C|92

Junction with 2 loops, call it J6797
Actual Branch 1 of junction J6797 - Nucleotides 4Y1M|1|B|G|35 to 4Y1M|1|B|C|73, length   2
Actual Branch 2 of junction J6797 - Nucleotides 4Y1M|1|B|G|74 to 4Y1M|1|B|A|93, length   4
  8 Junction

2B Branch 1 of 2 of junction J6797 - Nucleotides    35 to    73, length   2
pMakeNodes starting loop:     a=4Y1M|1|B|G|35 B=4Y1M|1|B|C|73
 10 Basepair    35   73 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J6797 - Nucleotides    74 to    93, length   4
pMakeNodes starting loop:     a=4Y1M|1|B|G|74 B=4Y1M|1|B|A|93
 13 Basepair    74   93 GA cWW 
No need to probe because of interaction between a=4Y1M|1|B|G|75 B=4Y1M|1|B|C|92
 14 Basepair    75   92 GC cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
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
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|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: 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: []
           numbranches: []
              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 C17 - G94 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J2760'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|G|18'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2760'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J2760'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A19 - A93 ID J2760'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2760'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 A19 - U34 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2760'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4Y1M|1|B|G|35 - 4Y1M|1|B|A|93 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J6797'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G35 - A93 ID J6797'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6797'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G35 - C73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 13

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: []
           numbranches: []
              NormCons: 1

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: 'J6797'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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 G74 - A93 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 G75 - 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]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J2760'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2760'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4Y1M|1|B|G|35 - 4Y1M|1|B|A|93 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_45582.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6797'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J6797'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_45582.1. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_45582.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8706

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J4_45801.2, number 27 of 65
pMakeNodes starting loop:     a=7A0S|1|X|C|245 B=7A0S|1|X|G|437
  2 Basepair   245  437 CG cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|C|246 B=7A0S|1|X|A|436
pMakeNodes probed for insert:  a=7A0S|1|X|C|246 B=7A0S|1|X|A|436
pMakeNodesJunction: a=7A0S|1|X|C|246 r=7A0S|1|X|C|246 s=7A0S|1|X|G|383 t=7A0S|1|X|A|384 u=B=7A0S|1|X|A|436
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|C|246 and 7A0S|1|X|G|383 and between 7A0S|1|X|A|384 and 7A0S|1|X|A|436
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|C|246 s=7A0S|1|X|G|383 t=7A0S|1|X|A|384 B=7A0S|1|X|A|436
pMakeNodesJunction: first branch starts at   7A0S|1|X|C|246
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|383
pMakeNodesJunction: second branch starts at  7A0S|1|X|A|384
pMakeNodesJunction: junction ends at         7A0S|1|X|A|436
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|C|246
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|G|383
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|388
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|434

Junction with 2 loops, call it J6550
Actual Branch 1 of junction J6550 - Nucleotides 7A0S|1|X|C|246 to 7A0S|1|X|G|383, length   2
Actual Branch 2 of junction J6550 - Nucleotides 7A0S|1|X|A|384 to 7A0S|1|X|A|436, length  15
  3 Junction

2B Branch 1 of 2 of junction J6550 - Nucleotides   246 to   383, length   2
pMakeNodes starting loop:     a=7A0S|1|X|C|246 B=7A0S|1|X|G|383
  5 Basepair   246  383 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J6550 - Nucleotides   384 to   436, length  15
pMakeNodes starting loop:     a=7A0S|1|X|A|384 B=7A0S|1|X|A|436
  7 Initial    384 (0 insertion) and  436 (0 insertion)
pMakeNodesJunction: a=7A0S|1|X|A|384 r=7A0S|1|X|A|384 s=7A0S|1|X|A|415 t=7A0S|1|X|U|416 u=B=7A0S|1|X|A|436
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|A|384 and 7A0S|1|X|A|415 and between 7A0S|1|X|U|416 and 7A0S|1|X|A|436
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|A|384 s=7A0S|1|X|A|415 t=7A0S|1|X|U|416 B=7A0S|1|X|A|436
pMakeNodesJunction: first branch starts at   7A0S|1|X|A|384
pMakeNodesJunction: first branch ends around 7A0S|1|X|A|415
pMakeNodesJunction: second branch starts at  7A0S|1|X|U|416
pMakeNodesJunction: junction ends at         7A0S|1|X|A|436
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|388
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|U|412
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|419
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|434
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     2


Junction with 2 loops, call it J1626
Actual Branch 1 of junction J1626 - Nucleotides 7A0S|1|X|A|384 to 7A0S|1|X|A|415, length   9
Actual Branch 2 of junction J1626 - Nucleotides 7A0S|1|X|U|416 to 7A0S|1|X|A|436, length   6
  8 Junction

2B Branch 1 of 2 of junction J1626 - Nucleotides   384 to   415, length   9
pMakeNodes starting loop:     a=7A0S|1|X|A|384 B=7A0S|1|X|A|415
 10 Basepair   384  415 AA tHH 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|385 B=7A0S|1|X|A|414
pMakeNodesProbeForInsertions:  a 7A0S|1|X|G|385 interacts with 7A0S|1|X|U|386
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|414 interacts with 7A0S|1|X|U|386
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|414 interacts with 7A0S|1|X|U|386
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7A0S|1|X|G|385 B=7A0S|1|X|A|414
pMakeNodes making a cluster near strand break a=7A0S|1|X|G|385 B=7A0S|1|X|A|414
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
 11 Cluster   7A0S|1|X|G|385:7A0S|1|X|U|386 7A0S|1|X|A|414:7A0S|1|X|A|414
    LR Inter  7A0S|1|X|U|386 7A0S|1|X|A|414 tWH 
    LL Inter  7A0S|1|X|G|385 7A0S|1|X|U|386 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=7A0S|1|X|A|387 B=7A0S|1|X|G|413
 12 Basepair   387  413 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|G|388 B=7A0S|1|X|U|412
 13 Basepair   388  412 GU cWW 
 14 Hairpin type *

2B Branch 2 of 2 of junction J1626 - Nucleotides   416 to   436, length   6
pMakeNodes starting loop:     a=7A0S|1|X|U|416 B=7A0S|1|X|A|436
    Insertion on left  7A0S|1|X|U|416
    Insertion on left  7A0S|1|X|C|417
    Insertion on right 7A0S|1|X|A|436
    Insertion on right 7A0S|1|X|A|435
pMakeNodesProbeForInsertions:  a 7A0S|1|X|G|419 interacts with 7A0S|1|X|C|434
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|434 interacts with 7A0S|1|X|G|419
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|434 interacts with 7A0S|1|X|G|419
 15 Initial    416 (2 insertion) and  436 (2 insertion)
 16 Basepair   419  434 GC cWW 
 17 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 18
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 18
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 18
pMakeMotifModelFromSSF:   9   Initial Left  4 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:  11   Cluster Left  5  6 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  15   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  16  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  17   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|U|416
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|C|417
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|A|435
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|434
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: 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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C245 - G437 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 18
             Insertion: []
                    id: 'J6550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C246 - A436 ID J6550'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J6550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 C246 - G383 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: 'J6550'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|384 - 7A0S|1|X|A|436 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 15]
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: 'J1626'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A384 - A436 ID J1626'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J1626'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 A384 - A415 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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 12
             LeftIndex: [5 6]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|X|G|385:7A0S|1|X|U|386 and 7A0S|1|X|A|414:7A0S|1|X|A|414'
              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: []
           numbranches: []
              NormCons: 0.2971
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]

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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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 A387 - G413 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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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 G388 - U412 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
                    id: 'J1626'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: 'AA'
               Comment: ' // Initial node 7A0S|1|X|U|416 - 7A0S|1|X|A|436 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 13
            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 7A0S|1|X|U|416'
              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]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 14
            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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 14
            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 7A0S|1|X|C|417'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 15
            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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 15
            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 7A0S|1|X|A|435'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 15
            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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 15
            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 7A0S|1|X|C|434'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G419 - C434 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 18
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 18
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 18
pMakeMotifModelFromSSF:   9   Initial Left  4 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:  11   Cluster Left  5  6 Right 11
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
pMakeMotifModelFromSSF:  16   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  17     Fixed Left 13 Right 18
pMakeMotifModelFromSSF:  18   Initial Left 14 Right 18
pMakeMotifModelFromSSF:  19     Fixed Left 14 Right 18
pMakeMotifModelFromSSF:  20   Initial Left 15 Right 18
pMakeMotifModelFromSSF:  21     Fixed Left 15 Right 18
pMakeMotifModelFromSSF:  22   Initial Left 15 Right 17
pMakeMotifModelFromSSF:  23     Fixed Left 15 Right 17
pMakeMotifModelFromSSF:  24   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  25  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  26   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J6550'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: 'J6550'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|384 - 7A0S|1|X|A|436 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_45801.2. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J1626'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
                    id: 'J1626'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: 'AA'
               Comment: ' // Initial node 7A0S|1|X|U|416 - 7A0S|1|X|A|436 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_45801.2. Nodes 9 and 16 both model an insertion before position 13. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 6 and 18
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 11 and 17
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 12 and 18
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 6 and 18
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 11 and 17
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 12 and 18
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_45801.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.6390
  -12.9057
  -12.1282
  -11.2831
  -12.2538
  -16.1335

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J4_46448.1, number 28 of 65
pMakeNodes starting loop:     a=6CB3|1|B|C|15 B=6CB3|1|B|G|90
  2 Basepair    15   90 CG cWW 
No need to probe because of interaction between a=6CB3|1|B|G|16 B=6CB3|1|B|A|89
pMakeNodes making a cluster near strand break a=6CB3|1|B|G|16 B=6CB3|1|B|A|89
pMakeNodesCluster: amax is 2 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 2 and then 9 to 10
aa is 2 bb is 9
  3 Cluster   6CB3|1|B|G|16:6CB3|1|B|G|16 6CB3|1|B|U|88:6CB3|1|B|A|89
    LR Inter  6CB3|1|B|G|16 6CB3|1|B|U|88 cWS 
    LR Inter  6CB3|1|B|G|16 6CB3|1|B|A|89 tSH 
pMakeNodesCluster a=3 B=8 at the end
pMakeNodesCluster a=3 B=8 at the end
pMakeNodes probe for inserts:  a=6CB3|1|B|U|17 B=6CB3|1|B|U|87
  4 Initial     17 (0 insertion) and   87 (0 insertion)
pMakeNodes probed for insert:  a=6CB3|1|B|U|17 B=6CB3|1|B|U|87
pMakeNodesJunction: a=6CB3|1|B|U|17 r=6CB3|1|B|U|17 s=6CB3|1|B|A|28 t=6CB3|1|B|A|29 u=B=6CB3|1|B|U|87
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6CB3|1|B|U|17 and 6CB3|1|B|A|28 and between 6CB3|1|B|A|29 and 6CB3|1|B|U|87
pMakeNodesJunction: about to make a junction: a=6CB3|1|B|U|17 s=6CB3|1|B|A|28 t=6CB3|1|B|A|29 B=6CB3|1|B|U|87
pMakeNodesJunction: first branch starts at   6CB3|1|B|U|17
pMakeNodesJunction: first branch ends around 6CB3|1|B|A|28
pMakeNodesJunction: second branch starts at  6CB3|1|B|A|29
pMakeNodesJunction: junction ends at         6CB3|1|B|U|87
pMakeNodesJunction: first branch strand start goes up to  6CB3|1|B|U|17
pMakeNodesJunction: first branch strand end goes down to  6CB3|1|B|A|28
pMakeNodesJunction: second branch strand start goes up to 6CB3|1|B|A|29
pMakeNodesJunction: last strand of junction goes down to  6CB3|1|B|U|87

Junction with 2 loops, call it J1189
Actual Branch 1 of junction J1189 - Nucleotides 6CB3|1|B|U|17 to 6CB3|1|B|A|28, length   2
Actual Branch 2 of junction J1189 - Nucleotides 6CB3|1|B|A|29 to 6CB3|1|B|U|87, length   4
  5 Junction

2B Branch 1 of 2 of junction J1189 - Nucleotides    17 to    28, length   2
pMakeNodes starting loop:     a=6CB3|1|B|U|17 B=6CB3|1|B|A|28
  7 Basepair    17   28 UA cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J1189 - Nucleotides    29 to    87, length   4
pMakeNodes starting loop:     a=6CB3|1|B|A|29 B=6CB3|1|B|U|87
  9 Initial     29 (0 insertion) and   87 (0 insertion)
pMakeNodesJunction: a=6CB3|1|B|A|29 r=6CB3|1|B|A|29 s=6CB3|1|B|U|69 t=6CB3|1|B|G|70 u=B=6CB3|1|B|U|87
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6CB3|1|B|A|29 and 6CB3|1|B|U|69 and between 6CB3|1|B|G|70 and 6CB3|1|B|U|87
pMakeNodesJunction: about to make a junction: a=6CB3|1|B|A|29 s=6CB3|1|B|U|69 t=6CB3|1|B|G|70 B=6CB3|1|B|U|87
pMakeNodesJunction: first branch starts at   6CB3|1|B|A|29
pMakeNodesJunction: first branch ends around 6CB3|1|B|U|69
pMakeNodesJunction: second branch starts at  6CB3|1|B|G|70
pMakeNodesJunction: junction ends at         6CB3|1|B|U|87
pMakeNodesJunction: first branch strand start goes up to  6CB3|1|B|A|29
pMakeNodesJunction: first branch strand end goes down to  6CB3|1|B|U|69
pMakeNodesJunction: second branch strand start goes up to 6CB3|1|B|G|70
pMakeNodesJunction: last strand of junction goes down to  6CB3|1|B|U|87

Junction with 2 loops, call it J4983
Actual Branch 1 of junction J4983 - Nucleotides 6CB3|1|B|A|29 to 6CB3|1|B|U|69, length   2
Actual Branch 2 of junction J4983 - Nucleotides 6CB3|1|B|G|70 to 6CB3|1|B|U|87, length   2
 10 Junction

2B Branch 1 of 2 of junction J4983 - Nucleotides    29 to    69, length   2
pMakeNodes starting loop:     a=6CB3|1|B|A|29 B=6CB3|1|B|U|69
 12 Basepair    29   69 AU cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J4983 - Nucleotides    70 to    87, length   2
pMakeNodes starting loop:     a=6CB3|1|B|G|70 B=6CB3|1|B|U|87
 15 Basepair    70   87 GU cWW 
 16 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 Right  9 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  10  Junction Left  5 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   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: 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: []
           numbranches: []

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 C15 - G90 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: 2
            RightIndex: [9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'UA'
               Comment: ' // Cluster node 6CB3|1|B|G|16:6CB3|1|B|G|16 and 6CB3|1|B|U|88:6CB3|1|B|A|89'
              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: 0.2580
           numbranches: []

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: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CB3|1|B|U|17 - 6CB3|1|B|U|87 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J1189'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U17 - U87 ID J1189'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

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: 'J1189'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U17 - A28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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
           numbranches: []

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: 'J1189'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CB3|1|B|A|29 - 6CB3|1|B|U|87 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J4983'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A29 - U87 ID J4983'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J4983'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A29 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 13

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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: 'J4983'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G70 - U87 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 16

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right  9 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  10  Junction Left  5 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J1189'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J1189'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CB3|1|B|A|29 - 6CB3|1|B|U|87 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_46448.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J4983'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J4983'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_46448.1. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_46448.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8542

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J4_47478.1, number 29 of 65
pMakeNodes starting loop:     a=1KH6|1|A|G|5 B=1KH6|1|A|C|49
  2 Basepair     5   49 GC cWW 
pMakeNodes probe for inserts:  a=1KH6|1|A|A|6 B=1KH6|1|A|C|48
    Insertion on left  1KH6|1|A|A|6
pMakeNodes probed for insert:  a=1KH6|1|A|A|7 B=1KH6|1|A|C|48
pMakeNodesJunction: a=1KH6|1|A|A|7 r=1KH6|1|A|A|7 s=1KH6|1|A|G|23 t=1KH6|1|A|A|24 u=B=1KH6|1|A|C|48
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 1KH6|1|A|A|7 and 1KH6|1|A|G|23 and between 1KH6|1|A|A|24 and 1KH6|1|A|C|48
pMakeNodesJunction: about to make a junction: a=1KH6|1|A|A|7 s=1KH6|1|A|G|23 t=1KH6|1|A|A|24 B=1KH6|1|A|C|48
pMakeNodesJunction: first branch starts at   1KH6|1|A|A|7
pMakeNodesJunction: first branch ends around 1KH6|1|A|G|23
pMakeNodesJunction: second branch starts at  1KH6|1|A|A|24
pMakeNodesJunction: junction ends at         1KH6|1|A|C|48
pMakeNodesJunction: first branch strand start goes up to  1KH6|1|A|C|8
pMakeNodesJunction: first branch strand end goes down to  1KH6|1|A|G|23
pMakeNodesJunction: second branch strand start goes up to 1KH6|1|A|A|24
pMakeNodesJunction: last strand of junction goes down to  1KH6|1|A|C|48
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J9597
Actual Branch 1 of junction J9597 - Nucleotides 1KH6|1|A|A|7 to 1KH6|1|A|G|23, length   3
Actual Branch 2 of junction J9597 - Nucleotides 1KH6|1|A|A|24 to 1KH6|1|A|C|48, length   5
  3 Junction

2B Branch 1 of 2 of junction J9597 - Nucleotides     7 to    23, length   3
pMakeNodes starting loop:     a=1KH6|1|A|A|7 B=1KH6|1|A|G|23
    Insertion on left  1KH6|1|A|A|7
pMakeNodesProbeForInsertions:  a 1KH6|1|A|C|8 interacts with 1KH6|1|A|G|23
pMakeNodesProbeForInsertions:  B 1KH6|1|A|G|23 interacts with 1KH6|1|A|C|8
pMakeNodesProbeForInsertions:  B 1KH6|1|A|G|23 interacts with 1KH6|1|A|C|8
  4 Initial      7 (1 insertion) and   23 (0 insertion)
  5 Basepair     8   23 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9597 - Nucleotides    24 to    48, length   5
pMakeNodes starting loop:     a=1KH6|1|A|A|24 B=1KH6|1|A|C|48
  7 Initial     24 (0 insertion) and   48 (0 insertion)
pMakeNodesJunction: a=1KH6|1|A|A|24 r=1KH6|1|A|A|24 s=1KH6|1|A|5BU|37 t=1KH6|1|A|5BU|38 u=B=1KH6|1|A|C|48
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1KH6|1|A|A|24 and 1KH6|1|A|5BU|37 and between 1KH6|1|A|5BU|38 and 1KH6|1|A|C|48
pMakeNodesJunction: about to make a junction: a=1KH6|1|A|A|24 s=1KH6|1|A|5BU|37 t=1KH6|1|A|5BU|38 B=1KH6|1|A|C|48
pMakeNodesJunction: first branch starts at   1KH6|1|A|A|24
pMakeNodesJunction: first branch ends around 1KH6|1|A|5BU|37
pMakeNodesJunction: second branch starts at  1KH6|1|A|5BU|38
pMakeNodesJunction: junction ends at         1KH6|1|A|C|48
pMakeNodesJunction: first branch strand start goes up to  1KH6|1|A|A|24
pMakeNodesJunction: first branch strand end goes down to  1KH6|1|A|5BU|37
pMakeNodesJunction: second branch strand start goes up to 1KH6|1|A|G|39
pMakeNodesJunction: last strand of junction goes down to  1KH6|1|A|C|48

Junction with 2 loops, call it J3403
Actual Branch 1 of junction J3403 - Nucleotides 1KH6|1|A|A|24 to 1KH6|1|A|5BU|37, length   2
Actual Branch 2 of junction J3403 - Nucleotides 1KH6|1|A|5BU|38 to 1KH6|1|A|C|48, length   3
  8 Junction

2B Branch 1 of 2 of junction J3403 - Nucleotides    24 to    37, length   2
pMakeNodes starting loop:     a=1KH6|1|A|A|24 B=1KH6|1|A|5BU|37
 10 Basepair    24   37 AU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J3403 - Nucleotides    38 to    48, length   3
pMakeNodes starting loop:     a=1KH6|1|A|5BU|38 B=1KH6|1|A|C|48
    Insertion on left  1KH6|1|A|5BU|38
pMakeNodesProbeForInsertions:  a 1KH6|1|A|G|39 interacts with 1KH6|1|A|C|48
pMakeNodesProbeForInsertions:  B 1KH6|1|A|C|48 interacts with 1KH6|1|A|G|39
pMakeNodesProbeForInsertions:  B 1KH6|1|A|C|48 interacts with 1KH6|1|A|G|39
 12 Initial     38 (1 insertion) and   48 (0 insertion)
 13 Basepair    39   48 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1KH6|1|A|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1KH6|1|A|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1KH6|1|A|5BU|38
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: []
           numbranches: []
              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: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G5 - C49 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J9597'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1KH6|1|A|A|6'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9597'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J9597'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A7 - C48 ID J9597'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9597'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|A|7 - 1KH6|1|A|G|23 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9597'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1KH6|1|A|A|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J3403'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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 C8 - 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]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9597'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|A|24 - 1KH6|1|A|C|48 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J3403'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A24 - C48 ID J3403'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3403'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A24 - U37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

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: 'J3403'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|5BU|38 - 1KH6|1|A|C|48 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1KH6|1|A|5BU|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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 G39 - 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]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9597'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|A|7 - 1KH6|1|A|G|23 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9597'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|A|24 - 1KH6|1|A|C|48 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_47478.1. Nodes 6 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J3403'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J3403'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 1KH6|1|A|5BU|38 - 1KH6|1|A|C|48 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_47478.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for cWS  between 3 and 6
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 3 and 8
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for cWS  between 3 and 6
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 3 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_47478.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2881

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J4_48692.1, number 30 of 65
pMakeNodes starting loop:     a=5SWD|1|B|A|21 B=5SWD|1|B|U|75
  2 Basepair    21   75 AU cWW 
No need to probe because of interaction between a=5SWD|1|B|A|23 B=5SWD|1|B|U|74
  3 Basepair    23   74 AU tHW 
pMakeNodes probe for inserts:  a=5SWD|1|B|A|24 B=5SWD|1|B|A|73
    Insertion on left  5SWD|1|B|A|24
    Insertion on right 5SWD|1|B|A|73
pMakeNodes probed for insert:  a=5SWD|1|B|U|25 B=5SWD|1|B|G|72
pMakeNodesJunction: a=5SWD|1|B|U|25 r=5SWD|1|B|U|25 s=5SWD|1|B|A|45 t=5SWD|1|B|G|46 u=B=5SWD|1|B|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5SWD|1|B|U|25 and 5SWD|1|B|A|45 and between 5SWD|1|B|G|46 and 5SWD|1|B|G|72
pMakeNodesJunction: about to make a junction: a=5SWD|1|B|U|25 s=5SWD|1|B|A|45 t=5SWD|1|B|G|46 B=5SWD|1|B|G|72
pMakeNodesJunction: first branch starts at   5SWD|1|B|U|25
pMakeNodesJunction: first branch ends around 5SWD|1|B|A|45
pMakeNodesJunction: second branch starts at  5SWD|1|B|G|46
pMakeNodesJunction: junction ends at         5SWD|1|B|G|72
pMakeNodesJunction: first branch strand start goes up to  5SWD|1|B|U|25
pMakeNodesJunction: first branch strand end goes down to  5SWD|1|B|A|45
pMakeNodesJunction: second branch strand start goes up to 5SWD|1|B|G|46
pMakeNodesJunction: last strand of junction goes down to  5SWD|1|B|G|72

Junction with 2 loops, call it J5852
Actual Branch 1 of junction J5852 - Nucleotides 5SWD|1|B|U|25 to 5SWD|1|B|A|45, length   2
Actual Branch 2 of junction J5852 - Nucleotides 5SWD|1|B|G|46 to 5SWD|1|B|G|72, length   4
  4 Junction

2B Branch 1 of 2 of junction J5852 - Nucleotides    25 to    45, length   2
pMakeNodes starting loop:     a=5SWD|1|B|U|25 B=5SWD|1|B|A|45
  6 Basepair    25   45 UA cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J5852 - Nucleotides    46 to    72, length   4
pMakeNodes starting loop:     a=5SWD|1|B|G|46 B=5SWD|1|B|G|72
  8 Initial     46 (0 insertion) and   72 (0 insertion)
pMakeNodesJunction: a=5SWD|1|B|G|46 r=5SWD|1|B|G|46 s=5SWD|1|B|C|53 t=5SWD|1|B|C|54 u=B=5SWD|1|B|G|72
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5SWD|1|B|G|46 and 5SWD|1|B|C|53 and between 5SWD|1|B|C|54 and 5SWD|1|B|G|72
pMakeNodesJunction: about to make a junction: a=5SWD|1|B|G|46 s=5SWD|1|B|C|53 t=5SWD|1|B|C|54 B=5SWD|1|B|G|72
pMakeNodesJunction: first branch starts at   5SWD|1|B|G|46
pMakeNodesJunction: first branch ends around 5SWD|1|B|C|53
pMakeNodesJunction: second branch starts at  5SWD|1|B|C|54
pMakeNodesJunction: junction ends at         5SWD|1|B|G|72
pMakeNodesJunction: first branch strand start goes up to  5SWD|1|B|G|46
pMakeNodesJunction: first branch strand end goes down to  5SWD|1|B|C|53
pMakeNodesJunction: second branch strand start goes up to 5SWD|1|B|C|54
pMakeNodesJunction: last strand of junction goes down to  5SWD|1|B|G|72

Junction with 2 loops, call it J2238
Actual Branch 1 of junction J2238 - Nucleotides 5SWD|1|B|G|46 to 5SWD|1|B|C|53, length   2
Actual Branch 2 of junction J2238 - Nucleotides 5SWD|1|B|C|54 to 5SWD|1|B|G|72, length   2
  9 Junction

2B Branch 1 of 2 of junction J2238 - Nucleotides    46 to    53, length   2
pMakeNodes starting loop:     a=5SWD|1|B|G|46 B=5SWD|1|B|C|53
 11 Basepair    46   53 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J2238 - Nucleotides    54 to    72, length   2
pMakeNodes starting loop:     a=5SWD|1|B|C|54 B=5SWD|1|B|G|72
 14 Basepair    54   72 CG cWW 
 15 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  Junction Left  4 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   9  Junction Left  6 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5SWD|1|B|A|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5SWD|1|B|G|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: 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: []
           numbranches: []
              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 A21 - U75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'AU'
               Comment: ' // Basepair A23 - U74 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]
           numbranches: []
              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: 'J5852'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5SWD|1|B|A|23'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5852'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 5SWD|1|B|G|72'
              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]
           numbranches: []
              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: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U25 - G72 ID J5852'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 - 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]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

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: 'J5852'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5SWD|1|B|G|46 - 5SWD|1|B|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J2238'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G46 - G72 ID J2238'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2238'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G46 - 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]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

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: 'J2238'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C54 - 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]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  Junction Left  6 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  17   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J5852'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J5852'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5SWD|1|B|G|46 - 5SWD|1|B|G|72 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_48692.1. Nodes 9 and 12 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J2238'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: 'J2238'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_48692.1. Nodes 14 and 17 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_48692.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4400

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J4_48907.1, number 31 of 65
pMakeNodes starting loop:     a=1NBS|1|B|G|90 B=1NBS|1|B|C|235
  2 Basepair    90  235 GC cWW 
pMakeNodes probe for inserts:  a=1NBS|1|B|C|91 B=1NBS|1|B|C|234
pMakeNodes probed for insert:  a=1NBS|1|B|C|91 B=1NBS|1|B|C|234
pMakeNodesJunction: a=1NBS|1|B|C|91 r=1NBS|1|B|C|91 s=1NBS|1|B|G|112 t=1NBS|1|B|G|113 u=B=1NBS|1|B|C|234
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 1NBS|1|B|C|91 and 1NBS|1|B|G|112 and between 1NBS|1|B|G|113 and 1NBS|1|B|C|234
pMakeNodesJunction: about to make a junction: a=1NBS|1|B|C|91 s=1NBS|1|B|G|112 t=1NBS|1|B|G|113 B=1NBS|1|B|C|234
pMakeNodesJunction: first branch starts at   1NBS|1|B|C|91
pMakeNodesJunction: first branch ends around 1NBS|1|B|G|112
pMakeNodesJunction: second branch starts at  1NBS|1|B|G|113
pMakeNodesJunction: junction ends at         1NBS|1|B|C|234
pMakeNodesJunction: first branch strand start goes up to  1NBS|1|B|C|91
pMakeNodesJunction: first branch strand end goes down to  1NBS|1|B|G|112
pMakeNodesJunction: second branch strand start goes up to 1NBS|1|B|G|113
pMakeNodesJunction: last strand of junction goes down to  1NBS|1|B|C|234

Junction with 2 loops, call it J7512
Actual Branch 1 of junction J7512 - Nucleotides 1NBS|1|B|C|91 to 1NBS|1|B|G|112, length   2
Actual Branch 2 of junction J7512 - Nucleotides 1NBS|1|B|G|113 to 1NBS|1|B|C|234, length   4
  3 Junction

2B Branch 1 of 2 of junction J7512 - Nucleotides    91 to   112, length   2
pMakeNodes starting loop:     a=1NBS|1|B|C|91 B=1NBS|1|B|G|112
  5 Basepair    91  112 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7512 - Nucleotides   113 to   234, length   4
pMakeNodes starting loop:     a=1NBS|1|B|G|113 B=1NBS|1|B|C|234
  7 Initial    113 (0 insertion) and  234 (0 insertion)
pMakeNodesJunction: a=1NBS|1|B|G|113 r=1NBS|1|B|G|113 s=1NBS|1|B|C|131 t=1NBS|1|B|G|132 u=B=1NBS|1|B|C|234
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1NBS|1|B|G|113 and 1NBS|1|B|C|131 and between 1NBS|1|B|G|132 and 1NBS|1|B|C|234
pMakeNodesJunction: about to make a junction: a=1NBS|1|B|G|113 s=1NBS|1|B|C|131 t=1NBS|1|B|G|132 B=1NBS|1|B|C|234
pMakeNodesJunction: first branch starts at   1NBS|1|B|G|113
pMakeNodesJunction: first branch ends around 1NBS|1|B|C|131
pMakeNodesJunction: second branch starts at  1NBS|1|B|G|132
pMakeNodesJunction: junction ends at         1NBS|1|B|C|234
pMakeNodesJunction: first branch strand start goes up to  1NBS|1|B|G|113
pMakeNodesJunction: first branch strand end goes down to  1NBS|1|B|C|131
pMakeNodesJunction: second branch strand start goes up to 1NBS|1|B|G|132
pMakeNodesJunction: last strand of junction goes down to  1NBS|1|B|C|234

Junction with 2 loops, call it J2550
Actual Branch 1 of junction J2550 - Nucleotides 1NBS|1|B|G|113 to 1NBS|1|B|C|131, length   2
Actual Branch 2 of junction J2550 - Nucleotides 1NBS|1|B|G|132 to 1NBS|1|B|C|234, length   2
  8 Junction

2B Branch 1 of 2 of junction J2550 - Nucleotides   113 to   131, length   2
pMakeNodes starting loop:     a=1NBS|1|B|G|113 B=1NBS|1|B|C|131
 10 Basepair   113  131 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J2550 - Nucleotides   132 to   234, length   2
pMakeNodes starting loop:     a=1NBS|1|B|G|132 B=1NBS|1|B|C|234
 13 Basepair   132  234 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   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: 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: []
           numbranches: []
              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 G90 - C235 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: 'J7512'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C91 - C234 ID J7512'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J7512'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 C91 - G112 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 'J7512'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1NBS|1|B|G|113 - 1NBS|1|B|C|234 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J2550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G113 - C234 ID J2550'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J2550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 G113 - C131 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

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: 'J2550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G132 - C234 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 14

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J7512'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J7512'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 1NBS|1|B|G|113 - 1NBS|1|B|C|234 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_48907.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J2550'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J2550'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_48907.1. Nodes 9 and 12 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_48907.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9967
   -5.9967

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J4_51403.1, number 32 of 65
pMakeNodes starting loop:     a=5TBW|1|1|C|185 B=5TBW|1|1|G|231
  2 Basepair   185  231 CG cWW 
No need to probe because of interaction between a=5TBW|1|1|U|186 B=5TBW|1|1|U|230
  3 Basepair   186  230 UU cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|187 B=5TBW|1|1|G|229
    Insertion on right 5TBW|1|1|G|229
    Insertion on right 5TBW|1|1|U|228
pMakeNodes probed for insert:  a=5TBW|1|1|A|187 B=5TBW|1|1|G|227
  4 Basepair   187  227 AG cHH 
pMakeNodes probe for inserts:  a=5TBW|1|1|U|188 B=5TBW|1|1|C|226
pMakeNodes probed for insert:  a=5TBW|1|1|U|188 B=5TBW|1|1|C|226
pMakeNodesJunction: a=5TBW|1|1|U|188 r=5TBW|1|1|U|188 s=5TBW|1|1|U|207 t=5TBW|1|1|C|208 u=B=5TBW|1|1|C|226
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|188 and 5TBW|1|1|U|207 and between 5TBW|1|1|C|208 and 5TBW|1|1|C|226
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|188 s=5TBW|1|1|U|207 t=5TBW|1|1|C|208 B=5TBW|1|1|C|226
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|188
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|207
pMakeNodesJunction: second branch starts at  5TBW|1|1|C|208
pMakeNodesJunction: junction ends at         5TBW|1|1|C|226
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|189
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|205
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|C|208
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|226

Junction with 2 loops, call it J5059
Actual Branch 1 of junction J5059 - Nucleotides 5TBW|1|1|U|188 to 5TBW|1|1|U|207, length   5
Actual Branch 2 of junction J5059 - Nucleotides 5TBW|1|1|C|208 to 5TBW|1|1|C|226, length   5
  5 Junction

2B Branch 1 of 2 of junction J5059 - Nucleotides   188 to   207, length   5
pMakeNodes starting loop:     a=5TBW|1|1|U|188 B=5TBW|1|1|U|207
  7 Basepair   188  207 UU cSS 
pMakeNodes probe for inserts:  a=5TBW|1|1|G|189 B=5TBW|1|1|G|206
    Insertion on right 5TBW|1|1|G|206
pMakeNodesProbeForInsertions:  a 5TBW|1|1|G|189 interacts with 5TBW|1|1|C|205
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|205 interacts with 5TBW|1|1|G|189
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|205 interacts with 5TBW|1|1|G|189
pMakeNodes probed for insert:  a=5TBW|1|1|G|189 B=5TBW|1|1|C|205
  8 Basepair   189  205 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J5059 - Nucleotides   208 to   226, length   5
pMakeNodes starting loop:     a=5TBW|1|1|C|208 B=5TBW|1|1|C|226
 10 Initial    208 (0 insertion) and  226 (0 insertion)
pMakeNodesJunction: a=5TBW|1|1|C|208 r=5TBW|1|1|C|208 s=5TBW|1|1|G|212 t=5TBW|1|1|A|213 u=B=5TBW|1|1|C|226
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|C|208 and 5TBW|1|1|G|212 and between 5TBW|1|1|A|213 and 5TBW|1|1|C|226
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|C|208 s=5TBW|1|1|G|212 t=5TBW|1|1|A|213 B=5TBW|1|1|C|226
pMakeNodesJunction: first branch starts at   5TBW|1|1|C|208
pMakeNodesJunction: first branch ends around 5TBW|1|1|G|212
pMakeNodesJunction: second branch starts at  5TBW|1|1|A|213
pMakeNodesJunction: junction ends at         5TBW|1|1|C|226
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|C|208
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|G|212
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|214
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|226

Junction with 2 loops, call it J6990
Actual Branch 1 of junction J6990 - Nucleotides 5TBW|1|1|C|208 to 5TBW|1|1|G|212, length   2
Actual Branch 2 of junction J6990 - Nucleotides 5TBW|1|1|A|213 to 5TBW|1|1|C|226, length   3
 11 Junction

2B Branch 1 of 2 of junction J6990 - Nucleotides   208 to   212, length   2
pMakeNodes starting loop:     a=5TBW|1|1|C|208 B=5TBW|1|1|G|212
 13 Basepair   208  212 CG cWW 
 14 Hairpin type *

2B Branch 2 of 2 of junction J6990 - Nucleotides   213 to   226, length   3
pMakeNodes starting loop:     a=5TBW|1|1|A|213 B=5TBW|1|1|C|226
    Insertion on left  5TBW|1|1|A|213
pMakeNodesProbeForInsertions:  a 5TBW|1|1|G|214 interacts with 5TBW|1|1|C|226
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|226 interacts with 5TBW|1|1|G|214
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|226 interacts with 5TBW|1|1|G|214
 15 Initial    213 (1 insertion) and  226 (0 insertion)
 16 Basepair   214  226 GC cWW 
 17 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 14
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  11  Junction Left  9 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  15   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  16  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  17   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 right for 5TBW|1|1|G|229
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|U|228
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|206
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|213
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: []
           numbranches: []
              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 C185 - 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]
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'UGU'
               Comment: ' // Basepair U186 - U230 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 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 5TBW|1|1|G|229'
              NumLoops: []
                  Edge: 7
         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]
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J5059'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J5059'
        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 5TBW|1|1|U|228'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             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: 'U'
           RightLetter: 'GU'
               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]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 3
            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: 'G'
               Comment: ' // Basepair A187 - G227 cHH '
              NumLoops: []
                  Edge: 7
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [6 10]
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J5059'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U188 - C226 ID J5059'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5059'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0.9950 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: 'GU'
               Comment: ' // Basepair U188 - U207 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]
           numbranches: []
              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: 'J6990'
        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 5TBW|1|1|G|206'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             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: '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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             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 G189 - C205 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J5059'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|C|208 - 5TBW|1|1|C|226 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [12 15]
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J6990'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C208 - C226 ID J6990'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6990'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C208 - G212 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: 1

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J6990'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|A|213 - 5TBW|1|1|C|226 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 5TBW|1|1|A|213'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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 G214 - C226 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  3 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   9  Junction Left  4 Right 13
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  5 Right  6
pMakeMotifModelFromSSF:  14  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  15   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  17  Junction Left  9 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  23   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J5059'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J5059'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|C|208 - 5TBW|1|1|C|226 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_51403.1. Nodes 10 and 16 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J6990'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J6990'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|A|213 - 5TBW|1|1|C|226 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_51403.1. Nodes 18 and 21 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a junction at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHS  between 11 and 14
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 11 and 14
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_51403.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.6907

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J4_54165.1, number 33 of 65
pMakeNodes starting loop:     a=7A0S|1|X|G|2622 B=7A0S|1|X|C|2751
  2 Basepair  2622 2751 GC cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|A|2623 B=7A0S|1|X|G|2750
    Insertion on left  7A0S|1|X|A|2623
    Insertion on left  7A0S|1|X|G|2624
pMakeNodes probed for insert:  a=7A0S|1|X|U|2625 B=7A0S|1|X|G|2750
pMakeNodesJunction: a=7A0S|1|X|U|2625 r=7A0S|1|X|U|2625 s=7A0S|1|X|A|2653 t=7A0S|1|X|A|2654 u=B=7A0S|1|X|G|2750
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|U|2625 and 7A0S|1|X|A|2653 and between 7A0S|1|X|A|2654 and 7A0S|1|X|G|2750
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|U|2625 s=7A0S|1|X|A|2653 t=7A0S|1|X|A|2654 B=7A0S|1|X|G|2750
pMakeNodesJunction: first branch starts at   7A0S|1|X|U|2625
pMakeNodesJunction: first branch ends around 7A0S|1|X|A|2653
pMakeNodesJunction: second branch starts at  7A0S|1|X|A|2654
pMakeNodesJunction: junction ends at         7A0S|1|X|G|2750
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|U|2625
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|A|2653
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|C|2655
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|2748

Junction with 2 loops, call it J8909
Actual Branch 1 of junction J8909 - Nucleotides 7A0S|1|X|U|2625 to 7A0S|1|X|A|2653, length   2
Actual Branch 2 of junction J8909 - Nucleotides 7A0S|1|X|A|2654 to 7A0S|1|X|G|2750, length  11
  3 Junction

2B Branch 1 of 2 of junction J8909 - Nucleotides  2625 to  2653, length   2
pMakeNodes starting loop:     a=7A0S|1|X|U|2625 B=7A0S|1|X|A|2653
  5 Basepair  2625 2653 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J8909 - Nucleotides  2654 to  2750, length  11
pMakeNodes starting loop:     a=7A0S|1|X|A|2654 B=7A0S|1|X|G|2750
  7 Initial   2654 (0 insertion) and 2750 (0 insertion)
pMakeNodesJunction: a=7A0S|1|X|A|2654 r=7A0S|1|X|A|2654 s=7A0S|1|X|G|2712 t=7A0S|1|X|A|2713 u=B=7A0S|1|X|G|2750
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|A|2654 and 7A0S|1|X|G|2712 and between 7A0S|1|X|A|2713 and 7A0S|1|X|G|2750
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|A|2654 s=7A0S|1|X|G|2712 t=7A0S|1|X|A|2713 B=7A0S|1|X|G|2750
pMakeNodesJunction: first branch starts at   7A0S|1|X|A|2654
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|2712
pMakeNodesJunction: second branch starts at  7A0S|1|X|A|2713
pMakeNodesJunction: junction ends at         7A0S|1|X|G|2750
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|C|2655
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|G|2711
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|2716
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|2748

Junction with 2 loops, call it J9592
Actual Branch 1 of junction J9592 - Nucleotides 7A0S|1|X|A|2654 to 7A0S|1|X|G|2712, length   4
Actual Branch 2 of junction J9592 - Nucleotides 7A0S|1|X|A|2713 to 7A0S|1|X|G|2750, length   7
  8 Junction

2B Branch 1 of 2 of junction J9592 - Nucleotides  2654 to  2712, length   4
pMakeNodes starting loop:     a=7A0S|1|X|A|2654 B=7A0S|1|X|G|2712
 10 Basepair  2654 2712 AG cWW 
No need to probe because of interaction between a=7A0S|1|X|C|2655 B=7A0S|1|X|G|2711
 11 Basepair  2655 2711 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J9592 - Nucleotides  2713 to  2750, length   7
pMakeNodes starting loop:     a=7A0S|1|X|A|2713 B=7A0S|1|X|G|2750
    Insertion on left  7A0S|1|X|A|2713
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|2714 interacts with 7A0S|1|X|G|2750
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2750 interacts with 7A0S|1|X|A|2714
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2750 interacts with 7A0S|1|X|A|2714
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 13 Initial   2713 (1 insertion) and 2750 (0 insertion)
 14 Basepair  2714 2750 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|C|2715 B=7A0S|1|X|A|2749
 15 Basepair  2715 2749 CA cWW 
No need to probe because of interaction between a=7A0S|1|X|G|2716 B=7A0S|1|X|C|2748
 16 Basepair  2716 2748 GC cWW 
 17 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 16
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 16
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
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  14  Basepair Left 11 Right 16
pMakeMotifModelFromSSF:  15  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  16  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  17   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|2623
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|2624
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|2713
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: []
           numbranches: []
              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: [0.0082 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: 'C'
               Comment: ' // Basepair G2622 - C2751 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J8909'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2623'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8909'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 7A0S|1|X|G|2624'
              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]
           numbranches: []
              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: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: 'J8909'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U2625 - G2750 ID J8909'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8909'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 U2625 - A2653 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: 'J8909'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|2654 - 7A0S|1|X|G|2750 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: 'J9592'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2654 - G2750 ID J9592'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J9592'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             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 A2654 - G2712 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 C2655 - G2711 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

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: 'J9592'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|2713 - 7A0S|1|X|G|2750 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 7A0S|1|X|A|2713'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             LeftIndex: 11
            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: 'G'
               Comment: ' // Basepair A2714 - G2750 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]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C2715 - A2749 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 23
             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 G2716 - C2748 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 16
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 16
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 16
pMakeMotifModelFromSSF:  20  Basepair Left 11 Right 16
pMakeMotifModelFromSSF:  21  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  22  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  23   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J8909'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: 'J8909'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|2654 - 7A0S|1|X|G|2750 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_54165.1. Nodes 8 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J9592'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: 'J9592'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|A|2713 - 7A0S|1|X|G|2750 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_54165.1. Nodes 13 and 17 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_54165.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.5425

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J4_57327.1, number 34 of 65
pMakeNodes starting loop:     a=4V7M|1|AY|U|6 B=4V7M|1|AY|A|66
  2 Basepair     6   66 UA cWW 
pMakeNodes probe for inserts:  a=4V7M|1|AY|A|7 B=4V7M|1|AY|U|65
    Insertion on left  4V7M|1|AY|A|7
    Insertion on left  4V7M|1|AY|C|9
    Insertion on left  4V7M|1|AY|G|10
    Insertion on left  4V7M|1|AY|C|11
    Insertion on right 4V7M|1|AY|U|65
pMakeNodes probed for insert:  a=4V7M|1|AY|C|12 B=4V7M|1|AY|G|64
pMakeNodesJunction: a=4V7M|1|AY|C|12 r=4V7M|1|AY|C|12 s=4V7M|1|AY|G|22 t=4V7M|1|AY|G|23 u=B=4V7M|1|AY|G|64
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V7M|1|AY|C|12 and 4V7M|1|AY|G|22 and between 4V7M|1|AY|G|23 and 4V7M|1|AY|G|64
pMakeNodesJunction: about to make a junction: a=4V7M|1|AY|C|12 s=4V7M|1|AY|G|22 t=4V7M|1|AY|G|23 B=4V7M|1|AY|G|64
pMakeNodesJunction: first branch starts at   4V7M|1|AY|C|12
pMakeNodesJunction: first branch ends around 4V7M|1|AY|G|22
pMakeNodesJunction: second branch starts at  4V7M|1|AY|G|23
pMakeNodesJunction: junction ends at         4V7M|1|AY|G|64
pMakeNodesJunction: first branch strand start goes up to  4V7M|1|AY|C|12
pMakeNodesJunction: first branch strand end goes down to  4V7M|1|AY|G|22
pMakeNodesJunction: second branch strand start goes up to 4V7M|1|AY|C|26
pMakeNodesJunction: last strand of junction goes down to  4V7M|1|AY|G|64

Junction with 2 loops, call it J5472
Actual Branch 1 of junction J5472 - Nucleotides 4V7M|1|AY|C|12 to 4V7M|1|AY|G|22, length   2
Actual Branch 2 of junction J5472 - Nucleotides 4V7M|1|AY|G|23 to 4V7M|1|AY|G|64, length   9
  3 Junction

2B Branch 1 of 2 of junction J5472 - Nucleotides    12 to    22, length   2
pMakeNodes starting loop:     a=4V7M|1|AY|C|12 B=4V7M|1|AY|G|22
  5 Basepair    12   22 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J5472 - Nucleotides    23 to    64, length   9
pMakeNodes starting loop:     a=4V7M|1|AY|G|23 B=4V7M|1|AY|G|64
    Insertion on left  4V7M|1|AY|G|23
    Insertion on left  4V7M|1|AY|C|24
  7 Initial     23 (2 insertion) and   64 (0 insertion)
pMakeNodesJunction: a=4V7M|1|AY|A|25 r=4V7M|1|AY|A|25 s=4V7M|1|AY|C|43 t=4V7M|1|AY|U|44 u=B=4V7M|1|AY|G|64
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V7M|1|AY|A|25 and 4V7M|1|AY|C|43 and between 4V7M|1|AY|U|44 and 4V7M|1|AY|G|64
pMakeNodesJunction: about to make a junction: a=4V7M|1|AY|A|25 s=4V7M|1|AY|C|43 t=4V7M|1|AY|U|44 B=4V7M|1|AY|G|64
pMakeNodesJunction: first branch starts at   4V7M|1|AY|A|25
pMakeNodesJunction: first branch ends around 4V7M|1|AY|C|43
pMakeNodesJunction: second branch starts at  4V7M|1|AY|U|44
pMakeNodesJunction: junction ends at         4V7M|1|AY|G|64
pMakeNodesJunction: first branch strand start goes up to  4V7M|1|AY|C|26
pMakeNodesJunction: first branch strand end goes down to  4V7M|1|AY|G|42
pMakeNodesJunction: second branch strand start goes up to 4V7M|1|AY|C|48
pMakeNodesJunction: last strand of junction goes down to  4V7M|1|AY|G|64

Junction with 2 loops, call it J1386
Actual Branch 1 of junction J1386 - Nucleotides 4V7M|1|AY|A|25 to 4V7M|1|AY|C|43, length   4
Actual Branch 2 of junction J1386 - Nucleotides 4V7M|1|AY|U|44 to 4V7M|1|AY|G|64, length   3
  8 Junction

2B Branch 1 of 2 of junction J1386 - Nucleotides    25 to    43, length   4
pMakeNodes starting loop:     a=4V7M|1|AY|A|25 B=4V7M|1|AY|C|43
 10 Basepair    25   43 AC cWW 
No need to probe because of interaction between a=4V7M|1|AY|C|26 B=4V7M|1|AY|G|42
 11 Basepair    26   42 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J1386 - Nucleotides    44 to    64, length   3
pMakeNodes starting loop:     a=4V7M|1|AY|U|44 B=4V7M|1|AY|G|64
    Insertion on left  4V7M|1|AY|U|44
pMakeNodesProbeForInsertions:  a 4V7M|1|AY|C|48 interacts with 4V7M|1|AY|G|64
pMakeNodesProbeForInsertions:  B 4V7M|1|AY|G|64 interacts with 4V7M|1|AY|C|48
pMakeNodesProbeForInsertions:  B 4V7M|1|AY|G|64 interacts with 4V7M|1|AY|C|48
 13 Initial     44 (1 insertion) and   64 (0 insertion)
 14 Basepair    48   64 CG cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  8 Right 16
pMakeMotifModelFromSSF:   8  Junction Left 10 Right 16
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  13   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  14  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  15   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V7M|1|AY|U|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|G|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|G|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|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: 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: []
           numbranches: []
              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-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: 'UACGC'
           RightLetter: 'UA'
               Comment: ' // Basepair U6 - A66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J5472'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V7M|1|AY|A|7'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5472'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4V7M|1|AY|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]
           numbranches: []
              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: '*'
           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: []
           numbranches: []
              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: 17
             Insertion: []
                    id: 'J5472'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V7M|1|AY|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J1386'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1386'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V7M|1|AY|G|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: '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]
           numbranches: []
              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 4V7M|1|AY|U|46'
              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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: 'J5472'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C12 - G64 ID J5472'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5472'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C12 - 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]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: 'J5472'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4V7M|1|AY|G|23 - 4V7M|1|AY|G|64 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 4V7M|1|AY|G|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 4V7M|1|AY|G|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: 'J1386'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A25 - G64 ID J1386'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J1386'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             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 A25 - 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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             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 C26 - G42 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 26

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: []
           numbranches: []
              NormCons: 1

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: 'J1386'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 4V7M|1|AY|U|44 - 4V7M|1|AY|G|64 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 29
             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 4V7M|1|AY|C|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 30
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 31
             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 C48 - 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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 33
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  6 Right 16
pMakeMotifModelFromSSF:  13  Junction Left  6 Right 16
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  17   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  18     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  20     Fixed Left  9 Right 16
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  22  Junction Left 10 Right 16
pMakeMotifModelFromSSF:  23   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  25  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  26   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  27   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  28     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  29   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  30  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  31   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Found a junction child at node 27
pNextNodeJunction: Found a hairpin at node 31
pNextNodeJunction: Finished at node 31 out of 31, type Hairpin
pNextNodeJunction: Finished at node 31 out of 31, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J5472'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: 'J5472'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4V7M|1|AY|G|23 - 4V7M|1|AY|G|64 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_57327.1. Nodes 14 and 17 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J1386'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: 'J1386'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 4V7M|1|AY|U|44 - 4V7M|1|AY|G|64 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_57327.1. Nodes 23 and 27 both model an insertion before position 14. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Found a junction child at node 27
pNextNodeJunction: Found a hairpin at node 31
pNextNodeJunction: Finished at node 31 out of 31, type Hairpin
pNextNodeJunction: Finished at node 31 out of 31, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_57327.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.9668

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J4_57344.1, number 35 of 65
pMakeNodes starting loop:     a=5UD5|1|C|C|7 B=5UD5|1|C|G|66
pMakeNodes making a cluster near strand break a=5UD5|1|C|C|7 B=5UD5|1|C|G|66
pMakeNodesCluster: amax is 2 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 11 to 11
aa is 2 bb is 11
  2 Cluster   5UD5|1|C|C|7:5UD5|1|C|U|9 5UD5|1|C|G|66:5UD5|1|C|G|66
    LR Inter  5UD5|1|C|C|7 5UD5|1|C|G|66 cWW 
    LR Inter  5UD5|1|C|U|9 5UD5|1|C|G|66 tHS 
    LL Inter  5UD5|1|C|C|7 5UD5|1|C|U|9 cSH 
pMakeNodesCluster a=3 B=10 at the end
pMakeNodesCluster a=3 B=10 at the end
pMakeNodes probe for inserts:  a=5UD5|1|C|G|10 B=5UD5|1|C|G|65
  3 Initial     10 (0 insertion) and   65 (0 insertion)
pMakeNodes probed for insert:  a=5UD5|1|C|G|10 B=5UD5|1|C|G|65
pMakeNodesJunction: a=5UD5|1|C|G|10 r=5UD5|1|C|G|10 s=5UD5|1|C|C|24 t=5UD5|1|C|G|25 u=B=5UD5|1|C|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5UD5|1|C|G|10 and 5UD5|1|C|C|24 and between 5UD5|1|C|G|25 and 5UD5|1|C|G|65
pMakeNodesJunction: about to make a junction: a=5UD5|1|C|G|10 s=5UD5|1|C|C|24 t=5UD5|1|C|G|25 B=5UD5|1|C|G|65
pMakeNodesJunction: first branch starts at   5UD5|1|C|G|10
pMakeNodesJunction: first branch ends around 5UD5|1|C|C|24
pMakeNodesJunction: second branch starts at  5UD5|1|C|G|25
pMakeNodesJunction: junction ends at         5UD5|1|C|G|65
pMakeNodesJunction: first branch strand start goes up to  5UD5|1|C|G|10
pMakeNodesJunction: first branch strand end goes down to  5UD5|1|C|C|24
pMakeNodesJunction: second branch strand start goes up to 5UD5|1|C|G|25
pMakeNodesJunction: last strand of junction goes down to  5UD5|1|C|G|65

Junction with 2 loops, call it J1492
Actual Branch 1 of junction J1492 - Nucleotides 5UD5|1|C|G|10 to 5UD5|1|C|C|24, length   2
Actual Branch 2 of junction J1492 - Nucleotides 5UD5|1|C|G|25 to 5UD5|1|C|G|65, length   6
  4 Junction

2B Branch 1 of 2 of junction J1492 - Nucleotides    10 to    24, length   2
pMakeNodes starting loop:     a=5UD5|1|C|G|10 B=5UD5|1|C|C|24
  6 Basepair    10   24 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1492 - Nucleotides    25 to    65, length   6
pMakeNodes starting loop:     a=5UD5|1|C|G|25 B=5UD5|1|C|G|65
  8 Initial     25 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=5UD5|1|C|G|25 r=5UD5|1|C|G|25 s=5UD5|1|C|C|45 t=5UD5|1|C|A|46 u=B=5UD5|1|C|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5UD5|1|C|G|25 and 5UD5|1|C|C|45 and between 5UD5|1|C|A|46 and 5UD5|1|C|G|65
pMakeNodesJunction: about to make a junction: a=5UD5|1|C|G|25 s=5UD5|1|C|C|45 t=5UD5|1|C|A|46 B=5UD5|1|C|G|65
pMakeNodesJunction: first branch starts at   5UD5|1|C|G|25
pMakeNodesJunction: first branch ends around 5UD5|1|C|C|45
pMakeNodesJunction: second branch starts at  5UD5|1|C|A|46
pMakeNodesJunction: junction ends at         5UD5|1|C|G|65
pMakeNodesJunction: first branch strand start goes up to  5UD5|1|C|G|25
pMakeNodesJunction: first branch strand end goes down to  5UD5|1|C|C|45
pMakeNodesJunction: second branch strand start goes up to 5UD5|1|C|C|49
pMakeNodesJunction: last strand of junction goes down to  5UD5|1|C|G|65

Junction with 2 loops, call it J2575
Actual Branch 1 of junction J2575 - Nucleotides 5UD5|1|C|G|25 to 5UD5|1|C|C|45, length   2
Actual Branch 2 of junction J2575 - Nucleotides 5UD5|1|C|A|46 to 5UD5|1|C|G|65, length   4
  9 Junction

2B Branch 1 of 2 of junction J2575 - Nucleotides    25 to    45, length   2
pMakeNodes starting loop:     a=5UD5|1|C|G|25 B=5UD5|1|C|C|45
 11 Basepair    25   45 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J2575 - Nucleotides    46 to    65, length   4
pMakeNodes starting loop:     a=5UD5|1|C|A|46 B=5UD5|1|C|G|65
    Insertion on left  5UD5|1|C|A|46
    Insertion on left  5UD5|1|C|G|47
pMakeNodesProbeForInsertions:  a 5UD5|1|C|C|49 interacts with 5UD5|1|C|G|65
pMakeNodesProbeForInsertions:  B 5UD5|1|C|G|65 interacts with 5UD5|1|C|C|49
pMakeNodesProbeForInsertions:  B 5UD5|1|C|G|65 interacts with 5UD5|1|C|C|49
 13 Initial     46 (2 insertion) and   65 (0 insertion)
 14 Basepair    49   65 CG cWW 
 15 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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  15   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UD5|1|C|A|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UD5|1|C|G|47
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 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: []
           numbranches: []
                  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: 'CU'
           RightLetter: 'G'
               Comment: ' // Cluster node 5UD5|1|C|C|7:5UD5|1|C|U|9 and 5UD5|1|C|G|66:5UD5|1|C|G|66'
              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
           numbranches: []
                  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: []
           RightLetter: []
               Comment: ' // Initial node 5UD5|1|C|G|10 - 5UD5|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J1492'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - G65 ID J1492'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J1492'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             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 - 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: []
           numbranches: []
                  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: 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
           numbranches: []
                  lpar: []
                  rpar: []

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: 'J1492'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5UD5|1|C|G|25 - 5UD5|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G25 - G65 ID J2575'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

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: 'J2575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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 G25 - 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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

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
           numbranches: []
                  lpar: []
                  rpar: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 5UD5|1|C|A|46 - 5UD5|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             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 5UD5|1|C|A|46'
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

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: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5UD5|1|C|G|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             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 C49 - G65 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 19

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  15   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  16     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  18  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  19   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J1492'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J1492'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5UD5|1|C|G|25 - 5UD5|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_57344.1. Nodes 5 and 8 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J2575'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: []
               Comment: ' // Initial node 5UD5|1|C|A|46 - 5UD5|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_57344.1. Nodes 10 and 13 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_57344.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5534

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J4_59634.1, number 36 of 65
pMakeNodes starting loop:     a=4V8N|1|CV|U|7 B=4V8N|1|CV|A|68
  2 Basepair     7   68 UA cWW 
pMakeNodes probe for inserts:  a=4V8N|1|CV|A|9 B=4V8N|1|CV|C|67
pMakeNodes probed for insert:  a=4V8N|1|CV|A|9 B=4V8N|1|CV|C|67
pMakeNodesJunction: a=4V8N|1|CV|A|9 r=4V8N|1|CV|A|9 s=4V8N|1|CV|A|25 t=4V8N|1|CV|G|26 u=B=4V8N|1|CV|C|67
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V8N|1|CV|A|9 and 4V8N|1|CV|A|25 and between 4V8N|1|CV|G|26 and 4V8N|1|CV|C|67
pMakeNodesJunction: about to make a junction: a=4V8N|1|CV|A|9 s=4V8N|1|CV|A|25 t=4V8N|1|CV|G|26 B=4V8N|1|CV|C|67
pMakeNodesJunction: first branch starts at   4V8N|1|CV|A|9
pMakeNodesJunction: first branch ends around 4V8N|1|CV|A|25
pMakeNodesJunction: second branch starts at  4V8N|1|CV|G|26
pMakeNodesJunction: junction ends at         4V8N|1|CV|C|67
pMakeNodesJunction: first branch strand start goes up to  4V8N|1|CV|U|12
pMakeNodesJunction: first branch strand end goes down to  4V8N|1|CV|A|25
pMakeNodesJunction: second branch strand start goes up to 4V8N|1|CV|G|28
pMakeNodesJunction: last strand of junction goes down to  4V8N|1|CV|C|67

Junction with 2 loops, call it J8407
Actual Branch 1 of junction J8407 - Nucleotides 4V8N|1|CV|A|9 to 4V8N|1|CV|A|25, length   5
Actual Branch 2 of junction J8407 - Nucleotides 4V8N|1|CV|G|26 to 4V8N|1|CV|C|67, length   8
  3 Junction

2B Branch 1 of 2 of junction J8407 - Nucleotides     9 to    25, length   5
pMakeNodes starting loop:     a=4V8N|1|CV|A|9 B=4V8N|1|CV|A|25
pMakeNodes making a cluster near strand break a=4V8N|1|CV|A|9 B=4V8N|1|CV|A|25
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 6 to 6
aa is 5 bb is 6
  5 Cluster   4V8N|1|CV|A|9:4V8N|1|CV|U|12 4V8N|1|CV|A|25:4V8N|1|CV|A|25
    LR Inter  4V8N|1|CV|A|9 4V8N|1|CV|A|25 tHH 
    LR Inter  4V8N|1|CV|U|12 4V8N|1|CV|A|25 cWW 
    Left  strand conserved insertion 4V8N|1|CV|G|10 at position 2
    Left  strand conserved insertion 4V8N|1|CV|C|11 at position 3
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J8407 - Nucleotides    26 to    67, length   8
pMakeNodes starting loop:     a=4V8N|1|CV|G|26 B=4V8N|1|CV|C|67
    Insertion on left  4V8N|1|CV|G|26
    Insertion on left  4V8N|1|CV|C|27
  7 Initial     26 (2 insertion) and   67 (0 insertion)
pMakeNodesJunction: a=4V8N|1|CV|G|28 r=4V8N|1|CV|G|28 s=4V8N|1|CV|U|46 t=4V8N|1|CV|G|47 u=B=4V8N|1|CV|C|67
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V8N|1|CV|G|28 and 4V8N|1|CV|U|46 and between 4V8N|1|CV|G|47 and 4V8N|1|CV|C|67
pMakeNodesJunction: about to make a junction: a=4V8N|1|CV|G|28 s=4V8N|1|CV|U|46 t=4V8N|1|CV|G|47 B=4V8N|1|CV|C|67
pMakeNodesJunction: first branch starts at   4V8N|1|CV|G|28
pMakeNodesJunction: first branch ends around 4V8N|1|CV|U|46
pMakeNodesJunction: second branch starts at  4V8N|1|CV|G|47
pMakeNodesJunction: junction ends at         4V8N|1|CV|C|67
pMakeNodesJunction: first branch strand start goes up to  4V8N|1|CV|G|28
pMakeNodesJunction: first branch strand end goes down to  4V8N|1|CV|U|46
pMakeNodesJunction: second branch strand start goes up to 4V8N|1|CV|G|51
pMakeNodesJunction: last strand of junction goes down to  4V8N|1|CV|C|67

Junction with 2 loops, call it J2542
Actual Branch 1 of junction J2542 - Nucleotides 4V8N|1|CV|G|28 to 4V8N|1|CV|U|46, length   2
Actual Branch 2 of junction J2542 - Nucleotides 4V8N|1|CV|G|47 to 4V8N|1|CV|C|67, length   4
  8 Junction

2B Branch 1 of 2 of junction J2542 - Nucleotides    28 to    46, length   2
pMakeNodes starting loop:     a=4V8N|1|CV|G|28 B=4V8N|1|CV|U|46
 10 Basepair    28   46 GU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J2542 - Nucleotides    47 to    67, length   4
pMakeNodes starting loop:     a=4V8N|1|CV|G|47 B=4V8N|1|CV|C|67
    Insertion on left  4V8N|1|CV|G|47
    Insertion on left  4V8N|1|CV|G|48
pMakeNodesProbeForInsertions:  a 4V8N|1|CV|G|51 interacts with 4V8N|1|CV|C|67
pMakeNodesProbeForInsertions:  B 4V8N|1|CV|C|67 interacts with 4V8N|1|CV|G|51
pMakeNodesProbeForInsertions:  B 4V8N|1|CV|C|67 interacts with 4V8N|1|CV|G|51
 12 Initial     47 (2 insertion) and   67 (0 insertion)
 13 Basepair    51   67 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  9 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  12   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  14   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V8N|1|CV|A|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V8N|1|CV|G|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V8N|1|CV|U|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V8N|1|CV|G|47
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: 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: []
           numbranches: []
          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: [0.9950 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 U7 - A68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: 'J8407'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A9 - C67 ID J8407'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: 'J8407'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4V8N|1|CV|A|9:4V8N|1|CV|U|12 and 4V8N|1|CV|A|25:4V8N|1|CV|A|25'
              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: []
           numbranches: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2477

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: []
           numbranches: []
          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: []
           numbranches: []
          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: 7
            RightIndex: 14
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4V8N|1|CV|G|26 - 4V8N|1|CV|C|67 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
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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: 'Fixed'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: 'J2542'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V8N|1|CV|A|25'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          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: 14
             Insertion: []
                    id: 'J2542'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            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: []
           numbranches: []
          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: 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 4V8N|1|CV|G|26'
              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]
           numbranches: []
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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: 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: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: 'J2542'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G28 - C67 ID J2542'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J2542'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
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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: 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 G28 - U46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J2542'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 4V8N|1|CV|G|47 - 4V8N|1|CV|C|67 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
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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: 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 4V8N|1|CV|U|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 12
            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 4V8N|1|CV|G|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
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          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
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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: 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 G51 - C67 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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 14
pMakeMotifModelFromSSF:   9     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  11     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  13  Junction Left  9 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  15  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  16   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  17   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  18     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  19   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  20     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  21   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  22  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  23   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: 'J8407'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4V8N|1|CV|G|26 - 4V8N|1|CV|C|67 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_59634.1. Nodes 4 and 8 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J2542'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J2542'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 4V8N|1|CV|G|47 - 4V8N|1|CV|C|67 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_59634.1. Nodes 14 and 17 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin
pNextNodeJunction: Finished at node 23 out of 23, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_59634.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.0345

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J4_59845.1, number 37 of 65
pMakeNodes starting loop:     a=6CK5|1|A|A|5 B=6CK5|1|A|U|106
  2 Basepair     5  106 AU cWW 
pMakeNodes probe for inserts:  a=6CK5|1|A|G|6 B=6CK5|1|A|G|105
    Insertion on left  6CK5|1|A|G|6
pMakeNodes probed for insert:  a=6CK5|1|A|U|7 B=6CK5|1|A|G|105
pMakeNodesJunction: a=6CK5|1|A|U|7 r=6CK5|1|A|U|7 s=6CK5|1|A|A|55 t=6CK5|1|A|G|56 u=B=6CK5|1|A|G|105
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6CK5|1|A|U|7 and 6CK5|1|A|A|55 and between 6CK5|1|A|G|56 and 6CK5|1|A|G|105
pMakeNodesJunction: about to make a junction: a=6CK5|1|A|U|7 s=6CK5|1|A|A|55 t=6CK5|1|A|G|56 B=6CK5|1|A|G|105
pMakeNodesJunction: first branch starts at   6CK5|1|A|U|7
pMakeNodesJunction: first branch ends around 6CK5|1|A|A|55
pMakeNodesJunction: second branch starts at  6CK5|1|A|G|56
pMakeNodesJunction: junction ends at         6CK5|1|A|G|105
pMakeNodesJunction: first branch strand start goes up to  6CK5|1|A|U|7
pMakeNodesJunction: first branch strand end goes down to  6CK5|1|A|A|55
pMakeNodesJunction: second branch strand start goes up to 6CK5|1|A|G|56
pMakeNodesJunction: last strand of junction goes down to  6CK5|1|A|G|100

Junction with 2 loops, call it J8142
Actual Branch 1 of junction J8142 - Nucleotides 6CK5|1|A|U|7 to 6CK5|1|A|A|55, length   2
Actual Branch 2 of junction J8142 - Nucleotides 6CK5|1|A|G|56 to 6CK5|1|A|G|105, length  11
  3 Junction

2B Branch 1 of 2 of junction J8142 - Nucleotides     7 to    55, length   2
pMakeNodes starting loop:     a=6CK5|1|A|U|7 B=6CK5|1|A|A|55
  5 Basepair     7   55 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J8142 - Nucleotides    56 to   105, length  11
pMakeNodes starting loop:     a=6CK5|1|A|G|56 B=6CK5|1|A|G|105
  7 Initial     56 (0 insertion) and  105 (0 insertion)
pMakeNodesJunction: a=6CK5|1|A|G|56 r=6CK5|1|A|G|56 s=6CK5|1|A|C|73 t=6CK5|1|A|A|74 u=B=6CK5|1|A|G|105
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6CK5|1|A|G|56 and 6CK5|1|A|C|73 and between 6CK5|1|A|A|74 and 6CK5|1|A|G|105
pMakeNodesJunction: about to make a junction: a=6CK5|1|A|G|56 s=6CK5|1|A|C|73 t=6CK5|1|A|A|74 B=6CK5|1|A|G|105
pMakeNodesJunction: first branch starts at   6CK5|1|A|G|56
pMakeNodesJunction: first branch ends around 6CK5|1|A|C|73
pMakeNodesJunction: second branch starts at  6CK5|1|A|A|74
pMakeNodesJunction: junction ends at         6CK5|1|A|G|105
pMakeNodesJunction: first branch strand start goes up to  6CK5|1|A|G|56
pMakeNodesJunction: first branch strand end goes down to  6CK5|1|A|C|73
pMakeNodesJunction: second branch strand start goes up to 6CK5|1|A|C|77
pMakeNodesJunction: last strand of junction goes down to  6CK5|1|A|G|100

Junction with 2 loops, call it J2435
Actual Branch 1 of junction J2435 - Nucleotides 6CK5|1|A|G|56 to 6CK5|1|A|C|73, length   2
Actual Branch 2 of junction J2435 - Nucleotides 6CK5|1|A|A|74 to 6CK5|1|A|G|105, length   9
  8 Junction

2B Branch 1 of 2 of junction J2435 - Nucleotides    56 to    73, length   2
pMakeNodes starting loop:     a=6CK5|1|A|G|56 B=6CK5|1|A|C|73
 10 Basepair    56   73 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J2435 - Nucleotides    74 to   105, length   9
pMakeNodes starting loop:     a=6CK5|1|A|A|74 B=6CK5|1|A|G|105
pMakeNodes making a cluster near strand break a=6CK5|1|A|A|74 B=6CK5|1|A|G|105
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 8 and then 15 to 15
aa is 8 bb is 15
 13 Cluster   6CK5|1|A|A|74:6CK5|1|A|C|75 6CK5|1|A|G|105:6CK5|1|A|G|105
    LR Inter  6CK5|1|A|A|74 6CK5|1|A|G|105 cSS 
    LR Inter  6CK5|1|A|C|75 6CK5|1|A|G|105 cSS 
pMakeNodesCluster a=9 B=14 at the end
pMakeNodesCluster a=9 B=14 at the end
pMakeNodes probe for inserts:  a=6CK5|1|A|A|76 B=6CK5|1|A|G|104
    Insertion on left  6CK5|1|A|A|76
    Insertion on right 6CK5|1|A|G|104
    Insertion on right 6CK5|1|A|U|102
    Insertion on right 6CK5|1|A|A|101
pMakeNodesProbeForInsertions:  a 6CK5|1|A|C|77 interacts with 6CK5|1|A|G|100
pMakeNodesProbeForInsertions:  B 6CK5|1|A|G|100 interacts with 6CK5|1|A|C|77
pMakeNodesProbeForInsertions:  B 6CK5|1|A|G|100 interacts with 6CK5|1|A|C|77
 14 Initial     76 (1 insertion) and  104 (3 insertion)
pMakeNodes probed for insert:  a=6CK5|1|A|C|77 B=6CK5|1|A|G|100
 15 Basepair    77  100 CG cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  13   Cluster Left  7  8 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CK5|1|A|G|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CK5|1|A|A|76
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6CK5|1|A|A|103
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6CK5|1|A|U|102
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6CK5|1|A|A|101
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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Basepair A5 - U106 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J8142'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6CK5|1|A|G|6'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J8142'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J8142'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U7 - G105 ID J8142'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J8142'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U7 - A55 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J8142'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CK5|1|A|G|56 - 6CK5|1|A|G|105 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J2435'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G56 - G105 ID J2435'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J2435'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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 G56 - C73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 13

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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J2435'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 16
             LeftIndex: [7 8]
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 6CK5|1|A|A|74:6CK5|1|A|C|75 and 6CK5|1|A|G|105:6CK5|1|A|G|105'
              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: []
           numbranches: []
              NormCons: 0.1949
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AUG'
               Comment: ' // Initial node 6CK5|1|A|A|76 - 6CK5|1|A|G|104 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             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 6CK5|1|A|A|76'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             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 6CK5|1|A|A|103'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             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 6CK5|1|A|U|102'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 6CK5|1|A|A|101'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             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 C77 - G100 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

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  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 15
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  15   Cluster Left  7  8 Right 15
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 10 Right 13
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  22   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  23     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  24   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  25  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  26   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J8142'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J8142'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6CK5|1|A|G|56 - 6CK5|1|A|G|105 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_59845.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J2435'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J2435'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_59845.1. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin
pNextNodeJunction: Finished at node 26 out of 26, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSW  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for tSW  between 2 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_59845.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8476
   -9.5307

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J4_60168.1, number 38 of 65
pMakeNodes starting loop:     a=4WF9|1|X|C|644 B=4WF9|1|X|G|701
pMakeNodes making a cluster near strand break a=4WF9|1|X|C|644 B=4WF9|1|X|G|701
pMakeNodesCluster: amax is 3 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 1 and then 20 to 20
aa is 1 bb is 20
  2 Cluster   4WF9|1|X|C|644:4WF9|1|X|C|644 4WF9|1|X|G|701:4WF9|1|X|G|701
    LR Inter  4WF9|1|X|C|644 4WF9|1|X|G|701 cWW 
pMakeNodesCluster a=2 B=19 at the end
pMakeNodesCluster a=2 B=19 at the end
pMakeNodes probe for inserts:  a=4WF9|1|X|A|645 B=4WF9|1|X|A|700
    Insertion on left  4WF9|1|X|A|645
    Insertion on right 4WF9|1|X|A|700
    Insertion on right 4WF9|1|X|U|699
    Insertion on right 4WF9|1|X|U|698
    Insertion on right 4WF9|1|X|U|697
  3 Initial    645 (1 insertion) and  700 (4 insertion)
pMakeNodes probed for insert:  a=4WF9|1|X|A|646 B=4WF9|1|X|C|695
pMakeNodesJunction: a=4WF9|1|X|A|646 r=4WF9|1|X|A|646 s=4WF9|1|X|G|670 t=4WF9|1|X|U|671 u=B=4WF9|1|X|C|695
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|A|646 and 4WF9|1|X|G|670 and between 4WF9|1|X|U|671 and 4WF9|1|X|C|695
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|A|646 s=4WF9|1|X|G|670 t=4WF9|1|X|U|671 B=4WF9|1|X|C|695
pMakeNodesJunction: first branch starts at   4WF9|1|X|A|646
pMakeNodesJunction: first branch ends around 4WF9|1|X|G|670
pMakeNodesJunction: second branch starts at  4WF9|1|X|U|671
pMakeNodesJunction: junction ends at         4WF9|1|X|C|695
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|647
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|C|669
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|G|673
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|G|694

Junction with 2 loops, call it J9292
Actual Branch 1 of junction J9292 - Nucleotides 4WF9|1|X|A|646 to 4WF9|1|X|G|670, length   4
Actual Branch 2 of junction J9292 - Nucleotides 4WF9|1|X|U|671 to 4WF9|1|X|C|695, length   9
  4 Junction

2B Branch 1 of 2 of junction J9292 - Nucleotides   646 to   670, length   4
pMakeNodes starting loop:     a=4WF9|1|X|A|646 B=4WF9|1|X|G|670
  6 Basepair   646  670 AG tSS 
No need to probe because of interaction between a=4WF9|1|X|G|647 B=4WF9|1|X|C|669
  7 Basepair   647  669 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J9292 - Nucleotides   671 to   695, length   9
pMakeNodes starting loop:     a=4WF9|1|X|U|671 B=4WF9|1|X|C|695
    Insertion on left  4WF9|1|X|U|671
    Insertion on left  4WF9|1|X|A|672
  9 Initial    671 (2 insertion) and  695 (0 insertion)
pMakeNodesJunction: a=4WF9|1|X|G|673 r=4WF9|1|X|G|673 s=4WF9|1|X|C|680 t=4WF9|1|X|G|681 u=B=4WF9|1|X|C|695
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|G|673 and 4WF9|1|X|C|680 and between 4WF9|1|X|G|681 and 4WF9|1|X|C|695
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|G|673 s=4WF9|1|X|C|680 t=4WF9|1|X|G|681 B=4WF9|1|X|C|695
pMakeNodesJunction: first branch starts at   4WF9|1|X|G|673
pMakeNodesJunction: first branch ends around 4WF9|1|X|C|680
pMakeNodesJunction: second branch starts at  4WF9|1|X|G|681
pMakeNodesJunction: junction ends at         4WF9|1|X|C|695
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|673
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|C|680
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|U|684
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|G|694
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J3499
Actual Branch 1 of junction J3499 - Nucleotides 4WF9|1|X|G|673 to 4WF9|1|X|C|680, length   2
Actual Branch 2 of junction J3499 - Nucleotides 4WF9|1|X|G|681 to 4WF9|1|X|C|695, length   5
 10 Junction

2B Branch 1 of 2 of junction J3499 - Nucleotides   673 to   680, length   2
pMakeNodes starting loop:     a=4WF9|1|X|G|673 B=4WF9|1|X|C|680
 12 Basepair   673  680 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J3499 - Nucleotides   681 to   695, length   5
pMakeNodes starting loop:     a=4WF9|1|X|G|681 B=4WF9|1|X|C|695
    Insertion on left  4WF9|1|X|G|681
pMakeNodesProbeForInsertions:  a 4WF9|1|X|A|682 interacts with 4WF9|1|X|C|695
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|695 interacts with 4WF9|1|X|A|682
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|695 interacts with 4WF9|1|X|A|682
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 14 Initial    681 (1 insertion) and  695 (0 insertion)
 15 Basepair   682  695 AC tSS 
No need to probe because of interaction between a=4WF9|1|X|U|684 B=4WF9|1|X|G|694
 16 Basepair   684  694 UG cWW 
 17 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 20
pMakeMotifModelFromSSF:   3   Initial Left  2 Right 19
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   9   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  10  Junction Left  9 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  14   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  15  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  16  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  17   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|645
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|U|698
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|U|697
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|G|696
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|C|695
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|671
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|672
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|G|681
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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Cluster node 4WF9|1|X|C|644:4WF9|1|X|C|644 and 4WF9|1|X|G|701:4WF9|1|X|G|701'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: 1
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Cluster Interaction 4WF9|1|X|C|644 - 4WF9|1|X|G|701 cWW '}
      JunctionDeletion: []
          InterIndices: [1 20]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'UUUA'
               Comment: ' // Initial node 4WF9|1|X|A|645 - 4WF9|1|X|A|700 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: 'J9292'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|645'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: 'J9292'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             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 4WF9|1|X|U|698'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 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: '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: []
           numbranches: []
                  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: 'Fixed'
              nextnode: 9
             LeftIndex: 3
            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|U|697'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: 'J9292'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UA'
           RightLetter: []
               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: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: 'J3499'
        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|G|696'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: 'J3499'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 3
            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 4WF9|1|X|C|695'
              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: []
           numbranches: []
                  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: 'Initial'
              nextnode: 14
             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: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J9292'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A646 - C695 ID J9292'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J9292'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             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 A646 - G670 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  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: 'Basepair'
              nextnode: 18
             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 G647 - C669 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             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
           numbranches: []
                  lpar: []
                  rpar: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J9292'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|U|671 - 4WF9|1|X|C|695 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 4WF9|1|X|U|671'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 4WF9|1|X|A|672'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: 'J3499'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G673 - C695 ID J3499'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J3499'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 27
             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 G673 - C680 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             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
           numbranches: []
                  lpar: []
                  rpar: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: 'J3499'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|G|681 - 4WF9|1|X|C|695 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 30
             LeftIndex: 11
            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 4WF9|1|X|G|681'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 32
             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 A682 - C695 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 33
             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: 'G'
               Comment: ' // Basepair U684 - G694 cWW '
              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: []
           numbranches: []
                  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: 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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 20
pMakeMotifModelFromSSF:   3   Initial Left  2 Right 19
pMakeMotifModelFromSSF:   4     Fixed Left  2 Right 19
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 19
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right 19
pMakeMotifModelFromSSF:   7   Initial Left  3 Right 18
pMakeMotifModelFromSSF:   8     Fixed Left  3 Right 18
pMakeMotifModelFromSSF:   9   Initial Left  3 Right 17
pMakeMotifModelFromSSF:  10     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:  11   Initial Left  3 Right 16
pMakeMotifModelFromSSF:  12     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:  13   Initial Left  3 Right 15
pMakeMotifModelFromSSF:  14  Junction Left  3 Right 15
pMakeMotifModelFromSSF:  15   Initial Left  3 Right  6
pMakeMotifModelFromSSF:  16  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:  17  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  18   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  19   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  20     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  21   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  22     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  23   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  24  Junction Left  9 Right 15
pMakeMotifModelFromSSF:  25   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  26  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  27   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  28   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  29     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  30   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  31  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  32  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  33   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a junction at node 24
pNextNodeJunction: Found a junction child at node 25
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a junction child at node 28
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J9292'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J9292'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|U|671 - 4WF9|1|X|C|695 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_60168.1. Nodes 15 and 19 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J3499'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: 'J3499'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|G|681 - 4WF9|1|X|C|695 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_60168.1. Nodes 25 and 28 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a junction at node 24
pNextNodeJunction: Found a junction child at node 25
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a junction child at node 28
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for rib  between 4 and 20
pConservedInteractionList: did not find a substitution probability matrix for rib  between 9 and 13
pConservedInteractionList: did not find a substitution probability matrix for rib  between 4 and 20
pConservedInteractionList: did not find a substitution probability matrix for rib  between 9 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_60168.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.0098
  -14.2763

Timestamp 18-Jul-2025 00:12:57
pMakeSCFGModels: Making JAR3D model for motif group J4_61477.2, number 39 of 65
pMakeNodes starting loop:     a=5J7L|1|DA|A|1772 B=5J7L|1|DA|U|1979
  2 Basepair  1772 1979 AU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1773 B=5J7L|1|DA|A|1978
    Insertion on right 5J7L|1|DA|A|1978
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1773 B=5J7L|1|DA|A|1977
  3 Basepair  1773 1977 AA tSW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|1774 B=5J7L|1|DA|U|1976
pMakeNodes probed for insert:  a=5J7L|1|DA|C|1774 B=5J7L|1|DA|U|1976
pMakeNodesJunction: a=5J7L|1|DA|C|1774 r=5J7L|1|DA|C|1774 s=5J7L|1|DA|C|1790 t=5J7L|1|DA|A|1791 u=B=5J7L|1|DA|U|1976
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|1774 and 5J7L|1|DA|C|1790 and between 5J7L|1|DA|A|1791 and 5J7L|1|DA|U|1976
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|1774 s=5J7L|1|DA|C|1790 t=5J7L|1|DA|A|1791 B=5J7L|1|DA|U|1976
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|1774
pMakeNodesJunction: first branch ends around 5J7L|1|DA|C|1790
pMakeNodesJunction: second branch starts at  5J7L|1|DA|A|1791
pMakeNodesJunction: junction ends at         5J7L|1|DA|U|1976
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|1776
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|C|1788
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|1792
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|G|1975

Junction with 2 loops, call it J1965
Actual Branch 1 of junction J1965 - Nucleotides 5J7L|1|DA|C|1774 to 5J7L|1|DA|C|1790, length   6
Actual Branch 2 of junction J1965 - Nucleotides 5J7L|1|DA|A|1791 to 5J7L|1|DA|U|1976, length   8
  4 Junction

2B Branch 1 of 2 of junction J1965 - Nucleotides  1774 to  1790, length   6
pMakeNodes starting loop:     a=5J7L|1|DA|C|1774 B=5J7L|1|DA|C|1790
  6 Basepair  1774 1790 CC tHS 
No need to probe because of interaction between a=5J7L|1|DA|U|1775 B=5J7L|1|DA|A|1789
  7 Basepair  1775 1789 UA tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|1776 B=5J7L|1|DA|C|1788
  8 Basepair  1776 1788 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J1965 - Nucleotides  1791 to  1976, length   8
pMakeNodes starting loop:     a=5J7L|1|DA|A|1791 B=5J7L|1|DA|U|1976
 10 Initial   1791 (0 insertion) and 1976 (0 insertion)
pMakeNodesJunction: a=5J7L|1|DA|A|1791 r=5J7L|1|DA|A|1791 s=5J7L|1|DA|G|1828 t=5J7L|1|DA|A|1829 u=B=5J7L|1|DA|U|1976
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|A|1791 and 5J7L|1|DA|G|1828 and between 5J7L|1|DA|A|1829 and 5J7L|1|DA|U|1976
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|A|1791 s=5J7L|1|DA|G|1828 t=5J7L|1|DA|A|1829 B=5J7L|1|DA|U|1976
pMakeNodesJunction: first branch starts at   5J7L|1|DA|A|1791
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|1828
pMakeNodesJunction: second branch starts at  5J7L|1|DA|A|1829
pMakeNodesJunction: junction ends at         5J7L|1|DA|U|1976
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|1792
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|U|1827
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|C|1830
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|G|1975

Junction with 2 loops, call it J2510
Actual Branch 1 of junction J2510 - Nucleotides 5J7L|1|DA|A|1791 to 5J7L|1|DA|G|1828, length   4
Actual Branch 2 of junction J2510 - Nucleotides 5J7L|1|DA|A|1829 to 5J7L|1|DA|U|1976, length   4
 11 Junction

2B Branch 1 of 2 of junction J2510 - Nucleotides  1791 to  1828, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|A|1791 B=5J7L|1|DA|G|1828
 13 Basepair  1791 1828 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|1792 B=5J7L|1|DA|U|1827
 14 Basepair  1792 1827 GU cWW 
 15 Hairpin type *

2B Branch 2 of 2 of junction J2510 - Nucleotides  1829 to  1976, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|A|1829 B=5J7L|1|DA|U|1976
 17 Basepair  1829 1976 AU tHS 
No need to probe because of interaction between a=5J7L|1|DA|C|1830 B=5J7L|1|DA|G|1975
 18 Basepair  1830 1975 CG cWW 
 19 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  11  Junction Left  9 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  16   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  17  Basepair Left 13 Right 16
pMakeMotifModelFromSSF:  18  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  19   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|1978
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: 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: []
           numbranches: []
              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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AU'
               Comment: ' // Basepair A1772 - U1979 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            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|1978'
              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]
           numbranches: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: 'J1965'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 17
             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 A1773 - A1977 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 10]
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: 'J1965'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1774 - U1976 ID J1965'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J1965'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             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: 'C'
               Comment: ' // Basepair C1774 - C1790 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]
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             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 U1775 - A1789 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]
           numbranches: []
              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 G1776 - C1788 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: 'J1965'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1791 - 5J7L|1|DA|U|1976 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [12 16]
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: 'J2510'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1791 - U1976 ID J2510'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J2510'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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 A1791 - G1828 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]
           numbranches: []
              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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1792 - U1827 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 17

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: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J2510'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 13
            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 A1829 - U1976 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]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 C1830 - G1975 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 18
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 17
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   6  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  13  Junction Left  9 Right 16
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  16  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  18   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  19  Basepair Left 13 Right 16
pMakeMotifModelFromSSF:  20  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  21   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J1965'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: 'J1965'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1791 - 5J7L|1|DA|U|1976 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_61477.2. Nodes 7 and 12 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J2510'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J2510'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_61477.2. Nodes 14 and 18 both model an insertion before position 13. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHS  between 2 and 9
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 2 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_61477.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.1901
  -12.1830
  -11.0851
  -11.0851

Timestamp 18-Jul-2025 00:12:58
pMakeSCFGModels: Making JAR3D model for motif group J4_61885.2, number 40 of 65
pMakeNodes starting loop:     a=4LFB|1|A|G|575 B=4LFB|1|A|C|880
  2 Basepair   575  880 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|576 B=4LFB|1|A|C|879
    Insertion on left  4LFB|1|A|G|576
pMakeNodes probed for insert:  a=4LFB|1|A|G|577 B=4LFB|1|A|C|879
pMakeNodesJunction: a=4LFB|1|A|G|577 r=4LFB|1|A|G|577 s=4LFB|1|A|C|764 t=4LFB|1|A|G|765 u=B=4LFB|1|A|C|879
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|G|577 and 4LFB|1|A|C|764 and between 4LFB|1|A|G|765 and 4LFB|1|A|C|879
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|G|577 s=4LFB|1|A|C|764 t=4LFB|1|A|G|765 B=4LFB|1|A|C|879
pMakeNodesJunction: first branch starts at   4LFB|1|A|G|577
pMakeNodesJunction: first branch ends around 4LFB|1|A|C|764
pMakeNodesJunction: second branch starts at  4LFB|1|A|G|765
pMakeNodesJunction: junction ends at         4LFB|1|A|C|879
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|G|577
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|C|764
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|G|769
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|879

Junction with 2 loops, call it J6160
Actual Branch 1 of junction J6160 - Nucleotides 4LFB|1|A|G|577 to 4LFB|1|A|C|764, length   2
Actual Branch 2 of junction J6160 - Nucleotides 4LFB|1|A|G|765 to 4LFB|1|A|C|879, length  17
  3 Junction

2B Branch 1 of 2 of junction J6160 - Nucleotides   577 to   764, length   2
pMakeNodes starting loop:     a=4LFB|1|A|G|577 B=4LFB|1|A|C|764
  5 Basepair   577  764 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J6160 - Nucleotides   765 to   879, length  17
pMakeNodes starting loop:     a=4LFB|1|A|G|765 B=4LFB|1|A|C|879
  7 Initial    765 (0 insertion) and  879 (0 insertion)
pMakeNodesJunction: a=4LFB|1|A|G|765 r=4LFB|1|A|G|765 s=4LFB|1|A|A|816 t=4LFB|1|A|C|817 u=B=4LFB|1|A|C|879
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|G|765 and 4LFB|1|A|A|816 and between 4LFB|1|A|C|817 and 4LFB|1|A|C|879
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|G|765 s=4LFB|1|A|A|816 t=4LFB|1|A|C|817 B=4LFB|1|A|C|879
pMakeNodesJunction: first branch starts at   4LFB|1|A|G|765
pMakeNodesJunction: first branch ends around 4LFB|1|A|A|816
pMakeNodesJunction: second branch starts at  4LFB|1|A|C|817
pMakeNodesJunction: junction ends at         4LFB|1|A|C|879
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|G|769
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|C|810
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|G|821
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|879

Junction with 2 loops, call it J4732
Actual Branch 1 of junction J4732 - Nucleotides 4LFB|1|A|G|765 to 4LFB|1|A|A|816, length  11
Actual Branch 2 of junction J4732 - Nucleotides 4LFB|1|A|C|817 to 4LFB|1|A|C|879, length   6
  8 Junction

2B Branch 1 of 2 of junction J4732 - Nucleotides   765 to   816, length  11
pMakeNodes starting loop:     a=4LFB|1|A|G|765 B=4LFB|1|A|A|816
 10 Basepair   765  816 GA cSS 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|766 B=4LFB|1|A|A|814
    Insertion on right 4LFB|1|A|A|814
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|766 interacts with 4LFB|1|A|U|813
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|813 interacts with 4LFB|1|A|A|766
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|813 interacts with 4LFB|1|A|A|766
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|A|766 B=4LFB|1|A|U|813
 11 Basepair   766  813 AU tHW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|767 B=4LFB|1|A|C|812
    Insertion on left  4LFB|1|A|A|767
    Insertion on right 4LFB|1|A|C|812
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|768 interacts with 4LFB|1|A|C|811
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|811 interacts with 4LFB|1|A|A|768
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|811 interacts with 4LFB|1|A|A|768
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|A|768 B=4LFB|1|A|C|811
 12 Basepair   768  811 AC bif 
No need to probe because of interaction between a=4LFB|1|A|G|769 B=4LFB|1|A|C|810
 13 Basepair   769  810 GC cWW 
 14 Hairpin type *

2B Branch 2 of 2 of junction J4732 - Nucleotides   817 to   879, length   6
pMakeNodes starting loop:     a=4LFB|1|A|C|817 B=4LFB|1|A|C|879
    Insertion on left  4LFB|1|A|C|817
    Insertion on left  4LFB|1|A|G|818
    Insertion on left  4LFB|1|A|A|819
    Insertion on left  4LFB|1|A|U|820
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|821 interacts with 4LFB|1|A|C|879
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|879 interacts with 4LFB|1|A|G|821
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|879 interacts with 4LFB|1|A|G|821
 15 Initial    817 (4 insertion) and  879 (0 insertion)
 16 Basepair   821  879 GC cWW 
 17 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 21
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 21
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 21
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 15
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right 15
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  15   Initial Left 16 Right 21
pMakeMotifModelFromSSF:  16  Basepair Left 20 Right 21
pMakeMotifModelFromSSF:  17   Hairpin Left 21 Right 20
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
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|G|576
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|814
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|767
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|812
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|816
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|817
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|818
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|819
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
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: 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: []
           numbranches: []
              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: [0.0826 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: '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]
           numbranches: []
              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: 'J6160'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|576'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 21
             Insertion: []
                    id: 'J6160'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 21
             Insertion: []
                    id: 'J6160'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G577 - C879 ID J6160'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J6160'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G577 - C764 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: 'J6160'
        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|765 - 4LFB|1|A|C|879 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 15]
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: 'J4732'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G765 - C879 ID J4732'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J4732'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            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: 'G'
           RightLetter: 'AA'
               Comment: ' // Basepair G765 - A816 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]
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             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 4LFB|1|A|A|814'
              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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             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: '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]
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 6
            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: 'AA'
           RightLetter: 'CU'
               Comment: ' // Basepair A766 - U813 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]
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             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 4LFB|1|A|A|767'
              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]
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: [5×5 double]
                     Z: []
           MiddleIndex: 21
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 4LFB|1|A|C|812'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
               Comment: ' // Basepair A768 - C811 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]
           numbranches: []
              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 G769 - C810 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

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: []
           numbranches: []
              NormCons: 1

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 16
            RightIndex: 21
             Insertion: []
                    id: 'J4732'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAU'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|817 - 4LFB|1|A|C|879 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 16
            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 4LFB|1|A|A|816'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 17
            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: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 27
             LeftIndex: 17
            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 4LFB|1|A|C|817'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 18
            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: []
           numbranches: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 29
             LeftIndex: 18
            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 4LFB|1|A|G|818'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 30
             LeftIndex: 19
            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: []
           numbranches: []
              NormCons: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 31
             LeftIndex: 19
            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 4LFB|1|A|A|819'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 32
             LeftIndex: 20
            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: []
           numbranches: []
              NormCons: []

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 33
             LeftIndex: 20
            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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G821 - C879 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 37
             LeftIndex: 21
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 21
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  3 Right 21
pMakeMotifModelFromSSF:   5  Junction Left  3 Right 21
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 21
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 21
pMakeMotifModelFromSSF:  11   Initial Left  5 Right 15
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  17   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  18     Fixed Left  8 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
pMakeMotifModelFromSSF:  23   Initial Left 16 Right 21
pMakeMotifModelFromSSF:  24     Fixed Left 16 Right 21
pMakeMotifModelFromSSF:  25   Initial Left 17 Right 21
pMakeMotifModelFromSSF:  26     Fixed Left 17 Right 21
pMakeMotifModelFromSSF:  27   Initial Left 18 Right 21
pMakeMotifModelFromSSF:  28     Fixed Left 18 Right 21
pMakeMotifModelFromSSF:  29   Initial Left 19 Right 21
pMakeMotifModelFromSSF:  30     Fixed Left 19 Right 21
pMakeMotifModelFromSSF:  31   Initial Left 20 Right 21
pMakeMotifModelFromSSF:  32  Basepair Left 20 Right 21
pMakeMotifModelFromSSF:  33   Hairpin Left 21 Right 20
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J6160'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: 'J6160'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|765 - 4LFB|1|A|C|879 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_61885.2. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J4732'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 16
            RightIndex: 21
             Insertion: []
                    id: 'J4732'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAU'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|817 - 4LFB|1|A|C|879 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_61885.2. Nodes 11 and 23 both model an insertion before position 16. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a junction child at node 23
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin
pNextNodeJunction: Finished at node 33 out of 33, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_61885.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.4143
  -11.4143
  -12.4359
  -13.9595

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J4_63076.1, number 41 of 65
pMakeNodes starting loop:     a=3HHN|1|E|A|54 B=3HHN|1|E|U|106
  2 Basepair    54  106 AU cWW 
pMakeNodes probe for inserts:  a=3HHN|1|E|C|55 B=3HHN|1|E|G|105
pMakeNodes probed for insert:  a=3HHN|1|E|C|55 B=3HHN|1|E|G|105
pMakeNodesJunction: a=3HHN|1|E|C|55 r=3HHN|1|E|C|55 s=3HHN|1|E|G|69 t=3HHN|1|E|A|71 u=B=3HHN|1|E|G|105
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3HHN|1|E|C|55 and 3HHN|1|E|G|69 and between 3HHN|1|E|A|71 and 3HHN|1|E|G|105
pMakeNodesJunction: about to make a junction: a=3HHN|1|E|C|55 s=3HHN|1|E|G|69 t=3HHN|1|E|A|71 B=3HHN|1|E|G|105
pMakeNodesJunction: first branch starts at   3HHN|1|E|C|55
pMakeNodesJunction: first branch ends around 3HHN|1|E|G|69
pMakeNodesJunction: second branch starts at  3HHN|1|E|A|71
pMakeNodesJunction: junction ends at         3HHN|1|E|G|105
pMakeNodesJunction: first branch strand start goes up to  3HHN|1|E|C|55
pMakeNodesJunction: first branch strand end goes down to  3HHN|1|E|G|69
pMakeNodesJunction: second branch strand start goes up to 3HHN|1|E|G|72
pMakeNodesJunction: last strand of junction goes down to  3HHN|1|E|G|105

Junction with 2 loops, call it J3516
Actual Branch 1 of junction J3516 - Nucleotides 3HHN|1|E|C|55 to 3HHN|1|E|G|69, length   2
Actual Branch 2 of junction J3516 - Nucleotides 3HHN|1|E|A|71 to 3HHN|1|E|G|105, length   5
  3 Junction

2B Branch 1 of 2 of junction J3516 - Nucleotides    55 to    69, length   2
pMakeNodes starting loop:     a=3HHN|1|E|C|55 B=3HHN|1|E|G|69
  5 Basepair    55   69 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J3516 - Nucleotides    71 to   105, length   5
pMakeNodes starting loop:     a=3HHN|1|E|A|71 B=3HHN|1|E|G|105
  7 Initial     71 (0 insertion) and  105 (0 insertion)
pMakeNodesJunction: a=3HHN|1|E|A|71 r=3HHN|1|E|A|71 s=3HHN|1|E|C|85 t=3HHN|1|E|C|86 u=B=3HHN|1|E|G|105
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3HHN|1|E|A|71 and 3HHN|1|E|C|85 and between 3HHN|1|E|C|86 and 3HHN|1|E|G|105
pMakeNodesJunction: about to make a junction: a=3HHN|1|E|A|71 s=3HHN|1|E|C|85 t=3HHN|1|E|C|86 B=3HHN|1|E|G|105
pMakeNodesJunction: first branch starts at   3HHN|1|E|A|71
pMakeNodesJunction: first branch ends around 3HHN|1|E|C|85
pMakeNodesJunction: second branch starts at  3HHN|1|E|C|86
pMakeNodesJunction: junction ends at         3HHN|1|E|G|105
pMakeNodesJunction: first branch strand start goes up to  3HHN|1|E|G|72
pMakeNodesJunction: first branch strand end goes down to  3HHN|1|E|C|85
pMakeNodesJunction: second branch strand start goes up to 3HHN|1|E|C|86
pMakeNodesJunction: last strand of junction goes down to  3HHN|1|E|G|105
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J8308
Actual Branch 1 of junction J8308 - Nucleotides 3HHN|1|E|A|71 to 3HHN|1|E|C|85, length   3
Actual Branch 2 of junction J8308 - Nucleotides 3HHN|1|E|C|86 to 3HHN|1|E|G|105, length   2
  8 Junction

2B Branch 1 of 2 of junction J8308 - Nucleotides    71 to    85, length   3
pMakeNodes starting loop:     a=3HHN|1|E|A|71 B=3HHN|1|E|C|85
    Insertion on left  3HHN|1|E|A|71
pMakeNodesProbeForInsertions:  a 3HHN|1|E|G|72 interacts with 3HHN|1|E|C|85
pMakeNodesProbeForInsertions:  B 3HHN|1|E|C|85 interacts with 3HHN|1|E|G|72
pMakeNodesProbeForInsertions:  B 3HHN|1|E|C|85 interacts with 3HHN|1|E|G|72
  9 Initial     71 (1 insertion) and   85 (0 insertion)
 10 Basepair    72   85 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J8308 - Nucleotides    86 to   105, length   2
pMakeNodes starting loop:     a=3HHN|1|E|C|86 B=3HHN|1|E|G|105
 13 Basepair    86  105 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  8
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HHN|1|E|C|70
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 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 A54 - U106 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: 'J3516'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C55 - G105 ID J3516'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J3516'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 C55 - 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 8
             Insertion: []
                    id: 'J3516'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3HHN|1|E|A|71 - 3HHN|1|E|G|105 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J8308'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A71 - G105 ID J8308'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8308'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 3HHN|1|E|A|71 - 3HHN|1|E|C|85 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             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 3HHN|1|E|C|70'
              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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             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: []
           numbranches: []
              NormCons: 1

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 G72 - 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]
           numbranches: []
              NormCons: []

Node 13

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: []
           numbranches: []
              NormCons: 1

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: 'J8308'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C86 - G105 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  8
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  6
pMakeMotifModelFromSSF:  10     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J3516'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.0238 0.9512 0.0238 0.0012]
       rightLetterDist: [0.1250 0.6250 0.1250 0.1250 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J3516'
        leftLengthDist: [0.0238 0.9512 0.0238 0.0012]
        leftLetterDist: [0.1250 0.6250 0.1250 0.1250 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3HHN|1|E|A|71 - 3HHN|1|E|G|105 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_63076.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: 'J8308'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 3HHN|1|E|A|71 - 3HHN|1|E|C|85 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J8308'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_63076.1. Nodes 9 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 4 and 7
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 4 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_63076.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2152
   -6.2152

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J4_64075.1, number 42 of 65
pMakeNodes starting loop:     a=5J7L|1|DA|C|1833 B=5J7L|1|DA|G|1972
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1833 B=5J7L|1|DA|G|1972
pMakeNodesCluster: amax is 2 bmin is 17, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 18 to 20
aa is 2 bb is 18
  2 Cluster   5J7L|1|DA|C|1833:5J7L|1|DA|U|1834 5J7L|1|DA|A|1969:5J7L|1|DA|G|1972
    LR Inter  5J7L|1|DA|C|1833 5J7L|1|DA|A|1969 tSS 
    LR Inter  5J7L|1|DA|U|1834 5J7L|1|DA|A|1970 cWH 
    LR Inter  5J7L|1|DA|C|1833 5J7L|1|DA|G|1972 cWW 
    RR Inter  5J7L|1|DA|A|1969 5J7L|1|DA|G|1972 cSS 
pMakeNodesCluster a=3 B=17 at the end
pMakeNodesCluster a=3 B=17 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|2MG|1835 B=5J7L|1|DA|G|1968
  3 Initial   1835 (0 insertion) and 1968 (0 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|2MG|1835 B=5J7L|1|DA|G|1968
pMakeNodesJunction: a=5J7L|1|DA|2MG|1835 r=5J7L|1|DA|2MG|1835 s=5J7L|1|DA|C|1905 t=5J7L|1|DA|G|1906 u=B=5J7L|1|DA|G|1968
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|2MG|1835 and 5J7L|1|DA|C|1905 and between 5J7L|1|DA|G|1906 and 5J7L|1|DA|G|1968
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|2MG|1835 s=5J7L|1|DA|C|1905 t=5J7L|1|DA|G|1906 B=5J7L|1|DA|G|1968
pMakeNodesJunction: first branch starts at   5J7L|1|DA|2MG|1835
pMakeNodesJunction: first branch ends around 5J7L|1|DA|C|1905
pMakeNodesJunction: second branch starts at  5J7L|1|DA|G|1906
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|1968
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|2MG|1835
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|C|1905
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|1906
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|C|1967

Junction with 2 loops, call it J5852
Actual Branch 1 of junction J5852 - Nucleotides 5J7L|1|DA|2MG|1835 to 5J7L|1|DA|C|1905, length   2
Actual Branch 2 of junction J5852 - Nucleotides 5J7L|1|DA|G|1906 to 5J7L|1|DA|G|1968, length  13
  4 Junction

2B Branch 1 of 2 of junction J5852 - Nucleotides  1835 to  1905, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|2MG|1835 B=5J7L|1|DA|C|1905
  6 Basepair  1835 1905 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J5852 - Nucleotides  1906 to  1968, length  13
pMakeNodes starting loop:     a=5J7L|1|DA|G|1906 B=5J7L|1|DA|G|1968
  8 Initial   1906 (0 insertion) and 1968 (0 insertion)
pMakeNodesJunction: a=5J7L|1|DA|G|1906 r=5J7L|1|DA|G|1906 s=5J7L|1|DA|C|1924 t=5J7L|1|DA|C|1925 u=B=5J7L|1|DA|G|1968
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|G|1906 and 5J7L|1|DA|C|1924 and between 5J7L|1|DA|C|1925 and 5J7L|1|DA|G|1968
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|G|1906 s=5J7L|1|DA|C|1924 t=5J7L|1|DA|C|1925 B=5J7L|1|DA|G|1968
pMakeNodesJunction: first branch starts at   5J7L|1|DA|G|1906
pMakeNodesJunction: first branch ends around 5J7L|1|DA|C|1924
pMakeNodesJunction: second branch starts at  5J7L|1|DA|C|1925
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|1968
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|1906
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|C|1924
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|1930
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|C|1967

Junction with 2 loops, call it J5497
Actual Branch 1 of junction J5497 - Nucleotides 5J7L|1|DA|G|1906 to 5J7L|1|DA|C|1924, length   2
Actual Branch 2 of junction J5497 - Nucleotides 5J7L|1|DA|C|1925 to 5J7L|1|DA|G|1968, length  11
  9 Junction

2B Branch 1 of 2 of junction J5497 - Nucleotides  1906 to  1924, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|G|1906 B=5J7L|1|DA|C|1924
 11 Basepair  1906 1924 GC cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J5497 - Nucleotides  1925 to  1968, length  11
pMakeNodes starting loop:     a=5J7L|1|DA|C|1925 B=5J7L|1|DA|G|1968
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|C|1925 interacts with 5J7L|1|DA|G|1929
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1968 interacts with 5J7L|1|DA|A|1932
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1968 interacts with 5J7L|1|DA|A|1932
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 13 Initial   1925 (0 insertion) and 1968 (0 insertion)
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1925 B=5J7L|1|DA|G|1968
pMakeNodesCluster: amax is 15 bmin is 16, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 14 and then 17 to 17
aa is 14 bb is 17
 14 Cluster   5J7L|1|DA|C|1925:5J7L|1|DA|A|1932 5J7L|1|DA|G|1968:5J7L|1|DA|G|1968
    LR Inter  5J7L|1|DA|A|1932 5J7L|1|DA|G|1968 tHS 
    LL Inter  5J7L|1|DA|U|1926 5J7L|1|DA|A|1928 tSH 
    LL Inter  5J7L|1|DA|C|1925 5J7L|1|DA|G|1929 tWW 
    LL Inter  5J7L|1|DA|G|1930 5J7L|1|DA|U|1931 cSH 
    Left  strand conserved insertion 5J7L|1|DA|A|1927 at position 3
pMakeNodesCluster a=15 B=16 at the end
pMakeNodesCluster a=15 B=16 at the end
No need to probe because of interaction between a=5J7L|1|DA|G|1933 B=5J7L|1|DA|C|1967
 15 Basepair  1933 1967 GC cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 18 19 20
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  14   Cluster Left  7  8  9 10 11 12 13 14 Right 17
pMakeMotifModelFromSSF:  15  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  16   Hairpin Left 16 Right 15
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: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 0 0 0 0 0 0 0 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: []
           numbranches: []
                  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: [18 19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CU'
           RightLetter: 'AAG'
               Comment: ' // Cluster node 5J7L|1|DA|C|1833:5J7L|1|DA|U|1834 and 5J7L|1|DA|A|1969:5J7L|1|DA|G|1972'
              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]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0156
           numbranches: []
                  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: 17
             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 5J7L|1|DA|2MG|1835 - 5J7L|1|DA|G|1968 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1835 - G1968 ID J5852'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             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 G1835 - C1905 cWW '
              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: []
           numbranches: []
                  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: 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
           numbranches: []
                  lpar: []
                  rpar: []

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: 'J5852'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|G|1906 - 5J7L|1|DA|G|1968 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: 'J5497'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1906 - G1968 ID J5497'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

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: 'J5497'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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 G1906 - C1924 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

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
           numbranches: []
                  lpar: []
                  rpar: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 17
             Insertion: []
                    id: 'J5497'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1968 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 15
             LeftIndex: [7 8 9 10 11 12 13 14]
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAAGGUA'
           RightLetter: 'G'
               Comment: ' // Cluster node 5J7L|1|DA|C|1925:5J7L|1|DA|A|1932 and 5J7L|1|DA|G|1968:5J7L|1|DA|G|1968'
              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]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []
                  lpar: []
                  rpar: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1933 - C1967 cWW '
              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: []
           numbranches: []
                  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: 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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 18 19 20
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  14   Cluster Left  7  8  9 10 11 12 13 14 Right 17
pMakeMotifModelFromSSF:  15   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  16  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  17   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J5852'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: 'J5852'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|G|1906 - 5J7L|1|DA|G|1968 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_64075.1. Nodes 5 and 8 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J5497'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 17
             Insertion: []
                    id: 'J5497'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1968 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_64075.1. Nodes 10 and 13 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWH  between 13 and 18
pConservedInteractionList: did not find a substitution probability matrix for tWH  between 13 and 18
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_64075.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.1880
  -13.6122
  -12.8715
  -12.8715

Timestamp 18-Jul-2025 00:13:00
pMakeSCFGModels: Making JAR3D model for motif group J4_64571.2, number 43 of 65
pMakeNodes starting loop:     a=5J7L|1|DA|C|1270 B=5J7L|1|DA|G|2010
  2 Basepair  1270 2010 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1274 B=5J7L|1|DA|A|2009
    Insertion on left  5J7L|1|DA|A|1274
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1275 B=5J7L|1|DA|A|2009
pMakeNodesJunction: a=5J7L|1|DA|A|1275 r=5J7L|1|DA|A|1275 s=5J7L|1|DA|U|1294 t=5J7L|1|DA|C|1295 u=B=5J7L|1|DA|A|2009
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|A|1275 and 5J7L|1|DA|U|1294 and between 5J7L|1|DA|C|1295 and 5J7L|1|DA|A|2009
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|A|1275 s=5J7L|1|DA|U|1294 t=5J7L|1|DA|C|1295 B=5J7L|1|DA|A|2009
pMakeNodesJunction: first branch starts at   5J7L|1|DA|A|1275
pMakeNodesJunction: first branch ends around 5J7L|1|DA|U|1294
pMakeNodesJunction: second branch starts at  5J7L|1|DA|C|1295
pMakeNodesJunction: junction ends at         5J7L|1|DA|A|2009
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|A|1276
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|U|1294
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|C|1295
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|A|2009
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J9171
Actual Branch 1 of junction J9171 - Nucleotides 5J7L|1|DA|A|1275 to 5J7L|1|DA|U|1294, length   3
Actual Branch 2 of junction J9171 - Nucleotides 5J7L|1|DA|C|1295 to 5J7L|1|DA|A|2009, length   5
  3 Junction

2B Branch 1 of 2 of junction J9171 - Nucleotides  1275 to  1294, length   3
pMakeNodes starting loop:     a=5J7L|1|DA|A|1275 B=5J7L|1|DA|U|1294
    Insertion on left  5J7L|1|DA|A|1275
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1276 interacts with 5J7L|1|DA|U|1294
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1294 interacts with 5J7L|1|DA|A|1276
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1294 interacts with 5J7L|1|DA|A|1276
  4 Initial   1275 (1 insertion) and 1294 (0 insertion)
  5 Basepair  1276 1294 AU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9171 - Nucleotides  1295 to  2009, length   5
pMakeNodes starting loop:     a=5J7L|1|DA|C|1295 B=5J7L|1|DA|A|2009
  7 Initial   1295 (0 insertion) and 2009 (0 insertion)
pMakeNodesJunction: a=5J7L|1|DA|C|1295 r=5J7L|1|DA|C|1295 s=5J7L|1|DA|G|1645 t=5J7L|1|DA|C|1646 u=B=5J7L|1|DA|A|2009
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|1295 and 5J7L|1|DA|G|1645 and between 5J7L|1|DA|C|1646 and 5J7L|1|DA|A|2009
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|1295 s=5J7L|1|DA|G|1645 t=5J7L|1|DA|C|1646 B=5J7L|1|DA|A|2009
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|1295
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|1645
pMakeNodesJunction: second branch starts at  5J7L|1|DA|C|1646
pMakeNodesJunction: junction ends at         5J7L|1|DA|A|2009
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|1295
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|1645
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|U|1648
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|A|2009

Junction with 2 loops, call it J2858
Actual Branch 1 of junction J2858 - Nucleotides 5J7L|1|DA|C|1295 to 5J7L|1|DA|G|1645, length   2
Actual Branch 2 of junction J2858 - Nucleotides 5J7L|1|DA|C|1646 to 5J7L|1|DA|A|2009, length   3
  8 Junction

2B Branch 1 of 2 of junction J2858 - Nucleotides  1295 to  1645, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|1295 B=5J7L|1|DA|G|1645
 10 Basepair  1295 1645 CG cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J2858 - Nucleotides  1646 to  2009, length   3
pMakeNodes starting loop:     a=5J7L|1|DA|C|1646 B=5J7L|1|DA|A|2009
    Insertion on left  5J7L|1|DA|C|1646
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|U|1648 interacts with 5J7L|1|DA|A|2009
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2009 interacts with 5J7L|1|DA|U|1648
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2009 interacts with 5J7L|1|DA|U|1648
 12 Initial   1646 (1 insertion) and 2009 (0 insertion)
 13 Basepair  1648 2009 UA cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1271
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1272
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|1294
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: []
           numbranches: []
              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 C1270 - G2010 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J9171'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1271'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9171'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J9171'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1275 - A2009 ID J9171'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9171'
        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|1275 - 5J7L|1|DA|U|1294 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9171'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1272'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J2858'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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 A1276 - U1294 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9171'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1295 - 5J7L|1|DA|A|2009 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J2858'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1295 - A2009 ID J2858'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2858'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1295 - G1645 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

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: 'J2858'
        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|1646 - 5J7L|1|DA|A|2009 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1294'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1648 - A2009 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J9171'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1275 - 5J7L|1|DA|U|1294 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9171'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1295 - 5J7L|1|DA|A|2009 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_64571.2. Nodes 6 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J2858'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J2858'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1646 - 5J7L|1|DA|A|2009 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_64571.2. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 6
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 6
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_64571.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.3329
  -10.3807
  -10.3807
  -11.3317

Timestamp 18-Jul-2025 00:13:01
pMakeSCFGModels: Making JAR3D model for motif group J4_65052.1, number 44 of 65
pMakeNodes starting loop:     a=6N2V|1|A|C|16 B=6N2V|1|A|G|86
  2 Basepair    16   86 CG cWW 
No need to probe because of interaction between a=6N2V|1|A|U|17 B=6N2V|1|A|U|85
  3 Basepair    17   85 UU cWW 
pMakeNodes probe for inserts:  a=6N2V|1|A|G|18 B=6N2V|1|A|C|84
    Insertion on right 6N2V|1|A|C|84
pMakeNodes probed for insert:  a=6N2V|1|A|G|18 B=6N2V|1|A|U|83
pMakeNodesJunction: a=6N2V|1|A|G|18 r=6N2V|1|A|G|18 s=6N2V|1|A|C|35 t=6N2V|1|A|G|36 u=B=6N2V|1|A|U|83
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6N2V|1|A|G|18 and 6N2V|1|A|C|35 and between 6N2V|1|A|G|36 and 6N2V|1|A|U|83
pMakeNodesJunction: about to make a junction: a=6N2V|1|A|G|18 s=6N2V|1|A|C|35 t=6N2V|1|A|G|36 B=6N2V|1|A|U|83
pMakeNodesJunction: first branch starts at   6N2V|1|A|G|18
pMakeNodesJunction: first branch ends around 6N2V|1|A|C|35
pMakeNodesJunction: second branch starts at  6N2V|1|A|G|36
pMakeNodesJunction: junction ends at         6N2V|1|A|U|83
pMakeNodesJunction: first branch strand start goes up to  6N2V|1|A|G|18
pMakeNodesJunction: first branch strand end goes down to  6N2V|1|A|C|35
pMakeNodesJunction: second branch strand start goes up to 6N2V|1|A|C|37
pMakeNodesJunction: last strand of junction goes down to  6N2V|1|A|U|83

Junction with 2 loops, call it J7572
Actual Branch 1 of junction J7572 - Nucleotides 6N2V|1|A|G|18 to 6N2V|1|A|C|35, length   2
Actual Branch 2 of junction J7572 - Nucleotides 6N2V|1|A|G|36 to 6N2V|1|A|U|83, length   5
  4 Junction

2B Branch 1 of 2 of junction J7572 - Nucleotides    18 to    35, length   2
pMakeNodes starting loop:     a=6N2V|1|A|G|18 B=6N2V|1|A|C|35
  6 Basepair    18   35 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7572 - Nucleotides    36 to    83, length   5
pMakeNodes starting loop:     a=6N2V|1|A|G|36 B=6N2V|1|A|U|83
    Insertion on left  6N2V|1|A|G|36
  8 Initial     36 (1 insertion) and   83 (0 insertion)
pMakeNodesJunction: a=6N2V|1|A|C|37 r=6N2V|1|A|C|37 s=6N2V|1|A|G|73 t=6N2V|1|A|A|74 u=B=6N2V|1|A|U|83
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6N2V|1|A|C|37 and 6N2V|1|A|G|73 and between 6N2V|1|A|A|74 and 6N2V|1|A|U|83
pMakeNodesJunction: about to make a junction: a=6N2V|1|A|C|37 s=6N2V|1|A|G|73 t=6N2V|1|A|A|74 B=6N2V|1|A|U|83
pMakeNodesJunction: first branch starts at   6N2V|1|A|C|37
pMakeNodesJunction: first branch ends around 6N2V|1|A|G|73
pMakeNodesJunction: second branch starts at  6N2V|1|A|A|74
pMakeNodesJunction: junction ends at         6N2V|1|A|U|83
pMakeNodesJunction: first branch strand start goes up to  6N2V|1|A|C|37
pMakeNodesJunction: first branch strand end goes down to  6N2V|1|A|G|73
pMakeNodesJunction: second branch strand start goes up to 6N2V|1|A|A|74
pMakeNodesJunction: last strand of junction goes down to  6N2V|1|A|U|83

Junction with 2 loops, call it J7537
Actual Branch 1 of junction J7537 - Nucleotides 6N2V|1|A|C|37 to 6N2V|1|A|G|73, length   2
Actual Branch 2 of junction J7537 - Nucleotides 6N2V|1|A|A|74 to 6N2V|1|A|U|83, length   2
  9 Junction

2B Branch 1 of 2 of junction J7537 - Nucleotides    37 to    73, length   2
pMakeNodes starting loop:     a=6N2V|1|A|C|37 B=6N2V|1|A|G|73
 11 Basepair    37   73 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J7537 - Nucleotides    74 to    83, length   2
pMakeNodes starting loop:     a=6N2V|1|A|A|74 B=6N2V|1|A|U|83
 14 Basepair    74   83 AU cWW 
 15 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  Junction Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9  Junction Left  6 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6N2V|1|A|C|84
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N2V|1|A|G|36
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: []
           numbranches: []
              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 C16 - G86 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'U'
           RightLetter: 'CU'
               Comment: ' // Basepair U17 - U85 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J7572'
        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 6N2V|1|A|C|84'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7572'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: 'J7572'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G18 - U83 ID J7572'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J7572'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             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 - 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]
           numbranches: []
              NormCons: []

Node 9

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: []
           numbranches: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J7572'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6N2V|1|A|G|36 - 6N2V|1|A|U|83 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             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 6N2V|1|A|G|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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J7537'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C37 - U83 ID J7537'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7537'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C37 - G73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

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: 'J7537'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 A74 - U83 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   9   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  Junction Left  6 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  17   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J7572'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J7572'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6N2V|1|A|G|36 - 6N2V|1|A|U|83 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_65052.1. Nodes 7 and 10 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J7537'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: 'J7537'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_65052.1. Nodes 14 and 17 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_65052.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.4224

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J4_65285.1, number 45 of 65
pMakeNodes starting loop:     a=2DU3|1|D|G|907 B=2DU3|1|D|C|965
  2 Basepair   907  965 GC cWW 
pMakeNodes probe for inserts:  a=2DU3|1|D|G|909 B=2DU3|1|D|G|964
    Insertion on left  2DU3|1|D|G|909
pMakeNodes probed for insert:  a=2DU3|1|D|G|910 B=2DU3|1|D|G|964
pMakeNodesJunction: a=2DU3|1|D|G|910 r=2DU3|1|D|G|910 s=2DU3|1|D|C|924 t=2DU3|1|D|G|925 u=B=2DU3|1|D|G|964
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 2DU3|1|D|G|910 and 2DU3|1|D|C|924 and between 2DU3|1|D|G|925 and 2DU3|1|D|G|964
pMakeNodesJunction: about to make a junction: a=2DU3|1|D|G|910 s=2DU3|1|D|C|924 t=2DU3|1|D|G|925 B=2DU3|1|D|G|964
pMakeNodesJunction: first branch starts at   2DU3|1|D|G|910
pMakeNodesJunction: first branch ends around 2DU3|1|D|C|924
pMakeNodesJunction: second branch starts at  2DU3|1|D|G|925
pMakeNodesJunction: junction ends at         2DU3|1|D|G|964
pMakeNodesJunction: first branch strand start goes up to  2DU3|1|D|G|910
pMakeNodesJunction: first branch strand end goes down to  2DU3|1|D|C|924
pMakeNodesJunction: second branch strand start goes up to 2DU3|1|D|C|927
pMakeNodesJunction: last strand of junction goes down to  2DU3|1|D|G|964

Junction with 2 loops, call it J3804
Actual Branch 1 of junction J3804 - Nucleotides 2DU3|1|D|G|910 to 2DU3|1|D|C|924, length   2
Actual Branch 2 of junction J3804 - Nucleotides 2DU3|1|D|G|925 to 2DU3|1|D|G|964, length   8
  3 Junction

2B Branch 1 of 2 of junction J3804 - Nucleotides   910 to   924, length   2
pMakeNodes starting loop:     a=2DU3|1|D|G|910 B=2DU3|1|D|C|924
  5 Basepair   910  924 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J3804 - Nucleotides   925 to   964, length   8
pMakeNodes starting loop:     a=2DU3|1|D|G|925 B=2DU3|1|D|G|964
    Insertion on left  2DU3|1|D|G|925
    Insertion on left  2DU3|1|D|G|926
  7 Initial    925 (2 insertion) and  964 (0 insertion)
pMakeNodesJunction: a=2DU3|1|D|C|927 r=2DU3|1|D|C|927 s=2DU3|1|D|G|941 t=2DU3|1|D|C|942 u=B=2DU3|1|D|G|964
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2DU3|1|D|C|927 and 2DU3|1|D|G|941 and between 2DU3|1|D|C|942 and 2DU3|1|D|G|964
pMakeNodesJunction: about to make a junction: a=2DU3|1|D|C|927 s=2DU3|1|D|G|941 t=2DU3|1|D|C|942 B=2DU3|1|D|G|964
pMakeNodesJunction: first branch starts at   2DU3|1|D|C|927
pMakeNodesJunction: first branch ends around 2DU3|1|D|G|941
pMakeNodesJunction: second branch starts at  2DU3|1|D|C|942
pMakeNodesJunction: junction ends at         2DU3|1|D|G|964
pMakeNodesJunction: first branch strand start goes up to  2DU3|1|D|C|927
pMakeNodesJunction: first branch strand end goes down to  2DU3|1|D|G|941
pMakeNodesJunction: second branch strand start goes up to 2DU3|1|D|C|948
pMakeNodesJunction: last strand of junction goes down to  2DU3|1|D|G|964

Junction with 2 loops, call it J5678
Actual Branch 1 of junction J5678 - Nucleotides 2DU3|1|D|C|927 to 2DU3|1|D|G|941, length   2
Actual Branch 2 of junction J5678 - Nucleotides 2DU3|1|D|C|942 to 2DU3|1|D|G|964, length   4
  8 Junction

2B Branch 1 of 2 of junction J5678 - Nucleotides   927 to   941, length   2
pMakeNodes starting loop:     a=2DU3|1|D|C|927 B=2DU3|1|D|G|941
 10 Basepair   927  941 CG cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J5678 - Nucleotides   942 to   964, length   4
pMakeNodes starting loop:     a=2DU3|1|D|C|942 B=2DU3|1|D|G|964
    Insertion on left  2DU3|1|D|C|942
    Insertion on left  2DU3|1|D|A|946
pMakeNodesProbeForInsertions:  a 2DU3|1|D|C|948 interacts with 2DU3|1|D|G|964
pMakeNodesProbeForInsertions:  B 2DU3|1|D|G|964 interacts with 2DU3|1|D|C|948
pMakeNodesProbeForInsertions:  B 2DU3|1|D|G|964 interacts with 2DU3|1|D|C|948
 12 Initial    942 (2 insertion) and  964 (0 insertion)
 13 Basepair   948  964 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   8  Junction Left  7 Right 12
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  14   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2DU3|1|D|U|908
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2DU3|1|D|C|924
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2DU3|1|D|G|925
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2DU3|1|D|G|941
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2DU3|1|D|C|942
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: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'C'
               Comment: ' // Basepair G907 - C965 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J3804'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2DU3|1|D|U|908'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3804'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J3804'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G910 - G964 ID J3804'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3804'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G910 - C924 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J3804'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 2DU3|1|D|G|925 - 2DU3|1|D|G|964 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             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 2DU3|1|D|C|924'
              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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             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: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J5678'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2DU3|1|D|G|925'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             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: '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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: 'J5678'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C927 - G964 ID J5678'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5678'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C927 - G941 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 17

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: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J5678'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: []
               Comment: ' // Initial node 2DU3|1|D|C|942 - 2DU3|1|D|G|964 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             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 2DU3|1|D|G|941'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             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 2DU3|1|D|C|942'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             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: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 24
             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 C948 - G964 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 26
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  14  Junction Left  7 Right 12
pMakeMotifModelFromSSF:  15   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  23  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  24   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J3804'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J3804'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 2DU3|1|D|G|925 - 2DU3|1|D|G|964 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_65285.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J5678'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J5678'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: []
               Comment: ' // Initial node 2DU3|1|D|C|942 - 2DU3|1|D|G|964 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_65285.1. Nodes 15 and 18 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin
pNextNodeJunction: Finished at node 24 out of 24, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_65285.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.8151
  -18.0213

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J4_69051.2, number 46 of 65
pMakeNodes starting loop:     a=5TBW|1|1|G|1492 B=5TBW|1|1|C|1836
  2 Basepair  1492 1836 GC cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|G|1493 B=5TBW|1|1|A|1835
    Insertion on left  5TBW|1|1|G|1493
pMakeNodes probed for insert:  a=5TBW|1|1|U|1494 B=5TBW|1|1|A|1835
pMakeNodesJunction: a=5TBW|1|1|U|1494 r=5TBW|1|1|U|1494 s=5TBW|1|1|U|1522 t=5TBW|1|1|A|1524 u=B=5TBW|1|1|A|1835
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|1494 and 5TBW|1|1|U|1522 and between 5TBW|1|1|A|1524 and 5TBW|1|1|A|1835
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|1494 s=5TBW|1|1|U|1522 t=5TBW|1|1|A|1524 B=5TBW|1|1|A|1835
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|1494
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|1522
pMakeNodesJunction: second branch starts at  5TBW|1|1|A|1524
pMakeNodesJunction: junction ends at         5TBW|1|1|A|1835
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|C|1496
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|G|1520
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|1525
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|G|1830
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     0


Junction with 2 loops, call it J758
Actual Branch 1 of junction J758 - Nucleotides 5TBW|1|1|U|1494 to 5TBW|1|1|U|1522, length   6
Actual Branch 2 of junction J758 - Nucleotides 5TBW|1|1|A|1524 to 5TBW|1|1|A|1835, length  11
  3 Junction

2B Branch 1 of 2 of junction J758 - Nucleotides  1494 to  1522, length   6
pMakeNodes starting loop:     a=5TBW|1|1|U|1494 B=5TBW|1|1|U|1522
  5 Basepair  1494 1522 UU tWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|U|1495 B=5TBW|1|1|G|1521
    Insertion on left  5TBW|1|1|U|1495
    Insertion on right 5TBW|1|1|G|1521
pMakeNodesProbeForInsertions:  a 5TBW|1|1|C|1496 interacts with 5TBW|1|1|G|1520
pMakeNodesProbeForInsertions:  B 5TBW|1|1|G|1520 interacts with 5TBW|1|1|C|1496
pMakeNodesProbeForInsertions:  B 5TBW|1|1|G|1520 interacts with 5TBW|1|1|C|1496
pMakeNodes probed for insert:  a=5TBW|1|1|C|1496 B=5TBW|1|1|G|1520
  6 Basepair  1496 1520 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J758 - Nucleotides  1524 to  1835, length  11
pMakeNodes starting loop:     a=5TBW|1|1|A|1524 B=5TBW|1|1|A|1835
    Insertion on right 5TBW|1|1|A|1835
  8 Initial   1524 (0 insertion) and 1835 (1 insertion)
  9 Basepair  1524 1834 AU tHW 
pMakeNodes probe for inserts:  a=5TBW|1|1|G|1525 B=5TBW|1|1|G|1833
    Insertion on right 5TBW|1|1|G|1833
    Insertion on right 5TBW|1|1|C|1832
    Insertion on right 5TBW|1|1|U|1831
    Insertion on right 5TBW|1|1|G|1830
pMakeNodes probed for insert:  a=5TBW|1|1|G|1525 B=5TBW|1|1|G|1829
pMakeNodesJunction: a=5TBW|1|1|G|1525 r=5TBW|1|1|G|1525 s=5TBW|1|1|C|1614 t=5TBW|1|1|C|1615 u=B=5TBW|1|1|G|1829
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|G|1525 and 5TBW|1|1|C|1614 and between 5TBW|1|1|C|1615 and 5TBW|1|1|G|1829
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|G|1525 s=5TBW|1|1|C|1614 t=5TBW|1|1|C|1615 B=5TBW|1|1|G|1829
pMakeNodesJunction: first branch starts at   5TBW|1|1|G|1525
pMakeNodesJunction: first branch ends around 5TBW|1|1|C|1614
pMakeNodesJunction: second branch starts at  5TBW|1|1|C|1615
pMakeNodesJunction: junction ends at         5TBW|1|1|G|1829
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|1525
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|1614
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|C|1615
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|G|1829

Junction with 2 loops, call it J539
Actual Branch 1 of junction J539 - Nucleotides 5TBW|1|1|G|1525 to 5TBW|1|1|C|1614, length   2
Actual Branch 2 of junction J539 - Nucleotides 5TBW|1|1|C|1615 to 5TBW|1|1|G|1829, length   2
 10 Junction

2B Branch 1 of 2 of junction J539 - Nucleotides  1525 to  1614, length   2
pMakeNodes starting loop:     a=5TBW|1|1|G|1525 B=5TBW|1|1|C|1614
 12 Basepair  1525 1614 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J539 - Nucleotides  1615 to  1829, length   2
pMakeNodes starting loop:     a=5TBW|1|1|C|1615 B=5TBW|1|1|G|1829
 15 Basepair  1615 1829 CG cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 19
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 19
pMakeMotifModelFromSSF:   9  Basepair Left  9 Right 18
pMakeMotifModelFromSSF:  10  Junction Left 10 Right 13
pMakeMotifModelFromSSF:  11   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  13   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  14   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  15  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  16   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
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 5TBW|1|1|G|1493
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|1495
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|1521
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|U|1834
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|C|1832
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|U|1831
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|1830
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|1829
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
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: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'C'
               Comment: ' // Basepair G1492 - C1836 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J758'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|G|1493'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J758'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: 'J758'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1494 - A1835 ID J758'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J758'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: 'GU'
               Comment: ' // Basepair U1494 - U1522 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]
           numbranches: []
              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: 'J758'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|U|1495'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'GUCGU'
               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]
           numbranches: []
              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: 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 5TBW|1|1|G|1521'
              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]
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J539'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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 C1496 - G1520 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 13

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: []
           numbranches: []
              NormCons: 1

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 19
             Insertion: []
                    id: 'J758'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'A'
               Comment: ' // Initial node 5TBW|1|1|A|1524 - 5TBW|1|1|A|1835 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 19
             Insertion: []
                    id: 'J539'
        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 5TBW|1|1|U|1834'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             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: '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]
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        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: 'A'
           RightLetter: 'GUCGU'
               Comment: ' // Basepair A1524 - U1834 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]
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            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 5TBW|1|1|C|1832'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             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 5TBW|1|1|U|1831'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 5TBW|1|1|G|1830'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             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: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             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 5TBW|1|1|G|1829'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             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: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J539'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1525 - G1829 ID J539'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J539'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 29
             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 G1525 - C1614 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 29

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: []
           numbranches: []
              NormCons: 1

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J539'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 32
             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 C1615 - G1829 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 36
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 19
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  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 19
pMakeMotifModelFromSSF:  15     Fixed Left  9 Right 19
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 18
pMakeMotifModelFromSSF:  17  Basepair Left  9 Right 18
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 17
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  20     Fixed Left 10 Right 16
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  22     Fixed Left 10 Right 15
pMakeMotifModelFromSSF:  23   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  24     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  25   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  26  Junction Left 10 Right 13
pMakeMotifModelFromSSF:  27   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  28  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  29   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  30   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  31  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  32   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a junction at node 26
pNextNodeJunction: Found a junction child at node 27
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 32
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J758'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.0082 0.9832 0.0082 4.0967e-04]
       rightLetterDist: [0.1875 0.0625 0.1875 0.5625 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 19
             Insertion: []
                    id: 'J758'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'A'
               Comment: ' // Initial node 5TBW|1|1|A|1524 - 5TBW|1|1|A|1835 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69051.2. Nodes 6 and 14 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J539'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J539'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69051.2. Nodes 27 and 30 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a junction at node 26
pNextNodeJunction: Found a junction child at node 27
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 32
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cWW  between 4 and 19
pConservedInteractionList: did not find a substitution probability matrix for cWW  between 4 and 19
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_69051.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.6977
   -9.1099
  -10.8916
   -8.3579
   -9.8173
  -10.9169

Timestamp 18-Jul-2025 00:13:03
pMakeSCFGModels: Making JAR3D model for motif group J4_69073.1, number 47 of 65
pMakeNodes starting loop:     a=6U8D|1|A|G|153 B=6U8D|1|A|C|239
  2 Basepair   153  239 GC cWW 
pMakeNodes probe for inserts:  a=6U8D|1|A|A|154 B=6U8D|1|A|C|238
    Insertion on left  6U8D|1|A|A|154
pMakeNodes probed for insert:  a=6U8D|1|A|A|155 B=6U8D|1|A|C|238
pMakeNodesJunction: a=6U8D|1|A|A|155 r=6U8D|1|A|A|155 s=6U8D|1|A|G|171 t=6U8D|1|A|A|172 u=B=6U8D|1|A|C|238
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6U8D|1|A|A|155 and 6U8D|1|A|G|171 and between 6U8D|1|A|A|172 and 6U8D|1|A|C|238
pMakeNodesJunction: about to make a junction: a=6U8D|1|A|A|155 s=6U8D|1|A|G|171 t=6U8D|1|A|A|172 B=6U8D|1|A|C|238
pMakeNodesJunction: first branch starts at   6U8D|1|A|A|155
pMakeNodesJunction: first branch ends around 6U8D|1|A|G|171
pMakeNodesJunction: second branch starts at  6U8D|1|A|A|172
pMakeNodesJunction: junction ends at         6U8D|1|A|C|238
pMakeNodesJunction: first branch strand start goes up to  6U8D|1|A|C|156
pMakeNodesJunction: first branch strand end goes down to  6U8D|1|A|G|171
pMakeNodesJunction: second branch strand start goes up to 6U8D|1|A|A|172
pMakeNodesJunction: last strand of junction goes down to  6U8D|1|A|C|238
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J5307
Actual Branch 1 of junction J5307 - Nucleotides 6U8D|1|A|A|155 to 6U8D|1|A|G|171, length   3
Actual Branch 2 of junction J5307 - Nucleotides 6U8D|1|A|A|172 to 6U8D|1|A|C|238, length   5
  3 Junction

2B Branch 1 of 2 of junction J5307 - Nucleotides   155 to   171, length   3
pMakeNodes starting loop:     a=6U8D|1|A|A|155 B=6U8D|1|A|G|171
    Insertion on left  6U8D|1|A|A|155
pMakeNodesProbeForInsertions:  a 6U8D|1|A|C|156 interacts with 6U8D|1|A|G|171
pMakeNodesProbeForInsertions:  B 6U8D|1|A|G|171 interacts with 6U8D|1|A|C|156
pMakeNodesProbeForInsertions:  B 6U8D|1|A|G|171 interacts with 6U8D|1|A|C|156
  4 Initial    155 (1 insertion) and  171 (0 insertion)
  5 Basepair   156  171 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J5307 - Nucleotides   172 to   238, length   5
pMakeNodes starting loop:     a=6U8D|1|A|A|172 B=6U8D|1|A|C|238
  7 Initial    172 (0 insertion) and  238 (0 insertion)
pMakeNodesJunction: a=6U8D|1|A|A|172 r=6U8D|1|A|A|172 s=6U8D|1|A|U|227 t=6U8D|1|A|U|228 u=B=6U8D|1|A|C|238
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6U8D|1|A|A|172 and 6U8D|1|A|U|227 and between 6U8D|1|A|U|228 and 6U8D|1|A|C|238
pMakeNodesJunction: about to make a junction: a=6U8D|1|A|A|172 s=6U8D|1|A|U|227 t=6U8D|1|A|U|228 B=6U8D|1|A|C|238
pMakeNodesJunction: first branch starts at   6U8D|1|A|A|172
pMakeNodesJunction: first branch ends around 6U8D|1|A|U|227
pMakeNodesJunction: second branch starts at  6U8D|1|A|U|228
pMakeNodesJunction: junction ends at         6U8D|1|A|C|238
pMakeNodesJunction: first branch strand start goes up to  6U8D|1|A|A|172
pMakeNodesJunction: first branch strand end goes down to  6U8D|1|A|U|227
pMakeNodesJunction: second branch strand start goes up to 6U8D|1|A|G|229
pMakeNodesJunction: last strand of junction goes down to  6U8D|1|A|C|238

Junction with 2 loops, call it J7791
Actual Branch 1 of junction J7791 - Nucleotides 6U8D|1|A|A|172 to 6U8D|1|A|U|227, length   2
Actual Branch 2 of junction J7791 - Nucleotides 6U8D|1|A|U|228 to 6U8D|1|A|C|238, length   3
  8 Junction

2B Branch 1 of 2 of junction J7791 - Nucleotides   172 to   227, length   2
pMakeNodes starting loop:     a=6U8D|1|A|A|172 B=6U8D|1|A|U|227
 10 Basepair   172  227 AU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J7791 - Nucleotides   228 to   238, length   3
pMakeNodes starting loop:     a=6U8D|1|A|U|228 B=6U8D|1|A|C|238
    Insertion on left  6U8D|1|A|U|228
pMakeNodesProbeForInsertions:  a 6U8D|1|A|G|229 interacts with 6U8D|1|A|C|238
pMakeNodesProbeForInsertions:  B 6U8D|1|A|C|238 interacts with 6U8D|1|A|G|229
pMakeNodesProbeForInsertions:  B 6U8D|1|A|C|238 interacts with 6U8D|1|A|G|229
 12 Initial    228 (1 insertion) and  238 (0 insertion)
 13 Basepair   229  238 GC cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6U8D|1|A|A|154
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6U8D|1|A|A|155
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6U8D|1|A|U|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: 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: []
           numbranches: []
              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: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G153 - C239 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J5307'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6U8D|1|A|A|154'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5307'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J5307'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A155 - C238 ID J5307'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J5307'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|A|155 - 6U8D|1|A|G|171 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J5307'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6U8D|1|A|A|155'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J7791'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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 C156 - G171 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J5307'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|A|172 - 6U8D|1|A|C|238 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J7791'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A172 - C238 ID J7791'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J7791'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A172 - U227 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

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: 'J7791'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|U|228 - 6U8D|1|A|C|238 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6U8D|1|A|U|228'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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 G229 - C238 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: 'J5307'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|A|155 - 6U8D|1|A|G|171 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J5307'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|A|172 - 6U8D|1|A|C|238 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69073.1. Nodes 6 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J7791'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J7791'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 6U8D|1|A|U|228 - 6U8D|1|A|C|238 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69073.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for cWS  between 3 and 6
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 3 and 8
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for cWS  between 3 and 6
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 3 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_69073.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2881

Timestamp 18-Jul-2025 00:13:04
pMakeSCFGModels: Making JAR3D model for motif group J4_69568.1, number 48 of 65
pMakeNodes starting loop:     a=5TBW|1|1|C|1451 B=5TBW|1|1|G|2353
  2 Basepair  1451 2353 CG cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|1453 B=5TBW|1|1|A|2352
    Insertion on left  5TBW|1|1|A|1453
    Insertion on left  5TBW|1|1|A|1454
pMakeNodes probed for insert:  a=5TBW|1|1|U|1457 B=5TBW|1|1|A|2352
pMakeNodesJunction: a=5TBW|1|1|U|1457 r=5TBW|1|1|U|1457 s=5TBW|1|1|A|1475 t=5TBW|1|1|G|1476 u=B=5TBW|1|1|A|2352
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|1457 and 5TBW|1|1|A|1475 and between 5TBW|1|1|G|1476 and 5TBW|1|1|A|2352
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|1457 s=5TBW|1|1|A|1475 t=5TBW|1|1|G|1476 B=5TBW|1|1|A|2352
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|1457
pMakeNodesJunction: first branch ends around 5TBW|1|1|A|1475
pMakeNodesJunction: second branch starts at  5TBW|1|1|G|1476
pMakeNodesJunction: junction ends at         5TBW|1|1|A|2352
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|U|1457
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|A|1475
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|1476
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|2352

Junction with 2 loops, call it J9340
Actual Branch 1 of junction J9340 - Nucleotides 5TBW|1|1|U|1457 to 5TBW|1|1|A|1475, length   2
Actual Branch 2 of junction J9340 - Nucleotides 5TBW|1|1|G|1476 to 5TBW|1|1|A|2352, length   6
  3 Junction

2B Branch 1 of 2 of junction J9340 - Nucleotides  1457 to  1475, length   2
pMakeNodes starting loop:     a=5TBW|1|1|U|1457 B=5TBW|1|1|A|1475
  5 Basepair  1457 1475 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9340 - Nucleotides  1476 to  2352, length   6
pMakeNodes starting loop:     a=5TBW|1|1|G|1476 B=5TBW|1|1|A|2352
  7 Initial   1476 (0 insertion) and 2352 (0 insertion)
pMakeNodesJunction: a=5TBW|1|1|G|1476 r=5TBW|1|1|G|1476 s=5TBW|1|1|U|1877 t=5TBW|1|1|G|1878 u=B=5TBW|1|1|A|2352
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|G|1476 and 5TBW|1|1|U|1877 and between 5TBW|1|1|G|1878 and 5TBW|1|1|A|2352
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|G|1476 s=5TBW|1|1|U|1877 t=5TBW|1|1|G|1878 B=5TBW|1|1|A|2352
pMakeNodesJunction: first branch starts at   5TBW|1|1|G|1476
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|1877
pMakeNodesJunction: second branch starts at  5TBW|1|1|G|1878
pMakeNodesJunction: junction ends at         5TBW|1|1|A|2352
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|1476
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|U|1877
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|U|1880
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|2352

Junction with 2 loops, call it J1299
Actual Branch 1 of junction J1299 - Nucleotides 5TBW|1|1|G|1476 to 5TBW|1|1|U|1877, length   2
Actual Branch 2 of junction J1299 - Nucleotides 5TBW|1|1|G|1878 to 5TBW|1|1|A|2352, length   4
  8 Junction

2B Branch 1 of 2 of junction J1299 - Nucleotides  1476 to  1877, length   2
pMakeNodes starting loop:     a=5TBW|1|1|G|1476 B=5TBW|1|1|U|1877
 10 Basepair  1476 1877 GU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J1299 - Nucleotides  1878 to  2352, length   4
pMakeNodes starting loop:     a=5TBW|1|1|G|1878 B=5TBW|1|1|A|2352
    Insertion on left  5TBW|1|1|G|1878
    Insertion on left  5TBW|1|1|A|1879
pMakeNodesProbeForInsertions:  a 5TBW|1|1|U|1880 interacts with 5TBW|1|1|A|2352
pMakeNodesProbeForInsertions:  B 5TBW|1|1|A|2352 interacts with 5TBW|1|1|U|1880
pMakeNodesProbeForInsertions:  B 5TBW|1|1|A|2352 interacts with 5TBW|1|1|U|1880
 12 Initial   1878 (2 insertion) and 2352 (0 insertion)
 13 Basepair  1880 2352 UA cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  14   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1452
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1453
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1475
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|1476
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: []
           numbranches: []
              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: [0.0082 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 C1451 - G2353 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J9340'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|A|1452'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9340'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 5TBW|1|1|A|1453'
              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]
           numbranches: []
              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: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J9340'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1457 - A2352 ID J9340'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9340'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 U1457 - A1475 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

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: 'J9340'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|1476 - 5TBW|1|1|A|2352 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J1299'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1476 - A2352 ID J1299'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1299'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G1476 - U1877 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1299'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|1878 - 5TBW|1|1|A|2352 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             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 5TBW|1|1|A|1475'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|G|1476'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1880 - A2352 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  21  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  22   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J9340'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J9340'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|1476 - 5TBW|1|1|A|2352 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69568.1. Nodes 8 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J1299'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1299'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|1878 - 5TBW|1|1|A|2352 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_69568.1. Nodes 13 and 16 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_69568.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5970

Timestamp 18-Jul-2025 00:13:04
pMakeSCFGModels: Making JAR3D model for motif group J4_70449.12, number 49 of 65
pMakeNodes starting loop:     a=3WQY|1|C|G|1607 B=3WQY|1|C|C|1666
  2 Basepair  1607 1666 GC cWW 
pMakeNodes probe for inserts:  a=3WQY|1|C|A|1609 B=3WQY|1|C|C|1665
    Insertion on left  3WQY|1|C|A|1609
pMakeNodes probed for insert:  a=3WQY|1|C|G|1610 B=3WQY|1|C|C|1665
pMakeNodesJunction: a=3WQY|1|C|G|1610 r=3WQY|1|C|G|1610 s=3WQY|1|C|C|1625 t=3WQY|1|C|G|1626 u=B=3WQY|1|C|C|1665
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3WQY|1|C|G|1610 and 3WQY|1|C|C|1625 and between 3WQY|1|C|G|1626 and 3WQY|1|C|C|1665
pMakeNodesJunction: about to make a junction: a=3WQY|1|C|G|1610 s=3WQY|1|C|C|1625 t=3WQY|1|C|G|1626 B=3WQY|1|C|C|1665
pMakeNodesJunction: first branch starts at   3WQY|1|C|G|1610
pMakeNodesJunction: first branch ends around 3WQY|1|C|C|1625
pMakeNodesJunction: second branch starts at  3WQY|1|C|G|1626
pMakeNodesJunction: junction ends at         3WQY|1|C|C|1665
pMakeNodesJunction: first branch strand start goes up to  3WQY|1|C|G|1610
pMakeNodesJunction: first branch strand end goes down to  3WQY|1|C|C|1625
pMakeNodesJunction: second branch strand start goes up to 3WQY|1|C|C|1627
pMakeNodesJunction: last strand of junction goes down to  3WQY|1|C|C|1665

Junction with 2 loops, call it J5688
Actual Branch 1 of junction J5688 - Nucleotides 3WQY|1|C|G|1610 to 3WQY|1|C|C|1625, length   2
Actual Branch 2 of junction J5688 - Nucleotides 3WQY|1|C|G|1626 to 3WQY|1|C|C|1665, length   8
  3 Junction

2B Branch 1 of 2 of junction J5688 - Nucleotides  1610 to  1625, length   2
pMakeNodes starting loop:     a=3WQY|1|C|G|1610 B=3WQY|1|C|C|1625
  5 Basepair  1610 1625 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J5688 - Nucleotides  1626 to  1665, length   8
pMakeNodes starting loop:     a=3WQY|1|C|G|1626 B=3WQY|1|C|C|1665
  7 Initial   1626 (0 insertion) and 1665 (0 insertion)
pMakeNodesJunction: a=3WQY|1|C|G|1626 r=3WQY|1|C|G|1626 s=3WQY|1|C|A|1644 t=3WQY|1|C|G|1645 u=B=3WQY|1|C|C|1665
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3WQY|1|C|G|1626 and 3WQY|1|C|A|1644 and between 3WQY|1|C|G|1645 and 3WQY|1|C|C|1665
pMakeNodesJunction: about to make a junction: a=3WQY|1|C|G|1626 s=3WQY|1|C|A|1644 t=3WQY|1|C|G|1645 B=3WQY|1|C|C|1665
pMakeNodesJunction: first branch starts at   3WQY|1|C|G|1626
pMakeNodesJunction: first branch ends around 3WQY|1|C|A|1644
pMakeNodesJunction: second branch starts at  3WQY|1|C|G|1645
pMakeNodesJunction: junction ends at         3WQY|1|C|C|1665
pMakeNodesJunction: first branch strand start goes up to  3WQY|1|C|C|1627
pMakeNodesJunction: first branch strand end goes down to  3WQY|1|C|G|1643
pMakeNodesJunction: second branch strand start goes up to 3WQY|1|C|G|1649
pMakeNodesJunction: last strand of junction goes down to  3WQY|1|C|C|1665

Junction with 2 loops, call it J4693
Actual Branch 1 of junction J4693 - Nucleotides 3WQY|1|C|G|1626 to 3WQY|1|C|A|1644, length   4
Actual Branch 2 of junction J4693 - Nucleotides 3WQY|1|C|G|1645 to 3WQY|1|C|C|1665, length   4
  8 Junction

2B Branch 1 of 2 of junction J4693 - Nucleotides  1626 to  1644, length   4
pMakeNodes starting loop:     a=3WQY|1|C|G|1626 B=3WQY|1|C|A|1644
 10 Basepair  1626 1644 GA cWW 
No need to probe because of interaction between a=3WQY|1|C|C|1627 B=3WQY|1|C|G|1643
 11 Basepair  1627 1643 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J4693 - Nucleotides  1645 to  1665, length   4
pMakeNodes starting loop:     a=3WQY|1|C|G|1645 B=3WQY|1|C|C|1665
    Insertion on left  3WQY|1|C|G|1645
    Insertion on left  3WQY|1|C|G|1646
pMakeNodesProbeForInsertions:  a 3WQY|1|C|G|1649 interacts with 3WQY|1|C|C|1665
pMakeNodesProbeForInsertions:  B 3WQY|1|C|C|1665 interacts with 3WQY|1|C|G|1649
pMakeNodesProbeForInsertions:  B 3WQY|1|C|C|1665 interacts with 3WQY|1|C|G|1649
 13 Initial   1645 (2 insertion) and 1665 (0 insertion)
 14 Basepair  1649 1665 GC cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 12
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
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  15   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3WQY|1|C|U|1608
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3WQY|1|C|A|1644
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3WQY|1|C|G|1645
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: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G1607 - C1666 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J5688'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3WQY|1|C|U|1608'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5688'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J5688'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1610 - C1665 ID J5688'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5688'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G1610 - C1625 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J5688'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3WQY|1|C|G|1626 - 3WQY|1|C|C|1665 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J4693'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1626 - C1665 ID J4693'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J4693'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1626 - A1644 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 C1627 - G1643 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 14

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: []
           numbranches: []
              NormCons: 1

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J4693'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 3WQY|1|C|G|1645 - 3WQY|1|C|C|1665 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             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 3WQY|1|C|A|1644'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 3WQY|1|C|G|1645'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 G1649 - C1665 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 12
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
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  20  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  21   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J5688'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J5688'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3WQY|1|C|G|1626 - 3WQY|1|C|C|1665 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_70449.12. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J4693'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J4693'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 3WQY|1|C|G|1645 - 3WQY|1|C|C|1665 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_70449.12. Nodes 11 and 15 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 9
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_70449.12_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3995
  -11.2515
   -9.1742
   -8.8332
   -9.0843
   -9.2416
   -9.1877
  -11.4990
  -11.3721
   -9.4830
   -8.6112
   -9.4830
   -9.7213
  -10.1505
   -9.4830
   -9.0670
   -9.2416
  -13.3540
   -9.1742
   -9.4830
  -12.4194
   -9.0544
  -17.5227
  -12.1906
   -9.0091
  -10.5626
  -10.9512
  -11.0376
  -10.5400
  -11.8609
   -9.4830
   -9.5447
  -14.3691
   -9.1742
  -11.2284
  -12.7620
  -15.4839
  -17.5227
  -17.5227
  -11.5816
  -11.8609
   -9.2416

Timestamp 18-Jul-2025 00:13:06
pMakeSCFGModels: Making JAR3D model for motif group J4_70672.1, number 50 of 65
pMakeNodes starting loop:     a=6DN2|1|X|C|8 B=6DN2|1|Y|G|105
  2 Basepair     8  105 CG cWW 
No need to probe because of interaction between a=6DN2|1|X|G|9 B=6DN2|1|Y|A|104
  3 Basepair     9  104 GA tSH 
pMakeNodes probe for inserts:  a=6DN2|1|X|G|10 B=6DN2|1|Y|G|103
    Insertion on left  6DN2|1|X|G|10
    Insertion on left  6DN2|1|X|G|11
    Insertion on right 6DN2|1|Y|G|103
    Insertion on right 6DN2|1|Y|A|102
    Insertion on right 6DN2|1|Y|G|101
    Insertion on right 6DN2|1|Y|A|99
pMakeNodes probed for insert:  a=6DN2|1|X|G|12 B=6DN2|1|Y|G|98
pMakeNodesJunction: a=6DN2|1|X|G|12 r=6DN2|1|X|G|12 s=6DN2|1|X|G|28 t=6DN2|1|X|A|29 u=B=6DN2|1|Y|G|98
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6DN2|1|X|G|12 and 6DN2|1|X|G|28 and between 6DN2|1|X|A|29 and 6DN2|1|Y|G|98
pMakeNodesJunction: about to make a junction: a=6DN2|1|X|G|12 s=6DN2|1|X|G|28 t=6DN2|1|X|A|29 B=6DN2|1|Y|G|98
pMakeNodesJunction: first branch starts at   6DN2|1|X|G|12
pMakeNodesJunction: first branch ends around 6DN2|1|X|G|28
pMakeNodesJunction: second branch starts at  6DN2|1|X|A|29
pMakeNodesJunction: junction ends at         6DN2|1|Y|G|98
pMakeNodesJunction: first branch strand start goes up to  6DN2|1|X|G|15
pMakeNodesJunction: first branch strand end goes down to  6DN2|1|X|C|27
pMakeNodesJunction: second branch strand start goes up to 6DN2|1|X|C|31
pMakeNodesJunction: last strand of junction goes down to  6DN2|1|Y|G|97
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J119
Actual Branch 1 of junction J119 - Nucleotides 6DN2|1|X|G|12 to 6DN2|1|X|G|28, length   6
Actual Branch 2 of junction J119 - Nucleotides 6DN2|1|X|A|29 to 6DN2|1|Y|G|98, length   8
  4 Junction

2B Branch 1 of 2 of junction J119 - Nucleotides    12 to    28, length   6
pMakeNodes starting loop:     a=6DN2|1|X|G|12 B=6DN2|1|X|G|28
    Insertion on left  6DN2|1|X|G|12
pMakeNodesProbeForInsertions:  a 6DN2|1|X|C|13 interacts with 6DN2|1|X|G|28
pMakeNodesProbeForInsertions:  B 6DN2|1|X|G|28 interacts with 6DN2|1|X|C|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6DN2|1|X|G|28 interacts with 6DN2|1|X|A|14
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  5 Initial     12 (1 insertion) and   28 (0 insertion)
pMakeNodes making a cluster near strand break a=6DN2|1|X|C|13 B=6DN2|1|X|G|28
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 7 and then 10 to 10
aa is 7 bb is 10
  6 Cluster   6DN2|1|X|C|13:6DN2|1|X|A|14 6DN2|1|X|G|28:6DN2|1|X|G|28
    LR Inter  6DN2|1|X|C|13 6DN2|1|X|G|28 cSW 
    LR Inter  6DN2|1|X|A|14 6DN2|1|X|G|28 tHS 
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=6DN2|1|X|G|15 B=6DN2|1|X|C|27
  7 Basepair    15   27 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J119 - Nucleotides    29 to    98, length   8
pMakeNodes starting loop:     a=6DN2|1|X|A|29 B=6DN2|1|Y|G|98
    Insertion on left  6DN2|1|X|A|29
    Insertion on left  6DN2|1|X|C|30
  9 Initial     29 (2 insertion) and   98 (0 insertion)
pMakeNodesJunction: a=6DN2|1|X|C|31 r=6DN2|1|X|C|31 s=6DN2|1|Y|G|84 t=6DN2|1|Y|A|85 u=B=6DN2|1|Y|G|98
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6DN2|1|X|C|31 and 6DN2|1|Y|G|84 and between 6DN2|1|Y|A|85 and 6DN2|1|Y|G|98
pMakeNodesJunction: about to make a junction: a=6DN2|1|X|C|31 s=6DN2|1|Y|G|84 t=6DN2|1|Y|A|85 B=6DN2|1|Y|G|98
pMakeNodesJunction: first branch starts at   6DN2|1|X|C|31
pMakeNodesJunction: first branch ends around 6DN2|1|Y|G|84
pMakeNodesJunction: second branch starts at  6DN2|1|Y|A|85
pMakeNodesJunction: junction ends at         6DN2|1|Y|G|98
pMakeNodesJunction: first branch strand start goes up to  6DN2|1|X|C|31
pMakeNodesJunction: first branch strand end goes down to  6DN2|1|Y|G|84
pMakeNodesJunction: second branch strand start goes up to 6DN2|1|Y|C|86
pMakeNodesJunction: last strand of junction goes down to  6DN2|1|Y|G|97

Junction with 2 loops, call it J3371
Actual Branch 1 of junction J3371 - Nucleotides 6DN2|1|X|C|31 to 6DN2|1|Y|G|84, length   2
Actual Branch 2 of junction J3371 - Nucleotides 6DN2|1|Y|A|85 to 6DN2|1|Y|G|98, length   4
 10 Junction

2B Branch 1 of 2 of junction J3371 - Nucleotides    31 to    84, length   2
pMakeNodes starting loop:     a=6DN2|1|X|C|31 B=6DN2|1|Y|G|84
 12 Basepair    31   84 CG cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J3371 - Nucleotides    85 to    98, length   4
pMakeNodes starting loop:     a=6DN2|1|Y|A|85 B=6DN2|1|Y|G|98
 15 Basepair    85   98 AG cWW 
No need to probe because of interaction between a=6DN2|1|Y|C|86 B=6DN2|1|Y|G|97
 16 Basepair    86   97 CG cWW 
 17 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  Junction Left  5 Right 18
pMakeMotifModelFromSSF:   5   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   6   Cluster Left  6  7 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   9   Initial Left 11 Right 18
pMakeMotifModelFromSSF:  10  Junction Left 13 Right 18
pMakeMotifModelFromSSF:  11   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  12  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  13   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  14   Initial Left 15 Right 18
pMakeMotifModelFromSSF:  15  Basepair Left 15 Right 18
pMakeMotifModelFromSSF:  16  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  17   Hairpin Left 17 Right 16
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DN2|1|X|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DN2|1|X|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DN2|1|Y|A|102
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DN2|1|Y|G|101
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DN2|1|Y|U|100
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DN2|1|Y|A|99
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DN2|1|X|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DN2|1|X|A|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DN2|1|X|C|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: 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: []
           numbranches: []
          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: 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: 'G'
               Comment: ' // Basepair C8 - G105 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          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: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 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: 'GGG'
           RightLetter: 'AGAGA'
               Comment: ' // Basepair G9 - A104 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]
           numbranches: []
          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: 22
             Insertion: []
                    id: 'J119'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DN2|1|X|G|10'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          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: 22
             Insertion: []
                    id: 'J119'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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: 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 6DN2|1|X|G|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]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2611

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             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: []
           numbranches: []
          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: 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 6DN2|1|Y|A|102'
              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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             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: '*'
           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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: 'J119'
        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 6DN2|1|Y|G|101'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: 'J3371'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: 'J3371'
        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 6DN2|1|Y|U|100'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             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: '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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 5
            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 6DN2|1|Y|A|99'
              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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: 'J3371'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: 'J119'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G12 - G98 ID J119'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J119'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6DN2|1|X|G|12 - 6DN2|1|X|G|28 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             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 6DN2|1|X|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 17
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

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: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          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]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Cluster node 6DN2|1|X|C|13:6DN2|1|X|A|14 and 6DN2|1|X|G|28:6DN2|1|X|G|28'
              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: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2611

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 23
             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 G15 - C27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 18
             Insertion: []
                    id: 'J119'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: []
               Comment: ' // Initial node 6DN2|1|X|A|29 - 6DN2|1|Y|G|98 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             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 6DN2|1|X|A|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DN2|1|X|C|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 13
            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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
                    id: 'J3371'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C31 - G98 ID J3371'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: 'J3371'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 32
             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 C31 - G84 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 33
             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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 34
             LeftIndex: 15
            RightIndex: 18
             Insertion: []
                    id: 'J3371'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 34

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 35
             LeftIndex: 15
            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: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A85 - 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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 35

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 36
             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 C86 - 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]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 36

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 38
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              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     Fixed Left  3 Right 22
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 22
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 22
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 22
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 22
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 21
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 21
pMakeMotifModelFromSSF:  11   Initial Left  5 Right 20
pMakeMotifModelFromSSF:  12     Fixed Left  5 Right 20
pMakeMotifModelFromSSF:  13   Initial Left  5 Right 19
pMakeMotifModelFromSSF:  14     Fixed Left  5 Right 19
pMakeMotifModelFromSSF:  15   Initial Left  5 Right 18
pMakeMotifModelFromSSF:  16  Junction Left  5 Right 18
pMakeMotifModelFromSSF:  17   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  18     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  19   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  20   Cluster Left  6  7 Right 10
pMakeMotifModelFromSSF:  21   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  22  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  23   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  24   Initial Left 11 Right 18
pMakeMotifModelFromSSF:  25     Fixed Left 11 Right 18
pMakeMotifModelFromSSF:  26   Initial Left 12 Right 18
pMakeMotifModelFromSSF:  27     Fixed Left 12 Right 18
pMakeMotifModelFromSSF:  28   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  29  Junction Left 13 Right 18
pMakeMotifModelFromSSF:  30   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  31  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  32   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  33   Initial Left 15 Right 18
pMakeMotifModelFromSSF:  34  Basepair Left 15 Right 18
pMakeMotifModelFromSSF:  35  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  36   Hairpin Left 17 Right 16
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a junction at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 32
pNextNodeJunction: Found a junction child at node 33
pNextNodeJunction: Found a hairpin at node 36
pNextNodeJunction: Finished at node 36 out of 36, type Hairpin
pNextNodeJunction: Finished at node 36 out of 36, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J119'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6DN2|1|X|G|12 - 6DN2|1|X|G|28 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 18
             Insertion: []
                    id: 'J119'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: []
               Comment: ' // Initial node 6DN2|1|X|A|29 - 6DN2|1|Y|G|98 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_70672.1. Nodes 17 and 24 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: 'J3371'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 34
             LeftIndex: 15
            RightIndex: 18
             Insertion: []
                    id: 'J3371'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J4_70672.1. Nodes 30 and 33 both model an insertion before position 15. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a junction at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 32
pNextNodeJunction: Found a junction child at node 33
pNextNodeJunction: Found a hairpin at node 36
pNextNodeJunction: Finished at node 36 out of 36, type Hairpin
pNextNodeJunction: Finished at node 36 out of 36, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 13
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_70672.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.7023
  -13.7023

Timestamp 18-Jul-2025 00:13:07
pMakeSCFGModels: Making JAR3D model for motif group J4_71729.2, number 51 of 65
pMakeNodes starting loop:     a=4Y4O|1|2A|C|297 B=4Y4O|1|2A|G|341
  2 Basepair   297  341 CG cWW 
No need to probe because of interaction between a=4Y4O|1|2A|G|298 B=4Y4O|1|2A|A|340
  3 Basepair   298  340 GA tSH 
pMakeNodes probe for inserts:  a=4Y4O|1|2A|A|299 B=4Y4O|1|2A|U|339
    Insertion on right 4Y4O|1|2A|U|339
pMakeNodes probed for insert:  a=4Y4O|1|2A|A|299 B=4Y4O|1|2A|G|338
pMakeNodes making a cluster near strand break a=4Y4O|1|2A|A|299 B=4Y4O|1|2A|G|338
pMakeNodesCluster: amax is 4 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 14 to 14
aa is 4 bb is 14
  4 Cluster   4Y4O|1|2A|A|299:4Y4O|1|2A|A|300 4Y4O|1|2A|G|338:4Y4O|1|2A|G|338
    LR Inter  4Y4O|1|2A|A|299 4Y4O|1|2A|G|338 cHH 
    LR Inter  4Y4O|1|2A|A|300 4Y4O|1|2A|G|338 wat 
pMakeNodesCluster a=5 B=13 at the end
pMakeNodesCluster a=5 B=13 at the end
pMakeNodes probe for inserts:  a=4Y4O|1|2A|G|301 B=4Y4O|1|2A|C|337
  5 Initial    301 (0 insertion) and  337 (0 insertion)
pMakeNodes probed for insert:  a=4Y4O|1|2A|G|301 B=4Y4O|1|2A|C|337
pMakeNodesJunction: a=4Y4O|1|2A|G|301 r=4Y4O|1|2A|G|301 s=4Y4O|1|2A|C|316 t=4Y4O|1|2A|G|317 u=B=4Y4O|1|2A|C|337
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|G|301 and 4Y4O|1|2A|C|316 and between 4Y4O|1|2A|G|317 and 4Y4O|1|2A|C|337
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|G|301 s=4Y4O|1|2A|C|316 t=4Y4O|1|2A|G|317 B=4Y4O|1|2A|C|337
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|G|301
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|C|316
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|G|317
pMakeNodesJunction: junction ends at         4Y4O|1|2A|C|337
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|G|301
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|C|316
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|C|319
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|C|337

Junction with 2 loops, call it J1621
Actual Branch 1 of junction J1621 - Nucleotides 4Y4O|1|2A|G|301 to 4Y4O|1|2A|C|316, length   2
Actual Branch 2 of junction J1621 - Nucleotides 4Y4O|1|2A|G|317 to 4Y4O|1|2A|C|337, length   7
  6 Junction

2B Branch 1 of 2 of junction J1621 - Nucleotides   301 to   316, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|G|301 B=4Y4O|1|2A|C|316
  8 Basepair   301  316 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J1621 - Nucleotides   317 to   337, length   7
pMakeNodes starting loop:     a=4Y4O|1|2A|G|317 B=4Y4O|1|2A|C|337
    Insertion on left  4Y4O|1|2A|G|317
    Insertion on left  4Y4O|1|2A|C|318
 10 Initial    317 (2 insertion) and  337 (0 insertion)
pMakeNodesJunction: a=4Y4O|1|2A|C|319 r=4Y4O|1|2A|C|319 s=4Y4O|1|2A|G|323 t=4Y4O|1|2A|A|324 u=B=4Y4O|1|2A|C|337
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|C|319 and 4Y4O|1|2A|G|323 and between 4Y4O|1|2A|A|324 and 4Y4O|1|2A|C|337
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|C|319 s=4Y4O|1|2A|G|323 t=4Y4O|1|2A|A|324 B=4Y4O|1|2A|C|337
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|C|319
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|G|323
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|A|324
pMakeNodesJunction: junction ends at         4Y4O|1|2A|C|337
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|C|319
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|G|323
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|G|325
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|C|337

Junction with 2 loops, call it J7942
Actual Branch 1 of junction J7942 - Nucleotides 4Y4O|1|2A|C|319 to 4Y4O|1|2A|G|323, length   2
Actual Branch 2 of junction J7942 - Nucleotides 4Y4O|1|2A|A|324 to 4Y4O|1|2A|C|337, length   3
 11 Junction

2B Branch 1 of 2 of junction J7942 - Nucleotides   319 to   323, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|C|319 B=4Y4O|1|2A|G|323
 13 Basepair   319  323 CG cWW 
 14 Hairpin type *

2B Branch 2 of 2 of junction J7942 - Nucleotides   324 to   337, length   3
pMakeNodes starting loop:     a=4Y4O|1|2A|A|324 B=4Y4O|1|2A|C|337
    Insertion on left  4Y4O|1|2A|A|324
pMakeNodesProbeForInsertions:  a 4Y4O|1|2A|G|325 interacts with 4Y4O|1|2A|C|337
pMakeNodesProbeForInsertions:  B 4Y4O|1|2A|C|337 interacts with 4Y4O|1|2A|G|325
pMakeNodesProbeForInsertions:  B 4Y4O|1|2A|C|337 interacts with 4Y4O|1|2A|G|325
 15 Initial    324 (1 insertion) and  337 (0 insertion)
 16 Basepair   325  337 GC cWW 
 17 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  3  4 Right 14
pMakeMotifModelFromSSF:   5   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   6  Junction Left  5 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  11  Junction Left  9 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  15   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  16  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  17   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Y4O|1|2A|U|339
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|G|317
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|C|318
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y4O|1|2A|A|324
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: []
           numbranches: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C297 - G341 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: [0.9950 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: 'UA'
               Comment: ' // Basepair G298 - A340 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: []
           numbranches: []

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: 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 4Y4O|1|2A|U|339'
              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: 0.7799
           numbranches: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             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: []
           numbranches: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [3 4]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'G'
               Comment: ' // Cluster node 4Y4O|1|2A|A|299:4Y4O|1|2A|A|300 and 4Y4O|1|2A|G|338:4Y4O|1|2A|G|338'
              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: 0.7799
           numbranches: []

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: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|301 - 4Y4O|1|2A|C|337 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [7 10]
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: 'J1621'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G301 - C337 ID J1621'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

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: 'J1621'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 G301 - C316 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 11

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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: 'J1621'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|317 - 4Y4O|1|2A|C|337 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 4Y4O|1|2A|G|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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: [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
           numbranches: []

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: 'J7942'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y4O|1|2A|C|318'
              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: []
           numbranches: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             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: '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: []
           numbranches: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [12 15]
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J7942'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C319 - C337 ID J7942'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

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: 'J7942'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 C319 - G323 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             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
           numbranches: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J7942'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|A|324 - 4Y4O|1|2A|C|337 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 4Y4O|1|2A|A|324'
              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: []
           numbranches: []

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 G325 - C337 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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  3 Right 14
pMakeMotifModelFromSSF:   6   Cluster Left  3  4 Right 14
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
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  Junction Left  9 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  23   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J1621'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J1621'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|G|317 - 4Y4O|1|2A|C|337 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_71729.2. Nodes 9 and 12 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J7942'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J7942'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4Y4O|1|2A|A|324 - 4Y4O|1|2A|C|337 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_71729.2. Nodes 18 and 21 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a junction child at node 21
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 8
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 11 and 14
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 8
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 11 and 14
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_71729.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7400
   -9.6992
   -8.9402
   -8.7404

Timestamp 18-Jul-2025 00:13:08
pMakeSCFGModels: Making JAR3D model for motif group J4_72305.3, number 52 of 65
pMakeNodes starting loop:     a=4QEI|1|C|C|7 B=4QEI|1|C|G|66
  2 Basepair     7   66 CG cWW 
pMakeNodes probe for inserts:  a=4QEI|1|C|G|9 B=4QEI|1|C|G|65
    Insertion on left  4QEI|1|C|G|9
pMakeNodes probed for insert:  a=4QEI|1|C|G|10 B=4QEI|1|C|G|65
pMakeNodesJunction: a=4QEI|1|C|G|10 r=4QEI|1|C|G|10 s=4QEI|1|C|U|25 t=4QEI|1|C|G|26 u=B=4QEI|1|C|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4QEI|1|C|G|10 and 4QEI|1|C|U|25 and between 4QEI|1|C|G|26 and 4QEI|1|C|G|65
pMakeNodesJunction: about to make a junction: a=4QEI|1|C|G|10 s=4QEI|1|C|U|25 t=4QEI|1|C|G|26 B=4QEI|1|C|G|65
pMakeNodesJunction: first branch starts at   4QEI|1|C|G|10
pMakeNodesJunction: first branch ends around 4QEI|1|C|U|25
pMakeNodesJunction: second branch starts at  4QEI|1|C|G|26
pMakeNodesJunction: junction ends at         4QEI|1|C|G|65
pMakeNodesJunction: first branch strand start goes up to  4QEI|1|C|G|10
pMakeNodesJunction: first branch strand end goes down to  4QEI|1|C|U|25
pMakeNodesJunction: second branch strand start goes up to 4QEI|1|C|G|26
pMakeNodesJunction: last strand of junction goes down to  4QEI|1|C|G|65

Junction with 2 loops, call it J3112
Actual Branch 1 of junction J3112 - Nucleotides 4QEI|1|C|G|10 to 4QEI|1|C|U|25, length   2
Actual Branch 2 of junction J3112 - Nucleotides 4QEI|1|C|G|26 to 4QEI|1|C|G|65, length   6
  3 Junction

2B Branch 1 of 2 of junction J3112 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=4QEI|1|C|G|10 B=4QEI|1|C|U|25
  5 Basepair    10   25 GU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J3112 - Nucleotides    26 to    65, length   6
pMakeNodes starting loop:     a=4QEI|1|C|G|26 B=4QEI|1|C|G|65
  7 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=4QEI|1|C|G|26 r=4QEI|1|C|G|26 s=4QEI|1|C|C|44 t=4QEI|1|C|G|45 u=B=4QEI|1|C|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4QEI|1|C|G|26 and 4QEI|1|C|C|44 and between 4QEI|1|C|G|45 and 4QEI|1|C|G|65
pMakeNodesJunction: about to make a junction: a=4QEI|1|C|G|26 s=4QEI|1|C|C|44 t=4QEI|1|C|G|45 B=4QEI|1|C|G|65
pMakeNodesJunction: first branch starts at   4QEI|1|C|G|26
pMakeNodesJunction: first branch ends around 4QEI|1|C|C|44
pMakeNodesJunction: second branch starts at  4QEI|1|C|G|45
pMakeNodesJunction: junction ends at         4QEI|1|C|G|65
pMakeNodesJunction: first branch strand start goes up to  4QEI|1|C|G|26
pMakeNodesJunction: first branch strand end goes down to  4QEI|1|C|C|44
pMakeNodesJunction: second branch strand start goes up to 4QEI|1|C|C|49
pMakeNodesJunction: last strand of junction goes down to  4QEI|1|C|G|65

Junction with 2 loops, call it J5285
Actual Branch 1 of junction J5285 - Nucleotides 4QEI|1|C|G|26 to 4QEI|1|C|C|44, length   2
Actual Branch 2 of junction J5285 - Nucleotides 4QEI|1|C|G|45 to 4QEI|1|C|G|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J5285 - Nucleotides    26 to    44, length   2
pMakeNodes starting loop:     a=4QEI|1|C|G|26 B=4QEI|1|C|C|44
 10 Basepair    26   44 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J5285 - Nucleotides    45 to    65, length   4
pMakeNodes starting loop:     a=4QEI|1|C|G|45 B=4QEI|1|C|G|65
    Insertion on left  4QEI|1|C|G|45
    Insertion on left  4QEI|1|C|A|46
pMakeNodesProbeForInsertions:  a 4QEI|1|C|C|49 interacts with 4QEI|1|C|G|65
pMakeNodesProbeForInsertions:  B 4QEI|1|C|G|65 interacts with 4QEI|1|C|C|49
pMakeNodesProbeForInsertions:  B 4QEI|1|C|G|65 interacts with 4QEI|1|C|C|49
 12 Initial     45 (2 insertion) and   65 (0 insertion)
 13 Basepair    49   65 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4QEI|1|C|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4QEI|1|C|C|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4QEI|1|C|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: 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: []
           numbranches: []
              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 C7 - G66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J3112'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4QEI|1|C|U|8'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3112'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: 'J3112'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - G65 ID J3112'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J3112'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G10 - 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]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J3112'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4QEI|1|C|G|26 - 4QEI|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J5285'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G26 - G65 ID J5285'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J5285'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G26 - 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]
           numbranches: []
              NormCons: []

Node 13

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: []
           numbranches: []
              NormCons: 1

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: 'J5285'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 4QEI|1|C|G|45 - 4QEI|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4QEI|1|C|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4QEI|1|C|G|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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 C49 - G65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J3112'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J3112'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4QEI|1|C|G|26 - 4QEI|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_72305.3. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J5285'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9980 0.0020 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J5285'
        leftLengthDist: [0.9980 0.0020 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: []
               Comment: ' // Initial node 4QEI|1|C|G|45 - 4QEI|1|C|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_72305.3. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 7
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_72305.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3470
  -10.3470
  -10.2764
  -11.8995
  -15.6592
  -12.8574

Timestamp 18-Jul-2025 00:13:09
pMakeSCFGModels: Making JAR3D model for motif group J4_75852.1, number 53 of 65
pMakeNodes starting loop:     a=6DME|1|A|A|4 B=6DME|1|A|U|99
  2 Basepair     4   99 AU cWW 
pMakeNodes probe for inserts:  a=6DME|1|A|G|5 B=6DME|1|A|G|98
    Insertion on left  6DME|1|A|G|5
pMakeNodes probed for insert:  a=6DME|1|A|U|6 B=6DME|1|A|G|98
pMakeNodesJunction: a=6DME|1|A|U|6 r=6DME|1|A|U|6 s=6DME|1|A|A|50 t=6DME|1|A|G|51 u=B=6DME|1|A|G|98
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6DME|1|A|U|6 and 6DME|1|A|A|50 and between 6DME|1|A|G|51 and 6DME|1|A|G|98
pMakeNodesJunction: about to make a junction: a=6DME|1|A|U|6 s=6DME|1|A|A|50 t=6DME|1|A|G|51 B=6DME|1|A|G|98
pMakeNodesJunction: first branch starts at   6DME|1|A|U|6
pMakeNodesJunction: first branch ends around 6DME|1|A|A|50
pMakeNodesJunction: second branch starts at  6DME|1|A|G|51
pMakeNodesJunction: junction ends at         6DME|1|A|G|98
pMakeNodesJunction: first branch strand start goes up to  6DME|1|A|U|6
pMakeNodesJunction: first branch strand end goes down to  6DME|1|A|A|50
pMakeNodesJunction: second branch strand start goes up to 6DME|1|A|G|51
pMakeNodesJunction: last strand of junction goes down to  6DME|1|A|G|94

Junction with 2 loops, call it J1656
Actual Branch 1 of junction J1656 - Nucleotides 6DME|1|A|U|6 to 6DME|1|A|A|50, length   2
Actual Branch 2 of junction J1656 - Nucleotides 6DME|1|A|G|51 to 6DME|1|A|G|98, length  11
  3 Junction

2B Branch 1 of 2 of junction J1656 - Nucleotides     6 to    50, length   2
pMakeNodes starting loop:     a=6DME|1|A|U|6 B=6DME|1|A|A|50
  5 Basepair     6   50 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1656 - Nucleotides    51 to    98, length  11
pMakeNodes starting loop:     a=6DME|1|A|G|51 B=6DME|1|A|G|98
  7 Initial     51 (0 insertion) and   98 (0 insertion)
pMakeNodesJunction: a=6DME|1|A|G|51 r=6DME|1|A|G|51 s=6DME|1|A|U|68 t=6DME|1|A|A|69 u=B=6DME|1|A|G|98
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6DME|1|A|G|51 and 6DME|1|A|U|68 and between 6DME|1|A|A|69 and 6DME|1|A|G|98
pMakeNodesJunction: about to make a junction: a=6DME|1|A|G|51 s=6DME|1|A|U|68 t=6DME|1|A|A|69 B=6DME|1|A|G|98
pMakeNodesJunction: first branch starts at   6DME|1|A|G|51
pMakeNodesJunction: first branch ends around 6DME|1|A|U|68
pMakeNodesJunction: second branch starts at  6DME|1|A|A|69
pMakeNodesJunction: junction ends at         6DME|1|A|G|98
pMakeNodesJunction: first branch strand start goes up to  6DME|1|A|G|51
pMakeNodesJunction: first branch strand end goes down to  6DME|1|A|U|68
pMakeNodesJunction: second branch strand start goes up to 6DME|1|A|C|72
pMakeNodesJunction: last strand of junction goes down to  6DME|1|A|G|94

Junction with 2 loops, call it J6019
Actual Branch 1 of junction J6019 - Nucleotides 6DME|1|A|G|51 to 6DME|1|A|U|68, length   2
Actual Branch 2 of junction J6019 - Nucleotides 6DME|1|A|A|69 to 6DME|1|A|G|98, length   9
  8 Junction

2B Branch 1 of 2 of junction J6019 - Nucleotides    51 to    68, length   2
pMakeNodes starting loop:     a=6DME|1|A|G|51 B=6DME|1|A|U|68
 10 Basepair    51   68 GU cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J6019 - Nucleotides    69 to    98, length   9
pMakeNodes starting loop:     a=6DME|1|A|A|69 B=6DME|1|A|G|98
pMakeNodes making a cluster near strand break a=6DME|1|A|A|69 B=6DME|1|A|G|98
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 8 and then 14 to 15
aa is 8 bb is 14
 13 Cluster   6DME|1|A|A|69:6DME|1|A|C|70 6DME|1|A|A|97:6DME|1|A|G|98
    LR Inter  6DME|1|A|C|70 6DME|1|A|A|97 cSS 
    LR Inter  6DME|1|A|A|69 6DME|1|A|G|98 cSS 
    LR Inter  6DME|1|A|C|70 6DME|1|A|G|98 cSS 
pMakeNodesCluster a=9 B=13 at the end
pMakeNodesCluster a=9 B=13 at the end
pMakeNodes probe for inserts:  a=6DME|1|A|A|71 B=6DME|1|A|A|96
    Insertion on left  6DME|1|A|A|71
pMakeNodesProbeForInsertions:  a 6DME|1|A|C|72 interacts with 6DME|1|A|G|94
pMakeNodesProbeForInsertions:  B 6DME|1|A|A|96 interacts with 6DME|1|A|C|95
pMakeNodesProbeForInsertions:  B 6DME|1|A|A|96 interacts with 6DME|1|A|C|95
 14 Initial     71 (1 insertion) and   96 (0 insertion)
pMakeNodes probed for insert:  a=6DME|1|A|C|72 B=6DME|1|A|A|96
pMakeNodes making a cluster near strand break a=6DME|1|A|C|72 B=6DME|1|A|A|96
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 10 to 10 and then 11 to 13
aa is 10 bb is 11
 15 Cluster   6DME|1|A|C|72:6DME|1|A|C|72 6DME|1|A|G|94:6DME|1|A|A|96
    LR Inter  6DME|1|A|C|72 6DME|1|A|G|94 cWW 
    RR Inter  6DME|1|A|C|95 6DME|1|A|A|96 cSH 
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  13   Cluster Left  7  8 Right 14 15
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  15   Cluster Left 10 Right 11 12 13
pMakeMotifModelFromSSF:  16   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 6DME|1|A|G|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DME|1|A|A|71
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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Basepair A4 - U99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J1656'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DME|1|A|G|5'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J1656'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: 'J1656'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U6 - G98 ID J1656'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'J1656'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U6 - A50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J1656'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6DME|1|A|G|51 - 6DME|1|A|G|98 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J6019'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G51 - G98 ID J6019'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6019'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'U'
               Comment: ' // Basepair G51 - U68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 13

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: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J6019'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 16
             LeftIndex: [7 8]
            RightIndex: [14 15]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'AG'
               Comment: ' // Cluster node 6DME|1|A|A|69:6DME|1|A|C|70 and 6DME|1|A|A|97:6DME|1|A|G|98'
              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: []
           numbranches: []
              NormCons: 0.0404
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 13
             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 6DME|1|A|A|71 - 6DME|1|A|A|96 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             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 6DME|1|A|A|71'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 20
             LeftIndex: 10
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'GCA'
               Comment: ' // Cluster node 6DME|1|A|C|72:6DME|1|A|C|72 and 6DME|1|A|G|94:6DME|1|A|A|96'
              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 3]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

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  Junction Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 15
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  15   Cluster Left  7  8 Right 14 15
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 13
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  19   Cluster Left 10 Right 11 12 13
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 10
pMakeMotifModelFromSSF:  21   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pUpdateModelWithSSF: J4_75852.1 allow insertions from initial node 20?
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


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J1656'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J1656'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6DME|1|A|G|51 - 6DME|1|A|G|98 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_75852.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6019'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J6019'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Motif J4_75852.1. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSW  between 2 and 7
pConservedInteractionList: did not find a substitution probability matrix for tSW  between 2 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_75852.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2038

Timestamp 18-Jul-2025 00:13:10
pMakeSCFGModels: Making JAR3D model for motif group J4_75971.1, number 54 of 65
pMakeNodes starting loop:     a=5TBW|1|1|U|3010 B=5TBW|1|1|G|3136
  2 Basepair  3010 3136 UG cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|3011 B=5TBW|1|1|U|3135
pMakeNodes probed for insert:  a=5TBW|1|1|A|3011 B=5TBW|1|1|U|3135
pMakeNodesJunction: a=5TBW|1|1|A|3011 r=5TBW|1|1|A|3011 s=5TBW|1|1|U|3042 t=5TBW|1|1|C|3043 u=B=5TBW|1|1|U|3135
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|A|3011 and 5TBW|1|1|U|3042 and between 5TBW|1|1|C|3043 and 5TBW|1|1|U|3135
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|A|3011 s=5TBW|1|1|U|3042 t=5TBW|1|1|C|3043 B=5TBW|1|1|U|3135
pMakeNodesJunction: first branch starts at   5TBW|1|1|A|3011
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|3042
pMakeNodesJunction: second branch starts at  5TBW|1|1|C|3043
pMakeNodesJunction: junction ends at         5TBW|1|1|U|3135
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|A|3012
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|U|3042
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|C|3043
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|3134
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J2629
Actual Branch 1 of junction J2629 - Nucleotides 5TBW|1|1|A|3011 to 5TBW|1|1|U|3042, length   3
Actual Branch 2 of junction J2629 - Nucleotides 5TBW|1|1|C|3043 to 5TBW|1|1|U|3135, length   6
  3 Junction

2B Branch 1 of 2 of junction J2629 - Nucleotides  3011 to  3042, length   3
pMakeNodes starting loop:     a=5TBW|1|1|A|3011 B=5TBW|1|1|U|3042
    Insertion on left  5TBW|1|1|A|3011
pMakeNodesProbeForInsertions:  a 5TBW|1|1|A|3012 interacts with 5TBW|1|1|U|3042
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|3042 interacts with 5TBW|1|1|A|3012
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|3042 interacts with 5TBW|1|1|A|3012
  4 Initial   3011 (1 insertion) and 3042 (0 insertion)
  5 Basepair  3012 3042 AU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2629 - Nucleotides  3043 to  3135, length   6
pMakeNodes starting loop:     a=5TBW|1|1|C|3043 B=5TBW|1|1|U|3135
  7 Initial   3043 (0 insertion) and 3135 (0 insertion)
pMakeNodesJunction: a=5TBW|1|1|C|3043 r=5TBW|1|1|C|3043 s=5TBW|1|1|G|3098 t=5TBW|1|1|C|3099 u=B=5TBW|1|1|U|3135
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|C|3043 and 5TBW|1|1|G|3098 and between 5TBW|1|1|C|3099 and 5TBW|1|1|U|3135
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|C|3043 s=5TBW|1|1|G|3098 t=5TBW|1|1|C|3099 B=5TBW|1|1|U|3135
pMakeNodesJunction: first branch starts at   5TBW|1|1|C|3043
pMakeNodesJunction: first branch ends around 5TBW|1|1|G|3098
pMakeNodesJunction: second branch starts at  5TBW|1|1|C|3099
pMakeNodesJunction: junction ends at         5TBW|1|1|U|3135
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|C|3043
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|G|3098
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|U|3100
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|3134

Junction with 2 loops, call it J6540
Actual Branch 1 of junction J6540 - Nucleotides 5TBW|1|1|C|3043 to 5TBW|1|1|G|3098, length   2
Actual Branch 2 of junction J6540 - Nucleotides 5TBW|1|1|C|3099 to 5TBW|1|1|U|3135, length   4
  8 Junction

2B Branch 1 of 2 of junction J6540 - Nucleotides  3043 to  3098, length   2
pMakeNodes starting loop:     a=5TBW|1|1|C|3043 B=5TBW|1|1|G|3098
 10 Basepair  3043 3098 CG cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J6540 - Nucleotides  3099 to  3135, length   4
pMakeNodes starting loop:     a=5TBW|1|1|C|3099 B=5TBW|1|1|U|3135
 13 Basepair  3099 3135 CU cWW 
No need to probe because of interaction between a=5TBW|1|1|U|3100 B=5TBW|1|1|A|3134
 14 Basepair  3100 3134 UA cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
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
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|3011
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 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: []
           numbranches: []
              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: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U3010 - G3136 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: 'J2629'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A3011 - U3135 ID J2629'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: 'J2629'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|A|3011 - 5TBW|1|1|U|3042 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             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 5TBW|1|1|A|3011'
              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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 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 A3012 - U3042 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2629'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|C|3043 - 5TBW|1|1|U|3135 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J6540'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C3043 - U3135 ID J6540'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6540'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C3043 - G3098 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 13

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: []
           numbranches: []
              NormCons: 1

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: 'J6540'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             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: 'U'
               Comment: ' // Basepair C3099 - U3135 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U3100 - A3134 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 17

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  4
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: 'J2629'
        leftLengthDist: 1
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|A|3011 - 5TBW|1|1|U|3042 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2629'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|C|3043 - 5TBW|1|1|U|3135 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_75971.1. Nodes 4 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6540'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J6540'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_75971.1. Nodes 11 and 14 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 2 and 5
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 2 and 5
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_75971.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7717

Timestamp 18-Jul-2025 00:13:10
pMakeSCFGModels: Making JAR3D model for motif group J4_76405.1, number 55 of 65
pMakeNodes starting loop:     a=2QUS|1|A|U|11 B=2QUS|1|A|A|54
  2 Basepair    11   54 UA cWW 
No need to probe because of interaction between a=2QUS|1|A|C|12 B=2QUS|1|A|A|53
pMakeNodes making a cluster near strand break a=2QUS|1|A|C|12 B=2QUS|1|A|A|53
pMakeNodesCluster: amax is 2 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 2 and then 11 to 12
aa is 2 bb is 11
  3 Cluster   2QUS|1|A|C|12:2QUS|1|A|C|12 2QUS|1|A|A|52:2QUS|1|A|A|53
    LR Inter  2QUS|1|A|C|12 2QUS|1|A|A|52 tSH 
    LR Inter  2QUS|1|A|C|12 2QUS|1|A|A|53 bif 
pMakeNodesCluster a=3 B=10 at the end
pMakeNodesCluster a=3 B=10 at the end
pMakeNodes probe for inserts:  a=2QUS|1|A|A|13 B=2QUS|1|A|A|51
    Insertion on right 2QUS|1|A|A|51
  4 Initial     13 (0 insertion) and   51 (1 insertion)
pMakeNodes probed for insert:  a=2QUS|1|A|A|13 B=2QUS|1|A|C|50
pMakeNodesJunction: a=2QUS|1|A|A|13 r=2QUS|1|A|A|13 s=2QUS|1|A|U|31 t=2QUS|1|A|C|32 u=B=2QUS|1|A|C|50
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 2QUS|1|A|A|13 and 2QUS|1|A|U|31 and between 2QUS|1|A|C|32 and 2QUS|1|A|C|50
pMakeNodesJunction: about to make a junction: a=2QUS|1|A|A|13 s=2QUS|1|A|U|31 t=2QUS|1|A|C|32 B=2QUS|1|A|C|50
pMakeNodesJunction: first branch starts at   2QUS|1|A|A|13
pMakeNodesJunction: first branch ends around 2QUS|1|A|U|31
pMakeNodesJunction: second branch starts at  2QUS|1|A|C|32
pMakeNodesJunction: junction ends at         2QUS|1|A|C|50
pMakeNodesJunction: first branch strand start goes up to  2QUS|1|A|A|13
pMakeNodesJunction: first branch strand end goes down to  2QUS|1|A|U|31
pMakeNodesJunction: second branch strand start goes up to 2QUS|1|A|C|32
pMakeNodesJunction: last strand of junction goes down to  2QUS|1|A|C|50

Junction with 2 loops, call it J6892
Actual Branch 1 of junction J6892 - Nucleotides 2QUS|1|A|A|13 to 2QUS|1|A|U|31, length   2
Actual Branch 2 of junction J6892 - Nucleotides 2QUS|1|A|C|32 to 2QUS|1|A|C|50, length   5
  5 Junction

2B Branch 1 of 2 of junction J6892 - Nucleotides    13 to    31, length   2
pMakeNodes starting loop:     a=2QUS|1|A|A|13 B=2QUS|1|A|U|31
  7 Basepair    13   31 AU cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6892 - Nucleotides    32 to    50, length   5
pMakeNodes starting loop:     a=2QUS|1|A|C|32 B=2QUS|1|A|C|50
  9 Initial     32 (0 insertion) and   50 (0 insertion)
pMakeNodesJunction: a=2QUS|1|A|C|32 r=2QUS|1|A|C|32 s=2QUS|1|A|G|37 t=2QUS|1|A|A|38 u=B=2QUS|1|A|C|50
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2QUS|1|A|C|32 and 2QUS|1|A|G|37 and between 2QUS|1|A|A|38 and 2QUS|1|A|C|50
pMakeNodesJunction: about to make a junction: a=2QUS|1|A|C|32 s=2QUS|1|A|G|37 t=2QUS|1|A|A|38 B=2QUS|1|A|C|50
pMakeNodesJunction: first branch starts at   2QUS|1|A|C|32
pMakeNodesJunction: first branch ends around 2QUS|1|A|G|37
pMakeNodesJunction: second branch starts at  2QUS|1|A|A|38
pMakeNodesJunction: junction ends at         2QUS|1|A|C|50
pMakeNodesJunction: first branch strand start goes up to  2QUS|1|A|C|32
pMakeNodesJunction: first branch strand end goes down to  2QUS|1|A|G|37
pMakeNodesJunction: second branch strand start goes up to 2QUS|1|A|G|39
pMakeNodesJunction: last strand of junction goes down to  2QUS|1|A|C|50

Junction with 2 loops, call it J7481
Actual Branch 1 of junction J7481 - Nucleotides 2QUS|1|A|C|32 to 2QUS|1|A|G|37, length   2
Actual Branch 2 of junction J7481 - Nucleotides 2QUS|1|A|A|38 to 2QUS|1|A|C|50, length   3
 10 Junction

2B Branch 1 of 2 of junction J7481 - Nucleotides    32 to    37, length   2
pMakeNodes starting loop:     a=2QUS|1|A|C|32 B=2QUS|1|A|G|37
 12 Basepair    32   37 CG cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J7481 - Nucleotides    38 to    50, length   3
pMakeNodes starting loop:     a=2QUS|1|A|A|38 B=2QUS|1|A|C|50
    Insertion on left  2QUS|1|A|A|38
pMakeNodesProbeForInsertions:  a 2QUS|1|A|G|39 interacts with 2QUS|1|A|C|50
pMakeNodesProbeForInsertions:  B 2QUS|1|A|C|50 interacts with 2QUS|1|A|G|39
pMakeNodesProbeForInsertions:  B 2QUS|1|A|C|50 interacts with 2QUS|1|A|G|39
 14 Initial     38 (1 insertion) and   50 (0 insertion)
 15 Basepair    39   50 GC cWW 
 16 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 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  10  Junction Left  5 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2QUS|1|A|A|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2QUS|1|A|A|38
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: []
           numbranches: []

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 U11 - A54 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: 2
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'AA'
               Comment: ' // Cluster node 2QUS|1|A|C|12:2QUS|1|A|C|12 and 2QUS|1|A|A|52:2QUS|1|A|A|53'
              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: 0.2813
           numbranches: []

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: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'A'
               Comment: ' // Initial node 2QUS|1|A|A|13 - 2QUS|1|A|A|51 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'J6892'
        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 2QUS|1|A|A|51'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: 'J6892'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: []
           numbranches: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: 'J6892'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A13 - C50 ID J6892'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J6892'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             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 A13 - 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: []
           numbranches: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             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
           numbranches: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J6892'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2QUS|1|A|C|32 - 2QUS|1|A|C|50 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [11 14]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J7481'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C32 - C50 ID J7481'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J7481'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             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 - 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: []
           numbranches: []

Node 15

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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: 'J7481'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 2QUS|1|A|A|38 - 2QUS|1|A|C|50 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2QUS|1|A|A|38'
              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: []
           numbranches: []

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G39 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 20

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   7  Junction Left  3 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   9  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:  10   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  12  Junction Left  5 Right  9
pMakeMotifModelFromSSF:  13   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  14  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  15   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  16   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  17     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  18   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  19  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  20   Hairpin Left  9 Right  8
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J6892'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J6892'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2QUS|1|A|C|32 - 2QUS|1|A|C|50 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_76405.1. Nodes 8 and 11 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J7481'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J7481'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 2QUS|1|A|A|38 - 2QUS|1|A|C|50 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J4_76405.1. Nodes 13 and 16 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_76405.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.4158

Timestamp 18-Jul-2025 00:13:11
pMakeSCFGModels: Making JAR3D model for motif group J4_77044.1, number 56 of 65
pMakeNodes starting loop:     a=5J7L|1|DA|G|2643 B=5J7L|1|DA|C|2771
  2 Basepair  2643 2771 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|2644 B=5J7L|1|DA|G|2770
    Insertion on left  5J7L|1|DA|G|2644
    Insertion on left  5J7L|1|DA|G|2645
pMakeNodes probed for insert:  a=5J7L|1|DA|C|2646 B=5J7L|1|DA|G|2770
pMakeNodesJunction: a=5J7L|1|DA|C|2646 r=5J7L|1|DA|C|2646 s=5J7L|1|DA|G|2674 t=5J7L|1|DA|A|2675 u=B=5J7L|1|DA|G|2770
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|2646 and 5J7L|1|DA|G|2674 and between 5J7L|1|DA|A|2675 and 5J7L|1|DA|G|2770
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|2646 s=5J7L|1|DA|G|2674 t=5J7L|1|DA|A|2675 B=5J7L|1|DA|G|2770
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|2646
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|2674
pMakeNodesJunction: second branch starts at  5J7L|1|DA|A|2675
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|2770
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|2646
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|2674
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|C|2676
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|U|2769

Junction with 2 loops, call it J4505
Actual Branch 1 of junction J4505 - Nucleotides 5J7L|1|DA|C|2646 to 5J7L|1|DA|G|2674, length   2
Actual Branch 2 of junction J4505 - Nucleotides 5J7L|1|DA|A|2675 to 5J7L|1|DA|G|2770, length   9
  3 Junction

2B Branch 1 of 2 of junction J4505 - Nucleotides  2646 to  2674, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|2646 B=5J7L|1|DA|G|2674
  5 Basepair  2646 2674 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J4505 - Nucleotides  2675 to  2770, length   9
pMakeNodes starting loop:     a=5J7L|1|DA|A|2675 B=5J7L|1|DA|G|2770
  7 Initial   2675 (0 insertion) and 2770 (0 insertion)
pMakeNodesJunction: a=5J7L|1|DA|A|2675 r=5J7L|1|DA|A|2675 s=5J7L|1|DA|G|2732 t=5J7L|1|DA|A|2733 u=B=5J7L|1|DA|G|2770
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|A|2675 and 5J7L|1|DA|G|2732 and between 5J7L|1|DA|A|2733 and 5J7L|1|DA|G|2770
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|A|2675 s=5J7L|1|DA|G|2732 t=5J7L|1|DA|A|2733 B=5J7L|1|DA|G|2770
pMakeNodesJunction: first branch starts at   5J7L|1|DA|A|2675
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|2732
pMakeNodesJunction: second branch starts at  5J7L|1|DA|A|2733
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|2770
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|2676
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|2731
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|2735
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|U|2769

Junction with 2 loops, call it J838
Actual Branch 1 of junction J838 - Nucleotides 5J7L|1|DA|A|2675 to 5J7L|1|DA|G|2732, length   4
Actual Branch 2 of junction J838 - Nucleotides 5J7L|1|DA|A|2733 to 5J7L|1|DA|G|2770, length   5
  8 Junction

2B Branch 1 of 2 of junction J838 - Nucleotides  2675 to  2732, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|A|2675 B=5J7L|1|DA|G|2732
 10 Basepair  2675 2732 AG cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|2676 B=5J7L|1|DA|G|2731
 11 Basepair  2676 2731 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J838 - Nucleotides  2733 to  2770, length   5
pMakeNodes starting loop:     a=5J7L|1|DA|A|2733 B=5J7L|1|DA|G|2770
    Insertion on left  5J7L|1|DA|A|2733
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|2734 interacts with 5J7L|1|DA|G|2770
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2770 interacts with 5J7L|1|DA|A|2734
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2770 interacts with 5J7L|1|DA|A|2734
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 13 Initial   2733 (1 insertion) and 2770 (0 insertion)
 14 Basepair  2734 2770 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|2735 B=5J7L|1|DA|U|2769
 15 Basepair  2735 2769 GU cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 14
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
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  14  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:  15  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  16   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2644
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2645
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2733
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: []
           numbranches: []
              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: [0.0082 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: 'GGG'
           RightLetter: 'C'
               Comment: ' // Basepair G2643 - C2771 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J4505'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2644'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J4505'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 5J7L|1|DA|G|2645'
              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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J4505'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C2646 - G2770 ID J4505'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J4505'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C2646 - G2674 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

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: []
           numbranches: []
              NormCons: 1

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: 'J4505'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|2675 - 5J7L|1|DA|G|2770 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J838'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2675 - G2770 ID J838'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J838'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             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 A2675 - G2732 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 C2676 - G2731 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

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: 'J838'
        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|2733 - 5J7L|1|DA|G|2770 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2733'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2734 - G2770 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]
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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: 'U'
               Comment: ' // Basepair G2735 - U2769 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  12  Junction Left  6 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  20  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:  21  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  22   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J4505'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J4505'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|2675 - 5J7L|1|DA|G|2770 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_77044.1. Nodes 8 and 11 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J838'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9940 0.0060 2.9999e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: 'J838'
        leftLengthDist: [0.9940 0.0060 2.9999e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|2733 - 5J7L|1|DA|G|2770 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_77044.1. Nodes 13 and 17 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a junction at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_77044.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0153
   -9.7746
  -10.3772

Timestamp 18-Jul-2025 00:13:11
pMakeSCFGModels: Making JAR3D model for motif group J4_78628.1, number 57 of 65
pMakeNodes starting loop:     a=5J7L|1|DA|G|1444 B=5J7L|1|DA|C|1547
  2 Basepair  1444 1547 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|1445 B=5J7L|1|DA|G|1546
pMakeNodes probed for insert:  a=5J7L|1|DA|G|1445 B=5J7L|1|DA|G|1546
pMakeNodesJunction: a=5J7L|1|DA|G|1445 r=5J7L|1|DA|G|1445 s=5J7L|1|DA|U|1466 t=5J7L|1|DA|U|1467 u=B=5J7L|1|DA|G|1546
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|G|1445 and 5J7L|1|DA|U|1466 and between 5J7L|1|DA|U|1467 and 5J7L|1|DA|G|1546
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|G|1445 s=5J7L|1|DA|U|1466 t=5J7L|1|DA|U|1467 B=5J7L|1|DA|G|1546
pMakeNodesJunction: first branch starts at   5J7L|1|DA|G|1445
pMakeNodesJunction: first branch ends around 5J7L|1|DA|U|1466
pMakeNodesJunction: second branch starts at  5J7L|1|DA|U|1467
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|1546
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|1445
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|U|1466
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|U|1467
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|G|1546

Junction with 2 loops, call it J2289
Actual Branch 1 of junction J2289 - Nucleotides 5J7L|1|DA|G|1445 to 5J7L|1|DA|U|1466, length   2
Actual Branch 2 of junction J2289 - Nucleotides 5J7L|1|DA|U|1467 to 5J7L|1|DA|G|1546, length   4
  3 Junction

2B Branch 1 of 2 of junction J2289 - Nucleotides  1445 to  1466, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|G|1445 B=5J7L|1|DA|U|1466
  5 Basepair  1445 1466 GU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2289 - Nucleotides  1467 to  1546, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|U|1467 B=5J7L|1|DA|G|1546
  7 Initial   1467 (0 insertion) and 1546 (0 insertion)
pMakeNodesJunction: a=5J7L|1|DA|U|1467 r=5J7L|1|DA|U|1467 s=5J7L|1|DA|A|1525 t=5J7L|1|DA|C|1526 u=B=5J7L|1|DA|G|1546
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|U|1467 and 5J7L|1|DA|A|1525 and between 5J7L|1|DA|C|1526 and 5J7L|1|DA|G|1546
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|U|1467 s=5J7L|1|DA|A|1525 t=5J7L|1|DA|C|1526 B=5J7L|1|DA|G|1546
pMakeNodesJunction: first branch starts at   5J7L|1|DA|U|1467
pMakeNodesJunction: first branch ends around 5J7L|1|DA|A|1525
pMakeNodesJunction: second branch starts at  5J7L|1|DA|C|1526
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|1546
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|U|1467
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|A|1525
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|C|1526
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|G|1546

Junction with 2 loops, call it J9133
Actual Branch 1 of junction J9133 - Nucleotides 5J7L|1|DA|U|1467 to 5J7L|1|DA|A|1525, length   2
Actual Branch 2 of junction J9133 - Nucleotides 5J7L|1|DA|C|1526 to 5J7L|1|DA|G|1546, length   2
  8 Junction

2B Branch 1 of 2 of junction J9133 - Nucleotides  1467 to  1525, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|U|1467 B=5J7L|1|DA|A|1525
 10 Basepair  1467 1525 UA cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9133 - Nucleotides  1526 to  1546, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|1526 B=5J7L|1|DA|G|1546
 13 Basepair  1526 1546 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   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: 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: []
           numbranches: []
              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 G1444 - C1547 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: 'J2289'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1445 - G1546 ID J2289'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J2289'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G1445 - U1466 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 'J2289'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|1467 - 5J7L|1|DA|G|1546 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1467 - G1546 ID J9133'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 U1467 - A1525 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

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: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 C1526 - G1546 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 14

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Junction Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J2289'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J2289'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|1467 - 5J7L|1|DA|G|1546 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_78628.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J9133'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9960 0.0040 9.9999e-06]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J9133'
        leftLengthDist: [0.9960 0.0040 9.9999e-06]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_78628.1. Nodes 9 and 12 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_78628.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8455
   -6.8214
   -8.8700
   -7.6657

Timestamp 18-Jul-2025 00:13:12
pMakeSCFGModels: Making JAR3D model for motif group J4_80682.1, number 58 of 65
pMakeNodes starting loop:     a=3ICQ|1|E|U|7 B=3ICQ|1|E|A|66
  2 Basepair     7   66 UA cWW 
pMakeNodes probe for inserts:  a=3ICQ|1|E|U|8 B=3ICQ|1|E|G|65
    Insertion on left  3ICQ|1|E|U|8
    Insertion on left  3ICQ|1|E|A|9
pMakeNodes probed for insert:  a=3ICQ|1|E|A|10 B=3ICQ|1|E|G|65
pMakeNodesJunction: a=3ICQ|1|E|A|10 r=3ICQ|1|E|A|10 s=3ICQ|1|E|C|25 t=3ICQ|1|E|G|26 u=B=3ICQ|1|E|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3ICQ|1|E|A|10 and 3ICQ|1|E|C|25 and between 3ICQ|1|E|G|26 and 3ICQ|1|E|G|65
pMakeNodesJunction: about to make a junction: a=3ICQ|1|E|A|10 s=3ICQ|1|E|C|25 t=3ICQ|1|E|G|26 B=3ICQ|1|E|G|65
pMakeNodesJunction: first branch starts at   3ICQ|1|E|A|10
pMakeNodesJunction: first branch ends around 3ICQ|1|E|C|25
pMakeNodesJunction: second branch starts at  3ICQ|1|E|G|26
pMakeNodesJunction: junction ends at         3ICQ|1|E|G|65
pMakeNodesJunction: first branch strand start goes up to  3ICQ|1|E|C|11
pMakeNodesJunction: first branch strand end goes down to  3ICQ|1|E|G|24
pMakeNodesJunction: second branch strand start goes up to 3ICQ|1|E|C|27
pMakeNodesJunction: last strand of junction goes down to  3ICQ|1|E|G|65

Junction with 2 loops, call it J1523
Actual Branch 1 of junction J1523 - Nucleotides 3ICQ|1|E|A|10 to 3ICQ|1|E|C|25, length   4
Actual Branch 2 of junction J1523 - Nucleotides 3ICQ|1|E|G|26 to 3ICQ|1|E|G|65, length  10
  3 Junction

2B Branch 1 of 2 of junction J1523 - Nucleotides    10 to    25, length   4
pMakeNodes starting loop:     a=3ICQ|1|E|A|10 B=3ICQ|1|E|C|25
  5 Basepair    10   25 AC cWW 
No need to probe because of interaction between a=3ICQ|1|E|C|11 B=3ICQ|1|E|G|24
  6 Basepair    11   24 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1523 - Nucleotides    26 to    65, length  10
pMakeNodes starting loop:     a=3ICQ|1|E|G|26 B=3ICQ|1|E|G|65
  8 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=3ICQ|1|E|G|26 r=3ICQ|1|E|G|26 s=3ICQ|1|E|A|44 t=3ICQ|1|E|G|45 u=B=3ICQ|1|E|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3ICQ|1|E|G|26 and 3ICQ|1|E|A|44 and between 3ICQ|1|E|G|45 and 3ICQ|1|E|G|65
pMakeNodesJunction: about to make a junction: a=3ICQ|1|E|G|26 s=3ICQ|1|E|A|44 t=3ICQ|1|E|G|45 B=3ICQ|1|E|G|65
pMakeNodesJunction: first branch starts at   3ICQ|1|E|G|26
pMakeNodesJunction: first branch ends around 3ICQ|1|E|A|44
pMakeNodesJunction: second branch starts at  3ICQ|1|E|G|45
pMakeNodesJunction: junction ends at         3ICQ|1|E|G|65
pMakeNodesJunction: first branch strand start goes up to  3ICQ|1|E|C|27
pMakeNodesJunction: first branch strand end goes down to  3ICQ|1|E|G|43
pMakeNodesJunction: second branch strand start goes up to 3ICQ|1|E|C|49
pMakeNodesJunction: last strand of junction goes down to  3ICQ|1|E|G|65

Junction with 2 loops, call it J8258
Actual Branch 1 of junction J8258 - Nucleotides 3ICQ|1|E|G|26 to 3ICQ|1|E|A|44, length   4
Actual Branch 2 of junction J8258 - Nucleotides 3ICQ|1|E|G|45 to 3ICQ|1|E|G|65, length   6
  9 Junction

2B Branch 1 of 2 of junction J8258 - Nucleotides    26 to    44, length   4
pMakeNodes starting loop:     a=3ICQ|1|E|G|26 B=3ICQ|1|E|A|44
 11 Basepair    26   44 GA cWW 
No need to probe because of interaction between a=3ICQ|1|E|C|27 B=3ICQ|1|E|G|43
 12 Basepair    27   43 CG cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J8258 - Nucleotides    45 to    65, length   6
pMakeNodes starting loop:     a=3ICQ|1|E|G|45 B=3ICQ|1|E|G|65
    Insertion on left  3ICQ|1|E|G|45
    Insertion on left  3ICQ|1|E|G|46
    Insertion on left  3ICQ|1|E|U|47
    Insertion on left  3ICQ|1|E|C|48
pMakeNodesProbeForInsertions:  a 3ICQ|1|E|C|49 interacts with 3ICQ|1|E|G|65
pMakeNodesProbeForInsertions:  B 3ICQ|1|E|G|65 interacts with 3ICQ|1|E|C|49
pMakeNodesProbeForInsertions:  B 3ICQ|1|E|G|65 interacts with 3ICQ|1|E|C|49
 14 Initial     45 (4 insertion) and   65 (0 insertion)
 15 Basepair    49   65 CG cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 17
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
pMakeMotifModelFromSSF:   8   Initial Left  8 Right 17
pMakeMotifModelFromSSF:   9  Junction Left  8 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  14   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  15  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  16   Hairpin Left 17 Right 16
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|G|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|G|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|U|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3ICQ|1|E|C|48
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: []
           numbranches: []
              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: 'UUA'
           RightLetter: 'A'
               Comment: ' // Basepair U7 - A66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J1523'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3ICQ|1|E|U|8'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J1523'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 3ICQ|1|E|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]
           numbranches: []
              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: '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]
           numbranches: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: 'J1523'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A10 - G65 ID J1523'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J1523'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             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 A10 - 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]
           numbranches: []
              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 C11 - G24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: 'J1523'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3ICQ|1|E|G|26 - 3ICQ|1|E|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 14]
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: 'J8258'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G26 - G65 ID J8258'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8258'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G26 - 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]
           numbranches: []
              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 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]
           numbranches: []
              NormCons: []

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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: 'J8258'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGUC'
           RightLetter: []
               Comment: ' // Initial node 3ICQ|1|E|G|45 - 3ICQ|1|E|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 12
            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 3ICQ|1|E|G|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 13
            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: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 13
            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 3ICQ|1|E|G|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 14
            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: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 14
            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 3ICQ|1|E|U|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 15
            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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 15
            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 3ICQ|1|E|C|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             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 C49 - G65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 30
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  4 Right 17
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 17
pMakeMotifModelFromSSF:  13  Junction Left  8 Right 17
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
pMakeMotifModelFromSSF:  18   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  19     Fixed Left 12 Right 17
pMakeMotifModelFromSSF:  20   Initial Left 13 Right 17
pMakeMotifModelFromSSF:  21     Fixed Left 13 Right 17
pMakeMotifModelFromSSF:  22   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  23     Fixed Left 14 Right 17
pMakeMotifModelFromSSF:  24   Initial Left 15 Right 17
pMakeMotifModelFromSSF:  25     Fixed Left 15 Right 17
pMakeMotifModelFromSSF:  26   Initial Left 16 Right 17
pMakeMotifModelFromSSF:  27  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:  28   Hairpin Left 17 Right 16
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J1523'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.4934 0.4934 0.0126 6.0168e-04]
       rightLetterDist: [0.5000 0.1667 0.1667 0.1667 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: 'J1523'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3ICQ|1|E|G|26 - 3ICQ|1|E|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_80682.1. Nodes 8 and 12 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J8258'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: 'J8258'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGUC'
           RightLetter: []
               Comment: ' // Initial node 3ICQ|1|E|G|45 - 3ICQ|1|E|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_80682.1. Nodes 14 and 18 both model an insertion before position 12. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 2 and 14
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 2 and 14
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_80682.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.9226
  -17.7102

Timestamp 18-Jul-2025 00:13:13
pMakeSCFGModels: Making JAR3D model for motif group J4_89787.1, number 59 of 65
pMakeNodes starting loop:     a=4V9F|1|0|C|1374 B=4V9F|1|0|G|2051
  2 Basepair  1374 2051 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1375 B=4V9F|1|0|G|2050
    Insertion on left  4V9F|1|0|A|1375
    Insertion on left  4V9F|1|0|G|1376
    Insertion on left  4V9F|1|0|C|1377
    Insertion on left  4V9F|1|0|A|1379
    Insertion on left  4V9F|1|0|A|1381
pMakeNodes probed for insert:  a=4V9F|1|0|G|1382 B=4V9F|1|0|G|2050
pMakeNodesJunction: a=4V9F|1|0|G|1382 r=4V9F|1|0|G|1382 s=4V9F|1|0|C|1400 t=4V9F|1|0|G|1401 u=B=4V9F|1|0|G|2050
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|1382 and 4V9F|1|0|C|1400 and between 4V9F|1|0|G|1401 and 4V9F|1|0|G|2050
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|1382 s=4V9F|1|0|C|1400 t=4V9F|1|0|G|1401 B=4V9F|1|0|G|2050
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|1382
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|1400
pMakeNodesJunction: second branch starts at  4V9F|1|0|G|1401
pMakeNodesJunction: junction ends at         4V9F|1|0|G|2050
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|1382
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|1400
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|1401
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|G|2050

Junction with 2 loops, call it J5383
Actual Branch 1 of junction J5383 - Nucleotides 4V9F|1|0|G|1382 to 4V9F|1|0|C|1400, length   2
Actual Branch 2 of junction J5383 - Nucleotides 4V9F|1|0|G|1401 to 4V9F|1|0|G|2050, length   7
  3 Junction

2B Branch 1 of 2 of junction J5383 - Nucleotides  1382 to  1400, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|1382 B=4V9F|1|0|C|1400
  5 Basepair  1382 1400 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J5383 - Nucleotides  1401 to  2050, length   7
pMakeNodes starting loop:     a=4V9F|1|0|G|1401 B=4V9F|1|0|G|2050
  7 Initial   1401 (0 insertion) and 2050 (0 insertion)
pMakeNodesJunction: a=4V9F|1|0|G|1401 r=4V9F|1|0|G|1401 s=4V9F|1|0|C|1721 t=4V9F|1|0|U|1722 u=B=4V9F|1|0|G|2050
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|1401 and 4V9F|1|0|C|1721 and between 4V9F|1|0|U|1722 and 4V9F|1|0|G|2050
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|1401 s=4V9F|1|0|C|1721 t=4V9F|1|0|U|1722 B=4V9F|1|0|G|2050
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|1401
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|1721
pMakeNodesJunction: second branch starts at  4V9F|1|0|U|1722
pMakeNodesJunction: junction ends at         4V9F|1|0|G|2050
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|1401
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|1721
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|C|1725
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|G|2050

Junction with 2 loops, call it J9961
Actual Branch 1 of junction J9961 - Nucleotides 4V9F|1|0|G|1401 to 4V9F|1|0|C|1721, length   2
Actual Branch 2 of junction J9961 - Nucleotides 4V9F|1|0|U|1722 to 4V9F|1|0|G|2050, length   5
  8 Junction

2B Branch 1 of 2 of junction J9961 - Nucleotides  1401 to  1721, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|1401 B=4V9F|1|0|C|1721
 10 Basepair  1401 1721 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9961 - Nucleotides  1722 to  2050, length   5
pMakeNodes starting loop:     a=4V9F|1|0|U|1722 B=4V9F|1|0|G|2050
    Insertion on left  4V9F|1|0|U|1722
    Insertion on left  4V9F|1|0|G|1723
    Insertion on left  4V9F|1|0|U|1724
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|1725 interacts with 4V9F|1|0|G|2050
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|2050 interacts with 4V9F|1|0|C|1725
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|2050 interacts with 4V9F|1|0|C|1725
 12 Initial   1722 (3 insertion) and 2050 (0 insertion)
 13 Basepair  1725 2050 CG cWW 
 14 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  7 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 15
pMakeMotifModelFromSSF:   8  Junction Left  9 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  12   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  13  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  14   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|1375
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|1376
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|1377
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|1378
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|1379
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|1401
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|1721
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|1722
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: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAGCAA'
           RightLetter: 'G'
               Comment: ' // Basepair C1374 - G2051 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J5383'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1375'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5383'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 4V9F|1|0|G|1376'
              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]
           numbranches: []
              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: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J5383'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1377'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'J9961'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J9961'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1378'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: '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]
           numbranches: []
              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 4V9F|1|0|A|1379'
              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: []
           numbranches: []
              NormCons: 1

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: 'J9961'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UGU'
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: 'J5383'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1382 - G2050 ID J5383'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J5383'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1382 - C1400 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

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: []
           numbranches: []
              NormCons: 1

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: 'J5383'
        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|0|G|1401 - 4V9F|1|0|G|2050 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: 'J9961'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1401 - G2050 ID J9961'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9961'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 G1401 - C1721 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

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: []
           numbranches: []
              NormCons: 1

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: 'J9961'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGU'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|U|1722 - 4V9F|1|0|G|2050 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 11
            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 4V9F|1|0|G|1401'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
           numbranches: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 12
            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 4V9F|1|0|C|1721'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 13
            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: []
           numbranches: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 28
             LeftIndex: 13
            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 4V9F|1|0|U|1722'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 30
             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 C1725 - G2050 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 32
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  7 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  18  Junction Left  9 Right 15
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  20  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  21   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  22   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  23     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 15
pMakeMotifModelFromSSF:  26   Initial Left 13 Right 15
pMakeMotifModelFromSSF:  27     Fixed Left 13 Right 15
pMakeMotifModelFromSSF:  28   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  29  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  30   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J5383'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: 'J5383'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|1401 - 4V9F|1|0|G|2050 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_89787.1. Nodes 14 and 17 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9961'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: 'J9961'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGU'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|U|1722 - 4V9F|1|0|G|2050 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_89787.1. Nodes 19 and 22 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a hairpin at node 30
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin
pNextNodeJunction: Finished at node 30 out of 30, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_89787.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.8358

Timestamp 18-Jul-2025 00:13:13
pMakeSCFGModels: Making JAR3D model for motif group J4_91813.1, number 60 of 65
pMakeNodes starting loop:     a=7A0S|1|X|A|1458 B=7A0S|1|X|U|1563
  2 Basepair  1458 1563 AU cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|1460 B=7A0S|1|X|G|1562
pMakeNodes probed for insert:  a=7A0S|1|X|G|1460 B=7A0S|1|X|G|1562
pMakeNodesJunction: a=7A0S|1|X|G|1460 r=7A0S|1|X|G|1460 s=7A0S|1|X|U|1481 t=7A0S|1|X|U|1482 u=B=7A0S|1|X|G|1562
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|G|1460 and 7A0S|1|X|U|1481 and between 7A0S|1|X|U|1482 and 7A0S|1|X|G|1562
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|G|1460 s=7A0S|1|X|U|1481 t=7A0S|1|X|U|1482 B=7A0S|1|X|G|1562
pMakeNodesJunction: first branch starts at   7A0S|1|X|G|1460
pMakeNodesJunction: first branch ends around 7A0S|1|X|U|1481
pMakeNodesJunction: second branch starts at  7A0S|1|X|U|1482
pMakeNodesJunction: junction ends at         7A0S|1|X|G|1562
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|1460
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|U|1481
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|U|1482
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|1558

Junction with 2 loops, call it J781
Actual Branch 1 of junction J781 - Nucleotides 7A0S|1|X|G|1460 to 7A0S|1|X|U|1481, length   2
Actual Branch 2 of junction J781 - Nucleotides 7A0S|1|X|U|1482 to 7A0S|1|X|G|1562, length  11
  3 Junction

2B Branch 1 of 2 of junction J781 - Nucleotides  1460 to  1481, length   2
pMakeNodes starting loop:     a=7A0S|1|X|G|1460 B=7A0S|1|X|U|1481
  5 Basepair  1460 1481 GU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J781 - Nucleotides  1482 to  1562, length  11
pMakeNodes starting loop:     a=7A0S|1|X|U|1482 B=7A0S|1|X|G|1562
  7 Initial   1482 (0 insertion) and 1562 (0 insertion)
pMakeNodesJunction: a=7A0S|1|X|U|1482 r=7A0S|1|X|U|1482 s=7A0S|1|X|G|1541 t=7A0S|1|X|G|1542 u=B=7A0S|1|X|G|1562
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|U|1482 and 7A0S|1|X|G|1541 and between 7A0S|1|X|G|1542 and 7A0S|1|X|G|1562
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|U|1482 s=7A0S|1|X|G|1541 t=7A0S|1|X|G|1542 B=7A0S|1|X|G|1562
pMakeNodesJunction: first branch starts at   7A0S|1|X|U|1482
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|1541
pMakeNodesJunction: second branch starts at  7A0S|1|X|G|1542
pMakeNodesJunction: junction ends at         7A0S|1|X|G|1562
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|U|1482
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|G|1541
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|1545
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|1558

Junction with 2 loops, call it J4426
Actual Branch 1 of junction J4426 - Nucleotides 7A0S|1|X|U|1482 to 7A0S|1|X|G|1541, length   2
Actual Branch 2 of junction J4426 - Nucleotides 7A0S|1|X|G|1542 to 7A0S|1|X|G|1562, length   9
  8 Junction

2B Branch 1 of 2 of junction J4426 - Nucleotides  1482 to  1541, length   2
pMakeNodes starting loop:     a=7A0S|1|X|U|1482 B=7A0S|1|X|G|1541
 10 Basepair  1482 1541 UG cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J4426 - Nucleotides  1542 to  1562, length   9
pMakeNodes starting loop:     a=7A0S|1|X|G|1542 B=7A0S|1|X|G|1562
 13 Basepair  1542 1562 GG bif 
No need to probe because of interaction between a=7A0S|1|X|G|1543 B=7A0S|1|X|A|1561
 14 Basepair  1543 1561 GA tSH 
pMakeNodes probe for inserts:  a=7A0S|1|X|A|1544 B=7A0S|1|X|A|1560
    Insertion on right 7A0S|1|X|A|1560
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|1544 interacts with 7A0S|1|X|G|1559
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|1559 interacts with 7A0S|1|X|A|1544
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|1559 interacts with 7A0S|1|X|A|1544
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7A0S|1|X|A|1544 B=7A0S|1|X|G|1559
 15 Basepair  1544 1559 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|G|1545 B=7A0S|1|X|C|1558
 16 Basepair  1545 1558 GC cWW 
 17 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right 13
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|1559
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: []
           numbranches: []
              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: [0.9950 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 A1458 - U1563 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: 'J781'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1460 - G1562 ID J781'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J781'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G1460 - 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 14
             Insertion: []
                    id: 'J781'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|1482 - 7A0S|1|X|G|1562 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 12]
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J4426'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1482 - G1562 ID J4426'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J4426'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 U1482 - G1541 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

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: []
           numbranches: []
              NormCons: 1

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J4426'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            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: 'G'
               Comment: ' // Basepair G1542 - G1562 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]
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 13
             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 G1543 - A1561 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]
           numbranches: []
              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: 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|1559'
              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]
           numbranches: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             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: '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]
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             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 A1544 - G1559 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]
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             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 G1545 - 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]
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right 13
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  17  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  18  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  19   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J781'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J781'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|1482 - 7A0S|1|X|G|1562 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_91813.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J4426'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J4426'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_91813.1. Nodes 9 and 12 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_91813.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4452

Timestamp 18-Jul-2025 00:13:14
pMakeSCFGModels: Making JAR3D model for motif group J4_91882.1, number 61 of 65
pMakeNodes starting loop:     a=2AKE|1|B|G|7 B=2AKE|1|B|C|66
  2 Basepair     7   66 GC cWW 
pMakeNodes probe for inserts:  a=2AKE|1|B|G|10 B=2AKE|1|B|U|65
pMakeNodes probed for insert:  a=2AKE|1|B|G|10 B=2AKE|1|B|U|65
pMakeNodesJunction: a=2AKE|1|B|G|10 r=2AKE|1|B|G|10 s=2AKE|1|B|C|25 t=2AKE|1|B|G|26 u=B=2AKE|1|B|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 2AKE|1|B|G|10 and 2AKE|1|B|C|25 and between 2AKE|1|B|G|26 and 2AKE|1|B|U|65
pMakeNodesJunction: about to make a junction: a=2AKE|1|B|G|10 s=2AKE|1|B|C|25 t=2AKE|1|B|G|26 B=2AKE|1|B|U|65
pMakeNodesJunction: first branch starts at   2AKE|1|B|G|10
pMakeNodesJunction: first branch ends around 2AKE|1|B|C|25
pMakeNodesJunction: second branch starts at  2AKE|1|B|G|26
pMakeNodesJunction: junction ends at         2AKE|1|B|U|65
pMakeNodesJunction: first branch strand start goes up to  2AKE|1|B|G|10
pMakeNodesJunction: first branch strand end goes down to  2AKE|1|B|C|25
pMakeNodesJunction: second branch strand start goes up to 2AKE|1|B|U|27
pMakeNodesJunction: last strand of junction goes down to  2AKE|1|B|U|65

Junction with 2 loops, call it J1066
Actual Branch 1 of junction J1066 - Nucleotides 2AKE|1|B|G|10 to 2AKE|1|B|C|25, length   2
Actual Branch 2 of junction J1066 - Nucleotides 2AKE|1|B|G|26 to 2AKE|1|B|U|65, length   8
  3 Junction

2B Branch 1 of 2 of junction J1066 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=2AKE|1|B|G|10 B=2AKE|1|B|C|25
  5 Basepair    10   25 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1066 - Nucleotides    26 to    65, length   8
pMakeNodes starting loop:     a=2AKE|1|B|G|26 B=2AKE|1|B|U|65
  7 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=2AKE|1|B|G|26 r=2AKE|1|B|G|26 s=2AKE|1|B|A|44 t=2AKE|1|B|U|47 u=B=2AKE|1|B|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2AKE|1|B|G|26 and 2AKE|1|B|A|44 and between 2AKE|1|B|U|47 and 2AKE|1|B|U|65
pMakeNodesJunction: about to make a junction: a=2AKE|1|B|G|26 s=2AKE|1|B|A|44 t=2AKE|1|B|U|47 B=2AKE|1|B|U|65
pMakeNodesJunction: first branch starts at   2AKE|1|B|G|26
pMakeNodesJunction: first branch ends around 2AKE|1|B|A|44
pMakeNodesJunction: second branch starts at  2AKE|1|B|U|47
pMakeNodesJunction: junction ends at         2AKE|1|B|U|65
pMakeNodesJunction: first branch strand start goes up to  2AKE|1|B|U|27
pMakeNodesJunction: first branch strand end goes down to  2AKE|1|B|A|43
pMakeNodesJunction: second branch strand start goes up to 2AKE|1|B|G|49
pMakeNodesJunction: last strand of junction goes down to  2AKE|1|B|U|65

Junction with 2 loops, call it J9618
Actual Branch 1 of junction J9618 - Nucleotides 2AKE|1|B|G|26 to 2AKE|1|B|A|44, length   4
Actual Branch 2 of junction J9618 - Nucleotides 2AKE|1|B|U|47 to 2AKE|1|B|U|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J9618 - Nucleotides    26 to    44, length   4
pMakeNodes starting loop:     a=2AKE|1|B|G|26 B=2AKE|1|B|A|44
 10 Basepair    26   44 GA cWW 
No need to probe because of interaction between a=2AKE|1|B|U|27 B=2AKE|1|B|A|43
 11 Basepair    27   43 UA cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J9618 - Nucleotides    47 to    65, length   4
pMakeNodes starting loop:     a=2AKE|1|B|U|47 B=2AKE|1|B|U|65
    Insertion on left  2AKE|1|B|U|47
    Insertion on left  2AKE|1|B|U|48
pMakeNodesProbeForInsertions:  a 2AKE|1|B|G|49 interacts with 2AKE|1|B|U|65
pMakeNodesProbeForInsertions:  B 2AKE|1|B|U|65 interacts with 2AKE|1|B|G|49
pMakeNodesProbeForInsertions:  B 2AKE|1|B|U|65 interacts with 2AKE|1|B|G|49
 13 Initial     47 (2 insertion) and   65 (0 insertion)
 14 Basepair    49   65 GU cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2AKE|1|B|A|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2AKE|1|B|A|44
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: 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: []
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - 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]
           numbranches: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: 'J1066'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - U65 ID J1066'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J1066'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             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 G10 - 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]
           numbranches: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             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: []
           numbranches: []
              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: 11
             Insertion: []
                    id: 'J1066'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2AKE|1|B|G|26 - 2AKE|1|B|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J9618'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G26 - U65 ID J9618'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J9618'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             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 G26 - 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]
           numbranches: []
              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 U27 - A43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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: 'J9618'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 2AKE|1|B|U|47 - 2AKE|1|B|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 2AKE|1|B|A|43'
              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]
           numbranches: []
              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: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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 2AKE|1|B|A|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G49 - U65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 19

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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
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 junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J1066'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J1066'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 2AKE|1|B|G|26 - 2AKE|1|B|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_91882.1. Nodes 4 and 7 both model an insertion before position 4. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J9618'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0 0.0238 0.9512 0.0238 0.0012]
       rightLetterDist: [0.0833 0.0833 0.4167 0.4167 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J9618'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 2AKE|1|B|U|47 - 2AKE|1|B|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_91882.1. Nodes 9 and 13 both model an insertion before position 8. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a junction at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_91882.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.4659
  -14.8904

Timestamp 18-Jul-2025 00:13:14
pMakeSCFGModels: Making JAR3D model for motif group J4_94519.1, number 62 of 65
pMakeNodes starting loop:     a=4V90|1|AV|A|7 B=4V90|1|AV|U|66
  2 Basepair     7   66 AU cWW 
pMakeNodes probe for inserts:  a=4V90|1|AV|A|9 B=4V90|1|AV|G|65
    Insertion on left  4V90|1|AV|A|9
pMakeNodes probed for insert:  a=4V90|1|AV|G|10 B=4V90|1|AV|G|65
pMakeNodesJunction: a=4V90|1|AV|G|10 r=4V90|1|AV|G|10 s=4V90|1|AV|C|25 t=4V90|1|AV|A|26 u=B=4V90|1|AV|G|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 6
pMakeNodesJunction: Found nested interactions between 4V90|1|AV|G|10 and 4V90|1|AV|C|25 and between 4V90|1|AV|A|26 and 4V90|1|AV|G|65
pMakeNodesJunction: about to make a junction: a=4V90|1|AV|G|10 s=4V90|1|AV|C|25 t=4V90|1|AV|A|26 B=4V90|1|AV|G|65
pMakeNodesJunction: first branch starts at   4V90|1|AV|G|10
pMakeNodesJunction: first branch ends around 4V90|1|AV|C|25
pMakeNodesJunction: second branch starts at  4V90|1|AV|A|26
pMakeNodesJunction: junction ends at         4V90|1|AV|G|65
pMakeNodesJunction: first branch strand start goes up to  4V90|1|AV|G|10
pMakeNodesJunction: first branch strand end goes down to  4V90|1|AV|C|25
pMakeNodesJunction: second branch strand start goes up to 4V90|1|AV|G|28
pMakeNodesJunction: last strand of junction goes down to  4V90|1|AV|G|65

Junction with 2 loops, call it J46
Actual Branch 1 of junction J46 - Nucleotides 4V90|1|AV|G|10 to 4V90|1|AV|C|25, length   2
Actual Branch 2 of junction J46 - Nucleotides 4V90|1|AV|A|26 to 4V90|1|AV|G|65, length  10
  3 Junction

2B Branch 1 of 2 of junction J46 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=4V90|1|AV|G|10 B=4V90|1|AV|C|25
  5 Basepair    10   25 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J46 - Nucleotides    26 to    65, length  10
pMakeNodes starting loop:     a=4V90|1|AV|A|26 B=4V90|1|AV|G|65
  7 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=4V90|1|AV|A|26 r=4V90|1|AV|A|26 s=4V90|1|AV|G|44 t=4V90|1|AV|U|45 u=B=4V90|1|AV|G|65
pMakeNodesJunction: a:s count 4
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V90|1|AV|A|26 and 4V90|1|AV|G|44 and between 4V90|1|AV|U|45 and 4V90|1|AV|G|65
pMakeNodesJunction: about to make a junction: a=4V90|1|AV|A|26 s=4V90|1|AV|G|44 t=4V90|1|AV|U|45 B=4V90|1|AV|G|65
pMakeNodesJunction: first branch starts at   4V90|1|AV|A|26
pMakeNodesJunction: first branch ends around 4V90|1|AV|G|44
pMakeNodesJunction: second branch starts at  4V90|1|AV|U|45
pMakeNodesJunction: junction ends at         4V90|1|AV|G|65
pMakeNodesJunction: first branch strand start goes up to  4V90|1|AV|G|28
pMakeNodesJunction: first branch strand end goes down to  4V90|1|AV|C|42
pMakeNodesJunction: second branch strand start goes up to 4V90|1|AV|C|49
pMakeNodesJunction: last strand of junction goes down to  4V90|1|AV|G|65

Junction with 2 loops, call it J7749
Actual Branch 1 of junction J7749 - Nucleotides 4V90|1|AV|A|26 to 4V90|1|AV|G|44, length   6
Actual Branch 2 of junction J7749 - Nucleotides 4V90|1|AV|U|45 to 4V90|1|AV|G|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J7749 - Nucleotides    26 to    44, length   6
pMakeNodes starting loop:     a=4V90|1|AV|A|26 B=4V90|1|AV|G|44
 10 Basepair    26   44 AG cWW 
No need to probe because of interaction between a=4V90|1|AV|G|27 B=4V90|1|AV|C|43
 11 Basepair    27   43 GC cWW 
No need to probe because of interaction between a=4V90|1|AV|G|28 B=4V90|1|AV|C|42
 12 Basepair    28   42 GC cWW 
 13 Hairpin type *

2B Branch 2 of 2 of junction J7749 - Nucleotides    45 to    65, length   4
pMakeNodes starting loop:     a=4V90|1|AV|U|45 B=4V90|1|AV|G|65
    Insertion on left  4V90|1|AV|U|45
    Insertion on left  4V90|1|AV|G|46
pMakeNodesProbeForInsertions:  a 4V90|1|AV|C|49 interacts with 4V90|1|AV|G|65
pMakeNodesProbeForInsertions:  B 4V90|1|AV|G|65 interacts with 4V90|1|AV|C|49
pMakeNodesProbeForInsertions:  B 4V90|1|AV|G|65 interacts with 4V90|1|AV|C|49
 14 Initial     45 (2 insertion) and   65 (0 insertion)
 15 Basepair    49   65 CG cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  14   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  15  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  16   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V90|1|AV|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V90|1|AV|G|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V90|1|AV|U|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: 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: []
           numbranches: []
              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: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A7 - U66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J46'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V90|1|AV|U|8'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J46'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: 'J46'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - G65 ID J46'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J46'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G10 - 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]
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             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: []
           numbranches: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: 'J46'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V90|1|AV|A|26 - 4V90|1|AV|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 14]
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: 'J7749'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A26 - G65 ID J7749'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J7749'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             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 A26 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G27 - 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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 G28 - C42 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: []
           numbranches: []
              NormCons: 1

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J7749'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: []
               Comment: ' // Initial node 4V90|1|AV|U|45 - 4V90|1|AV|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             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 4V90|1|AV|G|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             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: []
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 12
            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 4V90|1|AV|U|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             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: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             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 C49 - G65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 14
pMakeMotifModelFromSSF:  10  Junction Left  5 Right 14
pMakeMotifModelFromSSF:  11   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  16   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  17     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  18   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  19     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  20   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  21  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  22   Hairpin Left 14 Right 13
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: 'J46'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: 'J46'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V90|1|AV|A|26 - 4V90|1|AV|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_94519.1. Nodes 6 and 9 both model an insertion before position 5. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J7749'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9920 0.0080 4.9998e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: 'J7749'
        leftLengthDist: [0.9920 0.0080 4.9998e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: []
               Comment: ' // Initial node 4V90|1|AV|U|45 - 4V90|1|AV|G|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_94519.1. Nodes 11 and 16 both model an insertion before position 11. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 11
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 3 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_94519.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.6104
  -12.8037

Timestamp 18-Jul-2025 00:13:15
pMakeSCFGModels: Making JAR3D model for motif group J4_97835.1, number 63 of 65
pMakeNodes starting loop:     a=6ORD|1|QY|U|6 B=6ORD|1|QY|A|67
  2 Basepair     6   67 UA cWW 
pMakeNodes probe for inserts:  a=6ORD|1|QY|A|7 B=6ORD|1|QY|U|66
    Insertion on left  6ORD|1|QY|A|7
    Insertion on left  6ORD|1|QY|A|9
    Insertion on right 6ORD|1|QY|U|66
pMakeNodes probed for insert:  a=6ORD|1|QY|G|10 B=6ORD|1|QY|U|65
pMakeNodesJunction: a=6ORD|1|QY|G|10 r=6ORD|1|QY|G|10 s=6ORD|1|QY|C|25 t=6ORD|1|QY|G|26 u=B=6ORD|1|QY|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6ORD|1|QY|G|10 and 6ORD|1|QY|C|25 and between 6ORD|1|QY|G|26 and 6ORD|1|QY|U|65
pMakeNodesJunction: about to make a junction: a=6ORD|1|QY|G|10 s=6ORD|1|QY|C|25 t=6ORD|1|QY|G|26 B=6ORD|1|QY|U|65
pMakeNodesJunction: first branch starts at   6ORD|1|QY|G|10
pMakeNodesJunction: first branch ends around 6ORD|1|QY|C|25
pMakeNodesJunction: second branch starts at  6ORD|1|QY|G|26
pMakeNodesJunction: junction ends at         6ORD|1|QY|U|65
pMakeNodesJunction: first branch strand start goes up to  6ORD|1|QY|G|10
pMakeNodesJunction: first branch strand end goes down to  6ORD|1|QY|C|25
pMakeNodesJunction: second branch strand start goes up to 6ORD|1|QY|C|27
pMakeNodesJunction: last strand of junction goes down to  6ORD|1|QY|U|65

Junction with 2 loops, call it J8173
Actual Branch 1 of junction J8173 - Nucleotides 6ORD|1|QY|G|10 to 6ORD|1|QY|C|25, length   2
Actual Branch 2 of junction J8173 - Nucleotides 6ORD|1|QY|G|26 to 6ORD|1|QY|U|65, length   8
  3 Junction

2B Branch 1 of 2 of junction J8173 - Nucleotides    10 to    25, length   2
pMakeNodes starting loop:     a=6ORD|1|QY|G|10 B=6ORD|1|QY|C|25
  5 Basepair    10   25 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J8173 - Nucleotides    26 to    65, length   8
pMakeNodes starting loop:     a=6ORD|1|QY|G|26 B=6ORD|1|QY|U|65
  7 Initial     26 (0 insertion) and   65 (0 insertion)
pMakeNodesJunction: a=6ORD|1|QY|G|26 r=6ORD|1|QY|G|26 s=6ORD|1|QY|A|44 t=6ORD|1|QY|G|45 u=B=6ORD|1|QY|U|65
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6ORD|1|QY|G|26 and 6ORD|1|QY|A|44 and between 6ORD|1|QY|G|45 and 6ORD|1|QY|U|65
pMakeNodesJunction: about to make a junction: a=6ORD|1|QY|G|26 s=6ORD|1|QY|A|44 t=6ORD|1|QY|G|45 B=6ORD|1|QY|U|65
pMakeNodesJunction: first branch starts at   6ORD|1|QY|G|26
pMakeNodesJunction: first branch ends around 6ORD|1|QY|A|44
pMakeNodesJunction: second branch starts at  6ORD|1|QY|G|45
pMakeNodesJunction: junction ends at         6ORD|1|QY|U|65
pMakeNodesJunction: first branch strand start goes up to  6ORD|1|QY|C|27
pMakeNodesJunction: first branch strand end goes down to  6ORD|1|QY|G|43
pMakeNodesJunction: second branch strand start goes up to 6ORD|1|QY|A|49
pMakeNodesJunction: last strand of junction goes down to  6ORD|1|QY|U|65

Junction with 2 loops, call it J8686
Actual Branch 1 of junction J8686 - Nucleotides 6ORD|1|QY|G|26 to 6ORD|1|QY|A|44, length   4
Actual Branch 2 of junction J8686 - Nucleotides 6ORD|1|QY|G|45 to 6ORD|1|QY|U|65, length   4
  8 Junction

2B Branch 1 of 2 of junction J8686 - Nucleotides    26 to    44, length   4
pMakeNodes starting loop:     a=6ORD|1|QY|G|26 B=6ORD|1|QY|A|44
 10 Basepair    26   44 GA cWW 
No need to probe because of interaction between a=6ORD|1|QY|C|27 B=6ORD|1|QY|G|43
 11 Basepair    27   43 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J8686 - Nucleotides    45 to    65, length   4
pMakeNodes starting loop:     a=6ORD|1|QY|G|45 B=6ORD|1|QY|U|65
    Insertion on left  6ORD|1|QY|G|45
    Insertion on left  6ORD|1|QY|G|46
pMakeNodesProbeForInsertions:  a 6ORD|1|QY|A|49 interacts with 6ORD|1|QY|U|65
pMakeNodesProbeForInsertions:  B 6ORD|1|QY|U|65 interacts with 6ORD|1|QY|A|49
pMakeNodesProbeForInsertions:  B 6ORD|1|QY|U|65 interacts with 6ORD|1|QY|A|49
 13 Initial     45 (2 insertion) and   65 (0 insertion)
 14 Basepair    49   65 AU cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 13
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
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  14  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  15   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ORD|1|QY|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ORD|1|QY|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6ORD|1|QY|C|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ORD|1|QY|A|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ORD|1|QY|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: 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: []
           numbranches: []
              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: [0.0082 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: 'UAA'
           RightLetter: 'UA'
               Comment: ' // Basepair U6 - A67 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J8173'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6ORD|1|QY|A|7'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8173'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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 6ORD|1|QY|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]
           numbranches: []
              NormCons: []

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: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 14
             Insertion: []
                    id: 'J8173'
        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 6ORD|1|QY|C|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J8686'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J8173'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - U65 ID J8173'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J8173'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             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 - 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]
           numbranches: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             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: []
           numbranches: []
              NormCons: 1

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: 'J8173'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6ORD|1|QY|G|26 - 6ORD|1|QY|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [9 13]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J8686'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G26 - U65 ID J8686'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J8686'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 G26 - 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]
           numbranches: []
              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: '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]
           numbranches: []
              NormCons: []

Node 18

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: []
           numbranches: []
              NormCons: 1

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: 'J8686'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 6ORD|1|QY|G|45 - 6ORD|1|QY|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6ORD|1|QY|A|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             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: []
           numbranches: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             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 6ORD|1|QY|G|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: []
           numbranches: []
              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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A49 - U65 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  4 Right 13
pMakeMotifModelFromSSF:   9  Junction Left  4 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  12   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  13   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  14  Junction Left  6 Right 13
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
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  20     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  23   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J8173'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J8173'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6ORD|1|QY|G|26 - 6ORD|1|QY|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_97835.1. Nodes 10 and 13 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J8686'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: 'J8686'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 6ORD|1|QY|G|45 - 6ORD|1|QY|U|65 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_97835.1. Nodes 15 and 19 both model an insertion before position 10. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a junction at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin
pNextNodeJunction: Finished at node 25 out of 25, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cHS  between 4 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHS  between 4 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_97835.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.5543

Timestamp 18-Jul-2025 00:13:15
pMakeSCFGModels: Making JAR3D model for motif group J4_98739.1, number 64 of 65
pMakeNodes starting loop:     a=7A0S|1|X|C|611 B=7A0S|1|X|G|669
pMakeNodes making a cluster near strand break a=7A0S|1|X|C|611 B=7A0S|1|X|G|669
pMakeNodesCluster: amax is 3 bmin is 16, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 1 and then 23 to 23
aa is 1 bb is 23
  2 Cluster   7A0S|1|X|C|611:7A0S|1|X|C|611 7A0S|1|X|G|669:7A0S|1|X|G|669
    LR Inter  7A0S|1|X|C|611 7A0S|1|X|G|669 cWW 
pMakeNodesCluster a=2 B=22 at the end
pMakeNodesCluster a=2 B=22 at the end
pMakeNodes probe for inserts:  a=7A0S|1|X|G|612 B=7A0S|1|X|A|668
    Insertion on left  7A0S|1|X|G|612
    Insertion on left  7A0S|1|X|A|613
    Insertion on right 7A0S|1|X|A|668
    Insertion on right 7A0S|1|X|A|665
    Insertion on right 7A0S|1|X|C|664
    Insertion on right 7A0S|1|X|G|663
    Insertion on right 7A0S|1|X|G|662
  3 Initial    612 (2 insertion) and  668 (5 insertion)
pMakeNodes probed for insert:  a=7A0S|1|X|G|614 B=7A0S|1|X|C|661
pMakeNodesJunction: a=7A0S|1|X|G|614 r=7A0S|1|X|G|614 s=7A0S|1|X|C|635 t=7A0S|1|X|G|636 u=B=7A0S|1|X|C|661
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|G|614 and 7A0S|1|X|C|635 and between 7A0S|1|X|G|636 and 7A0S|1|X|C|661
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|G|614 s=7A0S|1|X|C|635 t=7A0S|1|X|G|636 B=7A0S|1|X|C|661
pMakeNodesJunction: first branch starts at   7A0S|1|X|G|614
pMakeNodesJunction: first branch ends around 7A0S|1|X|C|635
pMakeNodesJunction: second branch starts at  7A0S|1|X|G|636
pMakeNodesJunction: junction ends at         7A0S|1|X|C|661
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|614
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|C|635
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|639
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|G|659

Junction with 2 loops, call it J844
Actual Branch 1 of junction J844 - Nucleotides 7A0S|1|X|G|614 to 7A0S|1|X|C|635, length   2
Actual Branch 2 of junction J844 - Nucleotides 7A0S|1|X|G|636 to 7A0S|1|X|C|661, length  12
  4 Junction

2B Branch 1 of 2 of junction J844 - Nucleotides   614 to   635, length   2
pMakeNodes starting loop:     a=7A0S|1|X|G|614 B=7A0S|1|X|C|635
  6 Basepair   614  635 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J844 - Nucleotides   636 to   661, length  12
pMakeNodes starting loop:     a=7A0S|1|X|G|636 B=7A0S|1|X|C|661
    Insertion on left  7A0S|1|X|G|636
    Insertion on left  7A0S|1|X|G|637
    Insertion on left  7A0S|1|X|A|638
  8 Initial    636 (3 insertion) and  661 (0 insertion)
pMakeNodesJunction: a=7A0S|1|X|G|639 r=7A0S|1|X|G|639 s=7A0S|1|X|G|649 t=7A0S|1|X|U|650 u=B=7A0S|1|X|C|661
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|G|639 and 7A0S|1|X|G|649 and between 7A0S|1|X|U|650 and 7A0S|1|X|C|661
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|G|639 s=7A0S|1|X|G|649 t=7A0S|1|X|U|650 B=7A0S|1|X|C|661
pMakeNodesJunction: first branch starts at   7A0S|1|X|G|639
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|649
pMakeNodesJunction: second branch starts at  7A0S|1|X|U|650
pMakeNodesJunction: junction ends at         7A0S|1|X|C|661
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|639
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|C|646
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|U|650
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|G|659
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     2


Junction with 2 loops, call it J3997
Actual Branch 1 of junction J3997 - Nucleotides 7A0S|1|X|G|639 to 7A0S|1|X|G|649, length   5
Actual Branch 2 of junction J3997 - Nucleotides 7A0S|1|X|U|650 to 7A0S|1|X|C|661, length   4
  9 Junction

2B Branch 1 of 2 of junction J3997 - Nucleotides   639 to   649, length   5
pMakeNodes starting loop:     a=7A0S|1|X|G|639 B=7A0S|1|X|G|649
pMakeNodes making a cluster near strand break a=7A0S|1|X|G|639 B=7A0S|1|X|G|649
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 9 to 9 and then 10 to 13
aa is 9 bb is 10
 11 Cluster   7A0S|1|X|G|639:7A0S|1|X|G|639 7A0S|1|X|C|646:7A0S|1|X|G|649
    LR Inter  7A0S|1|X|G|639 7A0S|1|X|C|646 cWW 
    LR Inter  7A0S|1|X|G|639 7A0S|1|X|G|649 rib 
    Right strand conserved insertion 7A0S|1|X|G|647 at position 2
    Right strand conserved insertion 7A0S|1|X|A|648 at position 3
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
 12 Hairpin type *

2B Branch 2 of 2 of junction J3997 - Nucleotides   650 to   661, length   4
pMakeNodes starting loop:     a=7A0S|1|X|U|650 B=7A0S|1|X|C|661
    Insertion on right 7A0S|1|X|C|661
    Insertion on right 7A0S|1|X|G|660
pMakeNodesProbeForInsertions:  a 7A0S|1|X|U|650 interacts with 7A0S|1|X|G|659
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|659 interacts with 7A0S|1|X|U|650
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|659 interacts with 7A0S|1|X|U|650
 13 Initial    650 (0 insertion) and  661 (2 insertion)
 14 Basepair   650  659 UG cWW 
 15 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 23
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 23
pMakeMotifModelFromSSF:   3   Initial Left  2 Right 22
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 17
pMakeMotifModelFromSSF:   9  Junction Left  9 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  11   Cluster Left  9 Right 10 11 12 13
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  13   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  14  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  15   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|612
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|613
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|U|666
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|A|665
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|664
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|663
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|662
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|636
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|637
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|638
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|661
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|660
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: 23
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [23×23 double]
         Extensibility: [0 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Cluster node 7A0S|1|X|C|611:7A0S|1|X|C|611 and 7A0S|1|X|G|669:7A0S|1|X|G|669'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: 1
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Cluster Interaction 7A0S|1|X|C|611 - 7A0S|1|X|G|669 cWW '}
      JunctionDeletion: []
          InterIndices: [1 23]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'GGCAA'
               Comment: ' // Initial node 7A0S|1|X|G|612 - 7A0S|1|X|A|668 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 22
             Insertion: []
                    id: 'J844'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|612'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 22
             Insertion: []
                    id: 'J844'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            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 7A0S|1|X|A|613'
              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: []
           numbranches: []
                  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: 4
            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: [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
           numbranches: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 22
             Insertion: []
                    id: 'J844'
        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|U|666'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 21
             Insertion: []
                    id: 'J3997'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 21
             Insertion: []
                    id: 'J3997'
        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|A|665'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             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: 'G'
           RightLetter: 'CGAG'
               Comment: ' // New Initial node after Fixed node'
              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: 0.2505
           numbranches: []
                  lpar: []
                  rpar: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 4
            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 7A0S|1|X|C|664'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             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: '*'
           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
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 4
            RightIndex: 19
             Insertion: []
                    id: 'J3997'
        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|663'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             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 7A0S|1|X|G|662'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 15
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: 'J844'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G614 - C661 ID J844'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J844'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             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 G614 - C635 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             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
           numbranches: []
                  lpar: []
                  rpar: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: 'J844'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGA'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|G|636 - 7A0S|1|X|C|661 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             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 7A0S|1|X|G|636'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             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 7A0S|1|X|G|637'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 28
             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 7A0S|1|X|A|638'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 9
            RightIndex: 17
             Insertion: []
                    id: 'J3997'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G639 - C661 ID J3997'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: 2
                  lpar: []
                  rpar: []

Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J3997'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 32
             LeftIndex: 9
            RightIndex: [10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'CGAG'
               Comment: ' // Cluster node 7A0S|1|X|G|639:7A0S|1|X|G|639 and 7A0S|1|X|C|646:7A0S|1|X|G|649'
              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: 0.2505
           numbranches: []
                  lpar: []
                  rpar: []

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 33
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 34
             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
           numbranches: []
                  lpar: []
                  rpar: []

Node 34

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 35
             LeftIndex: 14
            RightIndex: 17
             Insertion: []
                    id: 'J3997'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'GC'
               Comment: ' // Initial node 7A0S|1|X|U|650 - 7A0S|1|X|C|661 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 35

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 36
             LeftIndex: 14
            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 7A0S|1|X|C|661'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 36

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 37
             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: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 37

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 38
             LeftIndex: 14
            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 7A0S|1|X|G|660'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 38

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 39
             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 Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 39

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 40
             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: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U650 - G659 cWW '
              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: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 40

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 41
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 23
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 23
pMakeMotifModelFromSSF:   3   Initial Left  2 Right 22
pMakeMotifModelFromSSF:   4     Fixed Left  2 Right 22
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 22
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right 22
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 22
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right 22
pMakeMotifModelFromSSF:   9   Initial Left  4 Right 21
pMakeMotifModelFromSSF:  10     Fixed Left  4 Right 21
pMakeMotifModelFromSSF:  11   Initial Left  4 Right 20
pMakeMotifModelFromSSF:  12     Fixed Left  4 Right 20
pMakeMotifModelFromSSF:  13   Initial Left  4 Right 19
pMakeMotifModelFromSSF:  14     Fixed Left  4 Right 19
pMakeMotifModelFromSSF:  15   Initial Left  4 Right 18
pMakeMotifModelFromSSF:  16     Fixed Left  4 Right 18
pMakeMotifModelFromSSF:  17   Initial Left  4 Right 17
pMakeMotifModelFromSSF:  18  Junction Left  4 Right 17
pMakeMotifModelFromSSF:  19   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  20  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  21   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  22   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  23     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  24   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  25     Fixed Left  7 Right 17
pMakeMotifModelFromSSF:  26   Initial Left  8 Right 17
pMakeMotifModelFromSSF:  27     Fixed Left  8 Right 17
pMakeMotifModelFromSSF:  28   Initial Left  9 Right 17
pMakeMotifModelFromSSF:  29  Junction Left  9 Right 17
pMakeMotifModelFromSSF:  30   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  31   Cluster Left  9 Right 10 11 12 13
pMakeMotifModelFromSSF:  32   Initial Left 10 Right  9
pMakeMotifModelFromSSF:  33   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  34   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  35     Fixed Left 14 Right 17
pMakeMotifModelFromSSF:  36   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  37     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  38   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  39  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  40   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a junction at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Found a junction child at node 34
pNextNodeJunction: Found a hairpin at node 40
pNextNodeJunction: Finished at node 40 out of 40, type Hairpin
pNextNodeJunction: Finished at node 40 out of 40, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J844'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: 'J844'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGA'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|G|636 - 7A0S|1|X|C|661 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_98739.1. Nodes 19 and 22 both model an insertion before position 6. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J3997'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 35
             LeftIndex: 14
            RightIndex: 17
             Insertion: []
                    id: 'J3997'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'GC'
               Comment: ' // Initial node 7A0S|1|X|U|650 - 7A0S|1|X|C|661 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J4_98739.1. Nodes 30 and 34 both model an insertion before position 14. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a junction child at node 22
pNextNodeJunction: Found a junction at node 29
pNextNodeJunction: Found a junction child at node 30
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Found a junction child at node 34
pNextNodeJunction: Found a hairpin at node 40
pNextNodeJunction: Finished at node 40 out of 40, type Hairpin
pNextNodeJunction: Finished at node 40 out of 40, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for rib  between 4 and 23
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 12 and 17
pConservedInteractionList: did not find a substitution probability matrix for bif  between 13 and 16
pConservedInteractionList: did not find a substitution probability matrix for rib  between 4 and 23
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 12 and 17
pConservedInteractionList: did not find a substitution probability matrix for bif  between 13 and 16
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_98739.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.8676

Timestamp 18-Jul-2025 00:13:16
pMakeSCFGModels: Making JAR3D model for motif group J4_99897.1, number 65 of 65
pMakeNodes starting loop:     a=3SUX|1|X|G|8||||17_555 B=3SUX|1|X|C|89
  2 Basepair     8   89 GC cWW 
pMakeNodes probe for inserts:  a=3SUX|1|X|U|9||||17_555 B=3SUX|1|X|G|88
    Insertion on left  3SUX|1|X|U|9||||17_555
pMakeNodes probed for insert:  a=3SUX|1|X|A|10||||17_555 B=3SUX|1|X|G|88
pMakeNodesJunction: a=3SUX|1|X|A|10||||17_555 r=3SUX|1|X|A|10||||17_555 s=3SUX|1|X|G|88||||17_555 t=3SUX|1|X|C|89||||17_555 u=B=3SUX|1|X|G|88
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3SUX|1|X|A|10||||17_555 and 3SUX|1|X|G|88||||17_555 and between 3SUX|1|X|C|89||||17_555 and 3SUX|1|X|G|88
pMakeNodesJunction: about to make a junction: a=3SUX|1|X|A|10||||17_555 s=3SUX|1|X|G|88||||17_555 t=3SUX|1|X|C|89||||17_555 B=3SUX|1|X|G|88
pMakeNodesJunction: first branch starts at   3SUX|1|X|A|10||||17_555
pMakeNodesJunction: first branch ends around 3SUX|1|X|G|88||||17_555
pMakeNodesJunction: second branch starts at  3SUX|1|X|C|89||||17_555
pMakeNodesJunction: junction ends at         3SUX|1|X|G|88
pMakeNodesJunction: first branch strand start goes up to  3SUX|1|X|G|11||||17_555
pMakeNodesJunction: first branch strand end goes down to  3SUX|1|X|C|87||||17_555
pMakeNodesJunction: second branch strand start goes up to 3SUX|1|X|C|89||||17_555
pMakeNodesJunction: last strand of junction goes down to  3SUX|1|X|C|87

Junction with 2 loops, call it J2598
Actual Branch 1 of junction J2598 - Nucleotides 3SUX|1|X|A|10||||17_555 to 3SUX|1|X|G|88||||17_555, length   4
Actual Branch 2 of junction J2598 - Nucleotides 3SUX|1|X|C|89||||17_555 to 3SUX|1|X|G|88, length   7
  3 Junction

2B Branch 1 of 2 of junction J2598 - Nucleotides    10 to    88, length   4
pMakeNodes starting loop:     a=3SUX|1|X|A|10||||17_555 B=3SUX|1|X|G|88||||17_555
  5 Basepair    10   88 AG cWW 
No need to probe because of interaction between a=3SUX|1|X|G|11||||17_555 B=3SUX|1|X|C|87||||17_555
  6 Basepair    11   87 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2598 - Nucleotides    89 to    88, length   7
pMakeNodes starting loop:     a=3SUX|1|X|C|89||||17_555 B=3SUX|1|X|G|88
  8 Initial     89 (0 insertion) and   88 (0 insertion)
pMakeNodesJunction: a=3SUX|1|X|C|89||||17_555 r=3SUX|1|X|C|89||||17_555 s=3SUX|1|X|G|8 t=3SUX|1|X|U|9 u=B=3SUX|1|X|G|88
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3SUX|1|X|C|89||||17_555 and 3SUX|1|X|G|8 and between 3SUX|1|X|U|9 and 3SUX|1|X|G|88
pMakeNodesJunction: about to make a junction: a=3SUX|1|X|C|89||||17_555 s=3SUX|1|X|G|8 t=3SUX|1|X|U|9 B=3SUX|1|X|G|88
pMakeNodesJunction: first branch starts at   3SUX|1|X|C|89||||17_555
pMakeNodesJunction: first branch ends around 3SUX|1|X|G|8
pMakeNodesJunction: second branch starts at  3SUX|1|X|U|9
pMakeNodesJunction: junction ends at         3SUX|1|X|G|88
pMakeNodesJunction: first branch strand start goes up to  3SUX|1|X|C|89||||17_555
pMakeNodesJunction: first branch strand end goes down to  3SUX|1|X|G|8
pMakeNodesJunction: second branch strand start goes up to 3SUX|1|X|G|11
pMakeNodesJunction: last strand of junction goes down to  3SUX|1|X|C|87

Junction with 2 loops, call it J8000
Actual Branch 1 of junction J8000 - Nucleotides 3SUX|1|X|C|89||||17_555 to 3SUX|1|X|G|8, length   2
Actual Branch 2 of junction J8000 - Nucleotides 3SUX|1|X|U|9 to 3SUX|1|X|G|88, length   5
  9 Junction

2B Branch 1 of 2 of junction J8000 - Nucleotides    89 to     8, length   2
pMakeNodes starting loop:     a=3SUX|1|X|C|89||||17_555 B=3SUX|1|X|G|8
 11 Basepair    89    8 CG cWW 
 12 Hairpin type *

2B Branch 2 of 2 of junction J8000 - Nucleotides     9 to    88, length   5
pMakeNodes starting loop:     a=3SUX|1|X|U|9 B=3SUX|1|X|G|88
    Insertion on left  3SUX|1|X|U|9
pMakeNodesProbeForInsertions:  a 3SUX|1|X|A|10 interacts with 3SUX|1|X|G|88
pMakeNodesProbeForInsertions:  B 3SUX|1|X|G|88 interacts with 3SUX|1|X|A|10
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3SUX|1|X|G|88 interacts with 3SUX|1|X|A|10
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
 13 Initial      9 (1 insertion) and   88 (0 insertion)
 14 Basepair    10   88 AG cWW 
No need to probe because of interaction between a=3SUX|1|X|G|11 B=3SUX|1|X|C|87
 15 Basepair    11   87 GC cWW 
 16 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Junction Left  3 Right 13
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
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 13
pMakeMotifModelFromSSF:   9  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  15  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  16   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|U|9||||17_555
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|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: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 1 1 0 0 0 0 0 1 1 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C89 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 'J2598'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|U|9||||17_555'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J2598'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: 'J2598'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A10 - G88 ID J2598'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              NormCons: []

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: 'J2598'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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: 'G'
               Comment: ' // Basepair A10 - G88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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 G11 - C87 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 9

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: []
           numbranches: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J2598'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3SUX|1|X|C|89||||17_555 - 3SUX|1|X|G|88 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Junction'
              nextnode: [10 13]
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J8000'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C89 - G88 ID J8000'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: 2
              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: 'J8000'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 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]
           numbranches: []
              NormCons: []

Node 14

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: []
           numbranches: []
              NormCons: 1

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: 'J8000'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 3SUX|1|X|U|9 - 3SUX|1|X|G|88 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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 3SUX|1|X|U|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

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: []
           numbranches: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             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: 'G'
               Comment: ' // Basepair A10 - G88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             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 G11 - C87 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             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: [17×2 double]
                  PIns: [0.0500 0.9500]
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              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  Junction Left  3 Right 13
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
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  11  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 13
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  18  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  20   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J2598'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J2598'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3SUX|1|X|C|89||||17_555 - 3SUX|1|X|G|88 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_99897.1. Nodes 6 and 10 both model an insertion before position 7. Nodes are above.
Fixing the second one to have length distribution concentrated on zero

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J8000'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.9899 0.0100 9.9990e-05]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J8000'
        leftLengthDist: [0.9899 0.0100 9.9990e-05]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 3SUX|1|X|U|9 - 3SUX|1|X|G|88 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J4_99897.1. Nodes 12 and 15 both model an insertion before position 9. Nodes are above.
Fixing the second one to have length distribution concentrated on zero
pNextNodeJunction: Found a junction at node 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\lib\J4_99897.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5479

There are 65 motif groups, of which 57 are structured
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     2     2
     2     2     2     3
     2     2     2     4
     2     2     3     2
     2     2     3     3
     2     2     4     3
     2     2     4     4
     2     2     4     5
     2     2     4     6
     2     2     5     3
     2     2     5     5
     2     3     2     2
     2     3     2     3
     2     3     2     4
     2     3     2     5
     2     3     3     2
     2     3     3     3
     2     3     3     4
     2     3     3     5
     2     3     3     6
     2     3     4     2
     2     3     4     3
     2     3     4     5
     2     3     5     2
     2     3     5     3
     2     3     5     4
     2     3     6     3
     2     3     6    12
     2     3     6    13
     2     3     7    12
     2     4     2     2
     2     4     2     3
     2     4     2     4
     2     4     2     6
     2     4     2     7
     2     4     2     8
     2     4     2     9
     2     4     3     2
     2     4     3     3
     2     4     3     4
     2     4     3     5
     2     4     3     6
     2     4     3     7
     2     4     3     8
     2     4     4     2
     2     4     4     3
     2     4     4     4
     2     4     4     6
     2     4     4     7
     2     4     4     8
     2     4     4     9
     2     4     5     3
     2     4     5     4
     2     4     5     5
     2     4     5     8
     2     4     6     3
     2     4     6     4
     2     4     6    12
     2     4     7     3
     2     4    14     9
     2     4    14    10
     2     4    15     9
     2     5     2     2
     2     5     2     3
     2     5     2     4
     2     5     2     5
     2     5     2     6
     2     5     2     7
     2     5     2     8
     2     5     2     9
     2     5     2    10
     2     5     3     3
     2     5     3     4
     2     5     3     6
     2     5     3     7
     2     5     3     9
     2     5     4     7
     2     5     4     8
     2     5     5     4
     2     5     5     7
     2     5     5     8
     2     5     5     9
     2     5     6     3
     2     5     6     4
     2     5     6     8
     2     5     7     3
     2     5     7     4
     2     5     8     3
     2     5    14     9
     2     6     2     4
     2     6     2     5
     2     6     2     6
     2     6     2     7
     2     6     2     8
     2     6     2     9
     2     6     3     4
     2     6     3     7
     2     6     4     6
     2     6     4     7
     2     6     5     6
     2     6     5     8
     2     6     6     3
     2     6     7     3
     2     6     7     4
     2     6     7     5
     2     6     8     4
     2     6     8     5
     2     6     9     4
     2     7     2     4
     2     7     2     7
     2     7     4     6
     2     7     7     4
     2     7     8     4
     2     8     5     6
     2     8     5     7
     2     8     6     6
     2     9     3     5
     2     9     3     6
     2     9     4     5
     2     9     5     6
     2    10     3     5
     2    10     6     3
     2    10     6     4
     2    10     7     3
     2    11     6     3
     2    22     3     4
     2    22     3     5
     2    22     4     4
     2    23     3     4
     3     2     2     2
     3     2     2     3
     3     2     4     3
     3     2     4     5
     3     3     2     4
     3     3     3     2
     3     3     3     3
     3     3     3     5
     3     3     4     2
     3     3     5     3
     3     3     5     5
     3     3     5     6
     3     3     6     5
     3     3     6    12
     3     4     2     2
     3     4     2     3
     3     4     2     6
     3     4     2     7
     3     4     2     8
     3     4     3     3
     3     4     3     4
     3     4     3     5
     3     4     3     6
     3     4     3     7
     3     4     4     4
     3     4     4     8
     3     4     5     4
     3     4     5     5
     3     4     6     3
     3     4    14     9
     3     5     2     4
     3     5     2     6
     3     5     2     9
     3     5     3     4
     3     5     3     5
     3     5     4     4
     3     5     4     7
     3     5     5     4
     3     5     5     5
     3     5     5     8
     3     5     6     3
     3     5     6     4
     3     5     7     3
     3     6     2     4
     3     6     2     7
     3     6     3     4
     3     6     4     4
     3     6     4     5
     3     6     4     6
     3     6     5     3
     3     6     5     4
     3     6     5     5
     3     6     6     3
     3     6     6     4
     3     6     6     5
     3     6     7     4
     3     6     8     4
     3     6    14     9
     3     6    14    10
     3     6    15     9
     3     7     3     5
     3     7     3     6
     3     7     4     4
     3     7     4     5
     3     7     4     6
     3     7     4     7
     3     7     5     3
     3     7     5     4
     3     7     5     6
     3     7     5     7
     3     7     5     8
     3     7     6     3
     3     7     6     4
     3     7     6     5
     3     7     6     7
     3     7     7     3
     3     7     7     4
     3     7    14     9
     3     8     3     5
     3     8     4     6
     3     8     5     6
     3     8     5     7
     3     8     6     3
     3     8     6     4
     3     9     3     5
     3     9     8     5
     3     9     8     6
     3     9     9     5
     3    10     6     3
     3    10     8     5
     3    22     3     4
     4     3     5     5
     4     4     3     4
     4     5     3     4
     4     5     4     7
     4     5     4     8
     4     5     5     4
     4     5     5     5
     4     5     5     6
     4     5     5     7
     4     5     5     8
     4     5     5     9
     4     5     5    11
     4     5     5    12
     4     5     6     5
     4     5     6     8
     4     5     6    11
     4     6     4     4
     4     6     4     7
     4     6     5     3
     4     6     5     4
     4     6     5     5
     4     6     5     8
     4     6     5    11
     4     6     6     4
     4     6    14     9
     4     7     3     5
     4     7     4     6
     4     7     5     7
     4     7     6     3
     4     7     6     4
     4     9     8     5
     5     5     4     7
     5     5     5     5
     5     5     5     6
     5     5     5     7
     5     5     5     8
     5     5     5    11
     5     5     6     6
     5     6     5     6
     6     5     5     6

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   260     4

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26508 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26852 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26916 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26462 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26598 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26720 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 27448 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26192 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 27247 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26726 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26376 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26755 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26274 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26408 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 26666 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     2     2
     2     2     2     3
     2     2     2     4
     2     2     3     2
     2     2     3     3
     2     2     4     3
     2     2     4     4
     2     2     4     5
     2     2     4     6
     2     2     5     3
     2     2     5     5
     2     3     2     2
     2     3     2     3
     2     3     2     4
     2     3     2     5
     2     3     3     2
     2     3     3     3
     2     3     3     4
     2     3     3     5
     2     3     3     6
     2     3     4     2
     2     3     4     3
     2     3     4     5
     2     3     5     2
     2     3     5     3
     2     3     5     4
     2     3     6     3
     2     3     6    12
     2     3     6    13
     2     3     7    12
     2     4     2     2
     2     4     2     3
     2     4     2     4
     2     4     2     6
     2     4     2     7
     2     4     2     8
     2     4     2     9
     2     4     3     2
     2     4     3     3
     2     4     3     4
     2     4     3     5
     2     4     3     6
     2     4     3     7
     2     4     3     8
     2     4     4     2
     2     4     4     3
     2     4     4     4
     2     4     4     6
     2     4     4     7
     2     4     4     8
     2     4     4     9
     2     4     5     3
     2     4     5     4
     2     4     5     5
     2     4     5     8
     2     4     6     3
     2     4     6     4
     2     4     6    12
     2     4     7     3
     2     4    14     9
     2     4    14    10
     2     4    15     9
     2     5     2     2
     2     5     2     3
     2     5     2     4
     2     5     2     5
     2     5     2     6
     2     5     2     7
     2     5     2     8
     2     5     2     9
     2     5     2    10
     2     5     3     3
     2     5     3     4
     2     5     3     6
     2     5     3     7
     2     5     3     9
     2     5     4     7
     2     5     4     8
     2     5     5     4
     2     5     5     7
     2     5     5     8
     2     5     5     9
     2     5     6     3
     2     5     6     4
     2     5     6     8
     2     5     7     3
     2     5     7     4
     2     5     8     3
     2     5    14     9
     2     6     2     4
     2     6     2     5
     2     6     2     6
     2     6     2     7
     2     6     2     8
     2     6     2     9
     2     6     3     4
     2     6     3     7
     2     6     4     6
     2     6     4     7
     2     6     5     6
     2     6     5     8
     2     6     6     3
     2     6     7     3
     2     6     7     4
     2     6     7     5
     2     6     8     4
     2     6     8     5
     2     6     9     4
     2     7     2     4
     2     7     2     7
     2     7     4     6
     2     7     7     4
     2     7     8     4
     2     8     5     6
     2     8     5     7
     2     8     6     6
     2     9     3     5
     2     9     3     6
     2     9     4     5
     2     9     5     6
     2    10     3     5
     2    10     6     3
     2    10     6     4
     2    10     7     3
     2    11     6     3
     2    22     3     4
     2    22     3     5
     2    22     4     4
     2    23     3     4
     3     2     2     2
     3     2     2     3
     3     2     4     3
     3     2     4     5
     3     3     2     4
     3     3     3     2
     3     3     3     3
     3     3     3     5
     3     3     4     2
     3     3     5     3
     3     3     5     5
     3     3     5     6
     3     3     6     5
     3     3     6    12
     3     4     2     2
     3     4     2     3
     3     4     2     6
     3     4     2     7
     3     4     2     8
     3     4     3     3
     3     4     3     4
     3     4     3     5
     3     4     3     6
     3     4     3     7
     3     4     4     4
     3     4     4     8
     3     4     5     4
     3     4     5     5
     3     4     6     3
     3     4    14     9
     3     5     2     4
     3     5     2     6
     3     5     2     9
     3     5     3     4
     3     5     3     5
     3     5     4     4
     3     5     4     7
     3     5     5     4
     3     5     5     5
     3     5     5     8
     3     5     6     3
     3     5     6     4
     3     5     7     3
     3     6     2     4
     3     6     2     7
     3     6     3     4
     3     6     4     4
     3     6     4     5
     3     6     4     6
     3     6     5     3
     3     6     5     4
     3     6     5     5
     3     6     6     3
     3     6     6     4
     3     6     6     5
     3     6     7     4
     3     6     8     4
     3     6    14     9
     3     6    14    10
     3     6    15     9
     3     7     3     5
     3     7     3     6
     3     7     4     4
     3     7     4     5
     3     7     4     6
     3     7     4     7
     3     7     5     3
     3     7     5     4
     3     7     5     6
     3     7     5     7
     3     7     5     8
     3     7     6     3
     3     7     6     4
     3     7     6     5
     3     7     6     7
     3     7     7     3
     3     7     7     4
     3     7    14     9
     3     8     3     5
     3     8     4     6
     3     8     5     6
     3     8     5     7
     3     8     6     3
     3     8     6     4
     3     9     3     5
     3     9     8     5
     3     9     8     6
     3     9     9     5
     3    10     6     3
     3    10     8     5
     3    22     3     4
     4     3     5     5
     4     4     3     4
     4     5     3     4
     4     5     4     7
     4     5     4     8
     4     5     5     4
     4     5     5     5
     4     5     5     6
     4     5     5     7
     4     5     5     8
     4     5     5     9
     4     5     5    11
     4     5     5    12
     4     5     6     5
     4     5     6     8
     4     5     6    11
     4     6     4     4
     4     6     4     7
     4     6     5     3
     4     6     5     4
     4     6     5     5
     4     6     5     8
     4     6     5    11
     4     6     6     4
     4     6    14     9
     4     7     3     5
     4     7     4     6
     4     7     5     7
     4     7     6     3
     4     7     6     4
     4     9     8     5
     5     5     4     7
     5     5     5     5
     5     5     5     6
     5     5     5     7
     5     5     5     8
     5     5     5    11
     5     5     6     6
     5     6     5     6
     6     5     5     6

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   260     4

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16366 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16469 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16314 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16825 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16442 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 15958 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16353 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16389 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16681 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 17179 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16603 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16686 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16464 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16391 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
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: Generating 7800 sequences required 16386 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     2     2
     2     2     2     3
     2     2     2     4
     2     2     3     2
     2     2     3     3
     2     2     4     3
     2     2     4     4
     2     2     4     5
     2     2     4     6
     2     2     5     3
     2     2     5     5
     2     3     2     2
     2     3     2     3
     2     3     2     4
     2     3     2     5
     2     3     3     2
     2     3     3     3
     2     3     3     4
     2     3     3     5
     2     3     3     6
     2     3     4     2
     2     3     4     3
     2     3     4     5
     2     3     5     2
     2     3     5     3
     2     3     5     4
     2     3     6     3
     2     3     6    12
     2     3     6    13
     2     3     7    12
     2     4     2     2
     2     4     2     3
     2     4     2     4
     2     4     2     6
     2     4     2     7
     2     4     2     8
     2     4     2     9
     2     4     3     2
     2     4     3     3
     2     4     3     4
     2     4     3     5
     2     4     3     6
     2     4     3     7
     2     4     3     8
     2     4     4     2
     2     4     4     3
     2     4     4     4
     2     4     4     6
     2     4     4     7
     2     4     4     8
     2     4     4     9
     2     4     5     3
     2     4     5     4
     2     4     5     5
     2     4     5     8
     2     4     6     3
     2     4     6     4
     2     4     6    12
     2     4     7     3
     2     4    14     9
     2     4    14    10
     2     4    15     9
     2     5     2     2
     2     5     2     3
     2     5     2     4
     2     5     2     5
     2     5     2     6
     2     5     2     7
     2     5     2     8
     2     5     2     9
     2     5     2    10
     2     5     3     3
     2     5     3     4
     2     5     3     6
     2     5     3     7
     2     5     3     9
     2     5     4     7
     2     5     4     8
     2     5     5     4
     2     5     5     7
     2     5     5     8
     2     5     5     9
     2     5     6     3
     2     5     6     4
     2     5     6     8
     2     5     7     3
     2     5     7     4
     2     5     8     3
     2     5    14     9
     2     6     2     4
     2     6     2     5
     2     6     2     6
     2     6     2     7
     2     6     2     8
     2     6     2     9
     2     6     3     4
     2     6     3     7
     2     6     4     6
     2     6     4     7
     2     6     5     6
     2     6     5     8
     2     6     6     3
     2     6     7     3
     2     6     7     4
     2     6     7     5
     2     6     8     4
     2     6     8     5
     2     6     9     4
     2     7     2     4
     2     7     2     7
     2     7     4     6
     2     7     7     4
     2     7     8     4
     2     8     5     6
     2     8     5     7
     2     8     6     6
     2     9     3     5
     2     9     3     6
     2     9     4     5
     2     9     5     6
     2    10     3     5
     2    10     6     3
     2    10     6     4
     2    10     7     3
     2    11     6     3
     2    22     3     4
     2    22     3     5
     2    22     4     4
     2    23     3     4
     3     2     2     2
     3     2     2     3
     3     2     4     3
     3     2     4     5
     3     3     2     4
     3     3     3     2
     3     3     3     3
     3     3     3     5
     3     3     4     2
     3     3     5     3
     3     3     5     5
     3     3     5     6
     3     3     6     5
     3     3     6    12
     3     4     2     2
     3     4     2     3
     3     4     2     6
     3     4     2     7
     3     4     2     8
     3     4     3     3
     3     4     3     4
     3     4     3     5
     3     4     3     6
     3     4     3     7
     3     4     4     4
     3     4     4     8
     3     4     5     4
     3     4     5     5
     3     4     6     3
     3     4    14     9
     3     5     2     4
     3     5     2     6
     3     5     2     9
     3     5     3     4
     3     5     3     5
     3     5     4     4
     3     5     4     7
     3     5     5     4
     3     5     5     5
     3     5     5     8
     3     5     6     3
     3     5     6     4
     3     5     7     3
     3     6     2     4
     3     6     2     7
     3     6     3     4
     3     6     4     4
     3     6     4     5
     3     6     4     6
     3     6     5     3
     3     6     5     4
     3     6     5     5
     3     6     6     3
     3     6     6     4
     3     6     6     5
     3     6     7     4
     3     6     8     4
     3     6    14     9
     3     6    14    10
     3     6    15     9
     3     7     3     5
     3     7     3     6
     3     7     4     4
     3     7     4     5
     3     7     4     6
     3     7     4     7
     3     7     5     3
     3     7     5     4
     3     7     5     6
     3     7     5     7
     3     7     5     8
     3     7     6     3
     3     7     6     4
     3     7     6     5
     3     7     6     7
     3     7     7     3
     3     7     7     4
     3     7    14     9
     3     8     3     5
     3     8     4     6
     3     8     5     6
     3     8     5     7
     3     8     6     3
     3     8     6     4
     3     9     3     5
     3     9     8     5
     3     9     8     6
     3     9     9     5
     3    10     6     3
     3    10     8     5
     3    22     3     4
     4     3     5     5
     4     4     3     4
     4     5     3     4
     4     5     4     7
     4     5     4     8
     4     5     5     4
     4     5     5     5
     4     5     5     6
     4     5     5     7
     4     5     5     8
     4     5     5     9
     4     5     5    11
     4     5     5    12
     4     5     6     5
     4     5     6     8
     4     5     6    11
     4     6     4     4
     4     6     4     7
     4     6     5     3
     4     6     5     4
     4     6     5     5
     4     6     5     8
     4     6     5    11
     4     6     6     4
     4     6    14     9
     4     7     3     5
     4     7     4     6
     4     7     5     7
     4     7     6     3
     4     7     6     4
     4     9     8     5
     5     5     4     7
     5     5     5     5
     5     5     5     6
     5     5     5     7
     5     5     5     8
     5     5     5    11
     5     5     6     6
     5     6     5     6
     6     5     5     6

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   260     4

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2
     2     2     2     2     2     2     2     2     2     2

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2865
    0.4297
    0.0928
    0.0982
    0.0846
    0.0082

    0.3005
    0.0960
    0.3106
    0.2929

    0.4306    0.1528    0.2326    0.1840
    0.2674    0.2209    0.2907    0.2209
    0.3034    0.0414    0.2586    0.3966
    0.4196    0.2589    0.1607    0.1607

pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Read random sequence variant file J4_RandomMotifSequences_1.fasta
max_rotation=3 r=0 n=1 a=CC*GC*GG*CG FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=1 n=1 a=GC*GG*CG*CC FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CC*GC FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=3 n=1 a=CG*CC*GC*GG FASTA(n).Sequence=CC*GC*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:15:25
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   7.0469 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:23:27
Parsing 7800 sequences from file J4_RandomMotifSequences_1.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5024 minutes
Read random sequence variant file J4_RandomMotifSequences_2.fasta
max_rotation=3 r=0 n=1 a=CG*CU*GG*CG FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=1 n=1 a=CU*GG*CG*CG FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CG*CU FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=3 n=1 a=CG*CG*CU*GG FASTA(n).Sequence=CG*CU*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:32:55
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.0893 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:35:36
Parsing 7800 sequences from file J4_RandomMotifSequences_2.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5515 minutes
Read random sequence variant file J4_RandomMotifSequences_3.fasta
max_rotation=3 r=0 n=1 a=CG*CC*GG*CG FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=1 n=1 a=CC*GG*CG*CG FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CG*CC FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=3 n=1 a=CG*CG*CC*GG FASTA(n).Sequence=CG*CC*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:45:07
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1323 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:47:52
Parsing 7800 sequences from file J4_RandomMotifSequences_3.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5977 minutes
Read random sequence variant file J4_RandomMotifSequences_4.fasta
max_rotation=3 r=0 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=1 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=2 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=3 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:57:26
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1550 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:00:17
Parsing 7800 sequences from file J4_RandomMotifSequences_4.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5684 minutes
Read random sequence variant file J4_RandomMotifSequences_5.fasta
max_rotation=3 r=0 n=1 a=UG*CC*GA*UA FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=1 n=1 a=CC*GA*UA*UG FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=2 n=1 a=GA*UA*UG*CC FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=3 n=1 a=UA*UG*CC*GA FASTA(n).Sequence=UG*CC*GA*UA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:09:49
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1339 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:12:34
Parsing 7800 sequences from file J4_RandomMotifSequences_5.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5953 minutes
Read random sequence variant file J4_RandomMotifSequences_6.fasta
max_rotation=3 r=0 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=1 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:22:07
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1481 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:24:51
Parsing 7800 sequences from file J4_RandomMotifSequences_6.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5516 minutes
Read random sequence variant file J4_RandomMotifSequences_7.fasta
max_rotation=3 r=0 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=1 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=2 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GC*GG*CC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:34:22
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1156 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:37:05
Parsing 7800 sequences from file J4_RandomMotifSequences_7.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5761 minutes
Read random sequence variant file J4_RandomMotifSequences_8.fasta
max_rotation=3 r=0 n=1 a=CA*UG*CG*CG FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=1 n=1 a=UG*CG*CG*CA FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=2 n=1 a=CG*CG*CA*UG FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=3 n=1 a=CG*CA*UG*CG FASTA(n).Sequence=CA*UG*CG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:46:37
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1255 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:49:21
Parsing 7800 sequences from file J4_RandomMotifSequences_8.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.6146 minutes
Read random sequence variant file J4_RandomMotifSequences_9.fasta
max_rotation=3 r=0 n=1 a=GU*GU*GC*GC FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=1 n=1 a=GU*GC*GC*GU FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GU*GU FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=3 n=1 a=GC*GU*GU*GC FASTA(n).Sequence=GU*GU*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:58:56
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1445 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:01:40
Parsing 7800 sequences from file J4_RandomMotifSequences_9.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5574 minutes
Read random sequence variant file J4_RandomMotifSequences_10.fasta
max_rotation=3 r=0 n=1 a=GC*GG*CU*GU FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=1 n=1 a=GG*CU*GU*GC FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=2 n=1 a=CU*GU*GC*GG FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=3 n=1 a=GU*GC*GG*CU FASTA(n).Sequence=GC*GG*CU*GU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:11:11
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1285 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:13:55
Parsing 7800 sequences from file J4_RandomMotifSequences_10.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5357 minutes
Read random sequence variant file J4_RandomMotifSequences_11.fasta
max_rotation=3 r=0 n=1 a=AC*GG*CU*AU FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=1 n=1 a=GG*CU*AU*AC FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=2 n=1 a=CU*AU*AC*GG FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=3 n=1 a=AU*AC*GG*CU FASTA(n).Sequence=AC*GG*CU*AU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:23:26
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1359 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:26:10
Parsing 7800 sequences from file J4_RandomMotifSequences_11.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5278 minutes
Read random sequence variant file J4_RandomMotifSequences_12.fasta
max_rotation=3 r=0 n=1 a=CC*GG*CG*CG FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=1 n=1 a=GG*CG*CG*CC FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=2 n=1 a=CG*CG*CC*GG FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=3 n=1 a=CG*CC*GG*CG FASTA(n).Sequence=CC*GG*CG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:35:40
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1189 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:38:23
Parsing 7800 sequences from file J4_RandomMotifSequences_12.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.4994 minutes
Read random sequence variant file J4_RandomMotifSequences_13.fasta
max_rotation=3 r=0 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=1 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=2 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GC*GG*CC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:47:51
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1313 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:50:35
Parsing 7800 sequences from file J4_RandomMotifSequences_13.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5085 minutes
Read random sequence variant file J4_RandomMotifSequences_14.fasta
max_rotation=3 r=0 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=1 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=3 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GG*CC*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:00:04
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1289 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:02:48
Parsing 7800 sequences from file J4_RandomMotifSequences_14.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.5592 minutes
Read random sequence variant file J4_RandomMotifSequences_15.fasta
max_rotation=3 r=0 n=1 a=UC*GG*CA*UA FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=1 n=1 a=GG*CA*UA*UC FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=2 n=1 a=CA*UA*UC*GG FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=3 n=1 a=UA*UC*GG*CA FASTA(n).Sequence=UC*GG*CA*UA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:12:20
Finding core edit distance of 7800 sequences against   65 models over    4 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.1191 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:03
Parsing 7800 sequences from file J4_RandomMotifSequences_15.fasta against 65 models over 4 rotations
Parsed against   50 models so far, total time estimate   9.6879 minutes
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_1.mat
max_rotation=3 r=0 n=1 a=CC*GC*GG*CG FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=1 n=1 a=GC*GG*CG*CC FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CC*GC FASTA(n).Sequence=CC*GC*GG*CG
max_rotation=3 r=3 n=1 a=CG*CC*GC*GG FASTA(n).Sequence=CC*GC*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:42
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_2.mat
max_rotation=3 r=0 n=1 a=CG*CU*GG*CG FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=1 n=1 a=CU*GG*CG*CG FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CG*CU FASTA(n).Sequence=CG*CU*GG*CG
max_rotation=3 r=3 n=1 a=CG*CG*CU*GG FASTA(n).Sequence=CG*CU*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:43
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_3.mat
max_rotation=3 r=0 n=1 a=CG*CC*GG*CG FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=1 n=1 a=CC*GG*CG*CG FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=2 n=1 a=GG*CG*CG*CC FASTA(n).Sequence=CG*CC*GG*CG
max_rotation=3 r=3 n=1 a=CG*CG*CC*GG FASTA(n).Sequence=CG*CC*GG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:44
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_4.mat
max_rotation=3 r=0 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=1 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=2 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
max_rotation=3 r=3 n=1 a=AU*AU*AU*AU FASTA(n).Sequence=AU*AU*AU*AU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:44
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_5.mat
max_rotation=3 r=0 n=1 a=UG*CC*GA*UA FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=1 n=1 a=CC*GA*UA*UG FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=2 n=1 a=GA*UA*UG*CC FASTA(n).Sequence=UG*CC*GA*UA
max_rotation=3 r=3 n=1 a=UA*UG*CC*GA FASTA(n).Sequence=UG*CC*GA*UA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:45
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_6.mat
max_rotation=3 r=0 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=1 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GC*GC FASTA(n).Sequence=GC*GC*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:46
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_7.mat
max_rotation=3 r=0 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=1 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=2 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GC*GG*CC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:46
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_8.mat
max_rotation=3 r=0 n=1 a=CA*UG*CG*CG FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=1 n=1 a=UG*CG*CG*CA FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=2 n=1 a=CG*CG*CA*UG FASTA(n).Sequence=CA*UG*CG*CG
max_rotation=3 r=3 n=1 a=CG*CA*UG*CG FASTA(n).Sequence=CA*UG*CG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:47
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_9.mat
max_rotation=3 r=0 n=1 a=GU*GU*GC*GC FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=1 n=1 a=GU*GC*GC*GU FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GU*GU FASTA(n).Sequence=GU*GU*GC*GC
max_rotation=3 r=3 n=1 a=GC*GU*GU*GC FASTA(n).Sequence=GU*GU*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:47
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_10.mat
max_rotation=3 r=0 n=1 a=GC*GG*CU*GU FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=1 n=1 a=GG*CU*GU*GC FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=2 n=1 a=CU*GU*GC*GG FASTA(n).Sequence=GC*GG*CU*GU
max_rotation=3 r=3 n=1 a=GU*GC*GG*CU FASTA(n).Sequence=GC*GG*CU*GU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:48
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_11.mat
max_rotation=3 r=0 n=1 a=AC*GG*CU*AU FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=1 n=1 a=GG*CU*AU*AC FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=2 n=1 a=CU*AU*AC*GG FASTA(n).Sequence=AC*GG*CU*AU
max_rotation=3 r=3 n=1 a=AU*AC*GG*CU FASTA(n).Sequence=AC*GG*CU*AU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:49
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_12.mat
max_rotation=3 r=0 n=1 a=CC*GG*CG*CG FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=1 n=1 a=GG*CG*CG*CC FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=2 n=1 a=CG*CG*CC*GG FASTA(n).Sequence=CC*GG*CG*CG
max_rotation=3 r=3 n=1 a=CG*CC*GG*CG FASTA(n).Sequence=CC*GG*CG*CG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:49
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_13.mat
max_rotation=3 r=0 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=1 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=2 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GC*GG*CC*GC
max_rotation=3 r=3 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GC*GG*CC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:50
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_14.mat
max_rotation=3 r=0 n=1 a=GG*CC*GC*GC FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=1 n=1 a=CC*GC*GC*GG FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=2 n=1 a=GC*GC*GG*CC FASTA(n).Sequence=GG*CC*GC*GC
max_rotation=3 r=3 n=1 a=GC*GG*CC*GC FASTA(n).Sequence=GG*CC*GC*GC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:50
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J4\3.48\diagnostic\J4_RandomMotifSequences_15.mat
max_rotation=3 r=0 n=1 a=UC*GG*CA*UA FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=1 n=1 a=GG*CA*UA*UC FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=2 n=1 a=CA*UA*UC*GG FASTA(n).Sequence=UC*GG*CA*UA
max_rotation=3 r=3 n=1 a=UA*UC*GG*CA FASTA(n).Sequence=UC*GG*CA*UA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:24:51
Evaluating how sequences fit models
Saved group data

GroupData = 

  1×65 <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\J4\3.48\J4_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J4\3.48\J4_GroupData.mat
