Timestamp 18-Jul-2025 00:12:34
pMakeSCFGModels: Looking for motifs in C:\Users\zirbel\Documents\JAR3D\Motifs\J3_3.48\mat
pMakeSCFGModels: Found 88 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 J3_00584.1
    {'> J3_00584.1  7A0S C 2769 G 2868'}    {'CACGGU*AAGCG*AGG'}

pCalculateTransitions:  processing J3_02067.1
    {'> J3_02067.1  4P95 G    7 U  260'}    {'GUAUC*GAAG*CAAU'}

pCalculateTransitions:  processing J3_04858.1
    {'> J3_04858.1  5J7L U 1344…'}    {'UCGACC*GAAA*UA'}    {'> J3_04858.1  5TBW U 1526…'}    {'UCGAUC*GGAAU*AA'}

pCalculateTransitions:  processing J3_05170.1
    {'> J3_05170.1  7A0S C  246 G  383'}    {'CAAACGGG*UU*GUAUG'}

pCalculateTransitions:  processing J3_06335.1
    {'> J3_06335.1  4V9F C  240 G  379'}    {'CAAAC*GUGUCAG*CAG'}

pCalculateTransitions:  processing J3_06579.1
    {'> J3_06579.1  2R8S C  138 G  180'}    {'CAAGU*GGCG*GUAUG'}

pCalculateTransitions:  processing J3_08394.2
  Columns 1 through 5

    {'> J3_08394.2  4…'}    {'CGUCAG*CGCAACC*…'}    {'> J3_08394.2  5…'}    {'CGUCAG*CGCAACC*…'}    {'> J3_08394.2  6…'}

  Column 6

    {'CGUCAG*CGCAACC*…'}

pCalculateTransitions:  processing J3_08465.1
    {'> J3_08465.1  4WF9 U 2118 G 2255'}    {'UUGCUAA*CCG*AGACAG'}

pCalculateTransitions:  processing J3_11279.1
    {'> J3_11279.1  4V88 C 1161…'}    {'CCAGCUAG*UAAU*GAUUACG'}    {'> J3_11279.1  4LFB C  936…'}    {'CAAGCUAG*UAAU*GAAUACG'}

pCalculateTransitions:  processing J3_11934.2
  Columns 1 through 5

    {'> J3_11934.2  1…'}    {'UGCGCCGA*GGC*AG'}    {'> J3_11934.2  6…'}    {'UGCGCCGA*GGC*AG'}    {'> J3_11934.2  5…'}

  Columns 6 through 8

    {'UAUACCGG*GGC*GG'}    {'> J3_11934.2  1…'}    {'UGCGCCGA*GGC*AG'}

pCalculateTransitions:  processing J3_13944.1
    {'> J3_13944.1  7A0S C   12…'}    {'CCCAUAG*CGC*GUCAG'}    {'> J3_13944.1  5J7L G   10…'}    {'GCCGUAG*CGC*GGAAC'}

pCalculateTransitions:  processing J3_15893.1
  Columns 1 through 5

    {'> J3_15893.1  6…'}    {'UUAAUC*GUAG*CGCA'}    {'> J3_15893.1  4…'}    {'UGAAUC*GUAG*CGAA'}    {'> J3_15893.1  6…'}

  Columns 6 through 10

    {'CGAAUC*GUAC*GGAG'}    {'> J3_15893.1  4…'}    {'UGAAUC*GUAG*CGAA'}    {'> J3_15893.1  4…'}    {'CGAAUC*GUAG*CGAG'}

pCalculateTransitions:  processing J3_18709.1
    {'> J3_18709.1  4V88 C 1037 G 1094'}    {'CUAUU*ACGC*AAAG'}

pCalculateTransitions:  processing J3_19256.1
    {'> J3_19256.1  7KGA G    5…'}    {'GCGACGA*AA*CCC'}    {'> J3_19256.1  7KGA G    5…'}    {'GCGACGA*AA*CCC'}

pCalculateTransitions:  processing J3_19286.1
    {'> J3_19286.1  5KPY C   18 G   78'}    {'CUGAUGAU*AUUG*CACG'}

pCalculateTransitions:  processing J3_19431.1
    {'> J3_19431.1  5TBW C    9 G  112'}    {'CCAUAU*AG*UG'}

pCalculateTransitions:  processing J3_20650.1
    {'> J3_20650.1  5BJO C    5 G   32'}    {'CGAGG*CUG*CACUG'}

pCalculateTransitions:  processing J3_22198.1
    {'> J3_22198.1  4RGE A   11 U   44'}    {'AGCC*GAG*CUAAU'}

pCalculateTransitions:  processing J3_25217.1
    {'> J3_25217.1  2RFK C   16 G   11'}    {'CG*UUCG*CGUG'}

pCalculateTransitions:  processing J3_25670.1
    {'> J3_25670.1  5TBW C 1631 G 1811'}    {'CACGUA*AC*UAG'}

pCalculateTransitions:  processing J3_28621.2
  Columns 1 through 5

    {'> J3_28621.2  4…'}    {'GGAUCUA*AGA*UAC'}    {'> J3_28621.2  6…'}    {'GGAUUUA*AAG*CAC'}    {'> J3_28621.2  1…'}

  Columns 6 through 10

    {'GGAUUUA*AAG*CAC'}    {'> J3_28621.2  5…'}    {'GGAUUUA*AAG*CAC'}    {'> J3_28621.2  5…'}    {'GACGCUA*AGG*CAC'}

  Columns 11 through 12

    {'> J3_28621.2  5…'}    {'GGAUUUA*AAG*CAC'}

pCalculateTransitions:  processing J3_30104.1
    {'> J3_30104.1  5J7L C 2789 G 2894'}    {'CUG*CC*GAG'}

pCalculateTransitions:  processing J3_32030.1
    {'> J3_32030.1  3NPQ C   13 G   48'}    {'CUGCAAG*CCCAG*CGG'}

pCalculateTransitions:  processing J3_32601.2
  Columns 1 through 5

    {'> J3_32601.2  4…'}    {'CAUCGUUAU*UA*AAG'}    {'> J3_32601.2  5…'}    {'CAUCGUAUU*UA*AAG'}    {'> J3_32601.2  4…'}

  Columns 6 through 8

    {'CAUCGUUAU*UA*AAG'}    {'> J3_32601.2  7…'}    {'CAUCGUUAU*UA*AAG'}

pCalculateTransitions:  processing J3_32852.2
  Columns 1 through 5

    {'> J3_32852.2  7…'}    {'CGUAAG*CGA*UAAG'}    {'> J3_32852.2  4…'}    {'CGUAAG*CGG*UCAG'}    {'> J3_32852.2  4…'}

  Columns 6 through 8

    {'CGAUUG*CAA*UAAG'}    {'> J3_32852.2  5…'}    {'CGGAAG*CAG*CAAG'}

pCalculateTransitions:  processing J3_32857.1
    {'> J3_32857.1  4LFB G1003A C 1038'}    {'GAAC*GGUGCC*GGAGCC'}

pCalculateTransitions:  processing J3_33851.1
    {'> J3_33851.1  5TBW A  828 U  897'}    {'AUAGC*GUAGU*CGAAU'}

pCalculateTransitions:  processing J3_35321.1
    {'> J3_35321.1  5TBW U  986 A 1098'}    {'UUAGAAG*CA*UUUGA'}

pCalculateTransitions:  processing J3_36387.1
    {'> J3_36387.1  4WFL C   10 G  102'}    {'CUAAG*CCGAAUCC*GUG'}

pCalculateTransitions:  processing J3_36499.1
    {'> J3_36499.1  4UYK C   10 G  135'}    {'CUAG*CGAAG*CGUG'}

pCalculateTransitions:  processing J3_37047.2
  Columns 1 through 5

    {'> J3_37047.2  4…'}    {'CAAUGCCC*AGUUC*…'}    {'> J3_37047.2  5…'}    {'CAAUGCGU*AGUCC*…'}    {'> J3_37047.2  4…'}

  Columns 6 through 8

    {'CACUGCGU*GCUGG*…'}    {'> J3_37047.2  6…'}    {'CAAUGCCC*AGUUC*…'}

pCalculateTransitions:  processing J3_37410.1
    {'> J3_37410.1  5TBW A 2432 U 2597'}    {'AUUGCUUA*UUAA*GACAUU'}

pCalculateTransitions:  processing J3_38151.1
    {'> J3_38151.1  6ZDP A 1294 U 1343'}    {'AAG*CAA*UGCU'}

pCalculateTransitions:  processing J3_38446.1
    {'> J3_38446.1  5TBW U  502 A  611'}    {'UCGAGGACUG*CGCAAG*GA'}

pCalculateTransitions:  processing J3_38616.1
    {'> J3_38616.1  4V88 A  881 U  947'}    {'AUCAUAAC*UACUGC*AUUU'}

pCalculateTransitions:  processing J3_39238.2
  Columns 1 through 5

    {'> J3_39238.2  4…'}    {'CGAUCUA*UAG*CGAG'}    {'> J3_39238.2  4…'}    {'UGAUCUA*UAG*CGAA'}    {'> J3_39238.2  7…'}

  Columns 6 through 10

    {'UGAGCUA*UAG*CGAA'}    {'> J3_39238.2  5…'}    {'UGAACUA*UAG*CGAA'}    {'> J3_39238.2  5…'}    {'UGAUCUA*UGG*CAAA'}

  Columns 11 through 12

    {'> J3_39238.2  4…'}    {'CGAGCUA*UAG*CGAG'}

pCalculateTransitions:  processing J3_41097.1
    {'> J3_41097.1  4KZ2 G    8…'}    {'GUG*CUUUG*UC'}    {'> J3_41097.1  3R4F G    4…'}    {'GUG*CUUUG*UC'}

pCalculateTransitions:  processing J3_42157.1
  Columns 1 through 5

    {'> J3_42157.1  5…'}    {'CAAGC*CCAAA*CGUG'}    {'> J3_42157.1  5…'}    {'GAAAU*GAUAA*CGUC'}    {'> J3_42157.1  4…'}

  Column 6

    {'UAAGC*GAGAA*CGUG'}

pCalculateTransitions:  processing J3_44724.2
  Columns 1 through 6

    {'> J3_44724.2  7…'}    {'CAGCG*AACG*AUG'}    {'> J3_44724.2  4…'}    {'CAGCG*AACG*AUG'}    {'> J3_44724.2  5…'}    {'CAGCG*AACG*AUG'}

  Columns 7 through 10

    {'> J3_44724.2  4…'}    {'CAAUG*UAGC*GUG'}    {'> J3_44724.2  4…'}    {'CAGCG*AACG*AUG'}

pCalculateTransitions:  processing J3_45941.1
    {'> J3_45941.1  4O26 A  173 U  217'}    {'ACGCC*GAA*UGUUGU'}

pCalculateTransitions:  processing J3_47248.1
    {'> J3_47248.1  4V88 U 1283 A 1424'}    {'UCUUAGC*GAGACG*CAAUA'}

pCalculateTransitions:  processing J3_47376.1
    {'> J3_47376.1  6P2H G   21 C   79'}    {'GU*ACC*GUCACC'}

pCalculateTransitions:  processing J3_47707.1
    {'> J3_47707.1  4WF9 A   56 U  113'}    {'ACGUUACUAACG*UGC*GAUUU'}

pCalculateTransitions:  processing J3_48314.1
    {'> J3_48314.1  5TBW C 3298 G 3390'}    {'CAUAG*AUG*CUG'}

pCalculateTransitions:  processing J3_51910.1
    {'> J3_51910.1  4R4V G  655 C  764'}    {'GAAC*GG*CACAAGC'}

pCalculateTransitions:  processing J3_52655.1
    {'> J3_52655.1  4…'}    {'UGGA*UAC*GGAA'}    {'> J3_52655.1  4…'}    {'UGGA*UAC*GGAA'}    {'> J3_52655.1  5…'}    {'UGGA*UAC*GGAA'}

pCalculateTransitions:  processing J3_52842.1
    {'> J3_52842.1  7A0S U 2789 A 2861'}    {'UCGUUA*GC*AUCA'}

pCalculateTransitions:  processing J3_52917.1
    {'> J3_52917.1  5TBW U 2886 A 2936'}    {'UAUCGUUAC*UA*AUA'}

pCalculateTransitions:  processing J3_56052.2
  Columns 1 through 6

    {'> J3_56052.2  5…'}    {'CGG*CUUG*CG'}    {'> J3_56052.2  6…'}    {'CGG*CUAG*CG'}    {'> J3_56052.2  1…'}    {'CGG*CUAG*CG'}

  Columns 7 through 8

    {'> J3_56052.2  1…'}    {'CGG*CUAG*CG'}

pCalculateTransitions:  processing J3_56708.1
    {'> J3_56708.1  3EGZ G    5 C   61'}    {'GAGAGCUAA*AACAU*AC'}

pCalculateTransitions:  processing J3_58090.1
    {'> J3_58090.1  6LAX C    6 G   50'}    {'CGUG*CGAUAAGUC*GG'}

pCalculateTransitions:  processing J3_58453.1
    {'> J3_58453.1  6JQ5 G   27 C   77'}    {'GUGGGC*AGAUUAA*AACC'}

pCalculateTransitions:  processing J3_59914.1
    {'> J3_59914.1  4KR9 U    8 G   28'}    {'UAG*CUU*AAG'}

pCalculateTransitions:  processing J3_64069.1
    {'> J3_64069.1  5J7L G 2812 C 2888'}    {'GAAC*GUUGAU*AAUGAAC'}

pCalculateTransitions:  processing J3_65070.2
  Columns 1 through 5

    {'> J3_65070.2  7…'}    {'GCGUGAAA*AG*CC'}    {'> J3_65070.2  5…'}    {'GCGCGAAA*AG*CC'}    {'> J3_65070.2  5…'}

  Column 6

    {'CUCGCGAAAAGUAUG…'}

pCalculateTransitions:  processing J3_65990.1
    {'> J3_65990.1  3PDR C   54 G  120'}    {'CUG*UCAACAG*UUAAUG'}

pCalculateTransitions:  processing J3_68440.1
    {'> J3_68440.1  6DB9 C    9 G   52'}    {'CUUGAAAAGCCUG*CA*UAUG'}

pCalculateTransitions:  processing J3_69441.1
    {'> J3_69441.1  4V9F C 2552 G 2602'}    {'CAUC*GUGA*UAUUAAAG'}

pCalculateTransitions:  processing J3_72575.1
    {'> J3_72575.1  3NDB G  145 C  233'}    {'GGUG*CUUUAC*GAC'}

pCalculateTransitions:  processing J3_72804.1
    {'> J3_72804.1  3IWN G    4 C   88'}    {'GCACAGGG*CAAAGC*GUUACC'}

pCalculateTransitions:  processing J3_75187.1
    {'> J3_75187.1  3PDR G   43 C  142'}    {'GAGAUACG*CUG*CUAUGC'}

pCalculateTransitions:  processing J3_79305.1
    {'> J3_79305.1  6CZR C 1099 G 1166'}    {'CGCGGACUG*CGA*GGAAGGAG'}

pCalculateTransitions:  processing J3_82061.2
    {'> J3_82061.2  5…'}    {'CCAG*CC*GCG'}    {'> J3_82061.2  7…'}    {'CCCUC*GU*AG'}    {'> J3_82061.2  5…'}    {'GCAG*CC*GCC'}

pCalculateTransitions:  processing J3_82365.1
    {'> J3_82365.1  4…'}    {'AACG*GAC*GUUU'}    {'> J3_82365.1  5…'}    {'UAUA*GAC*GGUG'}    {'> J3_82365.1  4…'}    {'CGCG*GAC*GGAG'}

pCalculateTransitions:  processing J3_82572.1
    {'> J3_82572.1  4LFB C  990…'}    {'CUUG*CAG*CUUACG'}    {'> J3_82572.1  5J7L C  990…'}    {'CUUG*CAG*CUUACG'}

pCalculateTransitions:  processing J3_83516.1
  Columns 1 through 5

    {'> J3_83516.1  4…'}    {'UUUAAUUCG*AAGAA…'}    {'> J3_83516.1  5…'}    {'UUUAAUUCG*AAGAA…'}    {'> J3_83516.1  4…'}

  Column 6

    {'CUUAAUUUG*GGAAA…'}

pCalculateTransitions:  processing J3_84189.2
  Columns 1 through 5

    {'> J3_84189.2  7…'}    {'CAAGCG*CAAA*CGUG'}    {'> J3_84189.2  4…'}    {'CAAGAACGUACGUAA…'}    {'> J3_84189.2  4…'}

  Column 6

    {'CAAGCG*CAAA*CGUG'}

pCalculateTransitions:  processing J3_84625.1
    {'> J3_84625.1  5J7L A   56…'}    {'ACGAUA*GCGAU*UU'}    {'> J3_84625.1  7A0S A   55…'}    {'ACGAAA*GCGAU*GU'}

pCalculateTransitions:  processing J3_85054.2
  Columns 1 through 5

    {'> J3_85054.2  4…'}    {'CUAAG*CGCAAAC*G…'}    {'> J3_85054.2  6…'}    {'CGAAG*CGUUAAG*C…'}    {'> J3_85054.2  4…'}

  Columns 6 through 8

    {'CGAAG*CGUUAAG*C…'}    {'> J3_85054.2  5…'}    {'CGGAG*CGUUAAG*C…'}

pCalculateTransitions:  processing J3_86907.1
    {'> J3_86907.1  6CZR G  932 C 1208'}    {'GUUUAAUUCG*AAGAACCUUA*CCGGGCGAC'}

pCalculateTransitions:  processing J3_89044.1
    {'> J3_89044.1  4R4V C  610 G  775'}    {'CGCAAUC*GUAG*CGAG'}

pCalculateTransitions:  processing J3_89368.2
  Columns 1 through 5

    {'> J3_89368.2  5…'}    {'CUGCUAA*CGG*ACAG'}    {'> J3_89368.2  7…'}    {'UUGCUAA*CGG*ACCG'}    {'> J3_89368.2  4…'}

  Column 6

    {'UUGCUAA*CGG*ACAG'}

pCalculateTransitions:  processing J3_89737.1
    {'> J3_89737.1  4V9F C    9 G  114'}    {'CCACAG*CGUUC*GUUCG'}

pCalculateTransitions:  processing J3_90256.1
    {'> J3_90256.1  6JQ6 G   27…'}    {'GUGGGCA*GACGU*AAAACC'}    {'> J3_90256.1  6JQ6 G   27…'}    {'GUGGGCA*GACAGACGGGUGCCAAA…'}

pCalculateTransitions:  processing J3_90744.1
    {'> J3_90744.1  4OJI U   12 A   41'}    {'UGCCGCG*AUAA*AA'}

pCalculateTransitions:  processing J3_91491.2
  Columns 1 through 6

    {'> J3_91491.2  4…'}    {'CUCGA*GCA*AAG'}    {'> J3_91491.2  4…'}    {'CUCGA*GCA*AAG'}    {'> J3_91491.2  4…'}    {'CUCGA*GUA*AAG'}

  Columns 7 through 12

    {'> J3_91491.2  7…'}    {'CUCGA*GUA*AAG'}    {'> J3_91491.2  5…'}    {'CUCGA*AUA*AAG'}    {'> J3_91491.2  5…'}    {'CUAUA*GCA*AAG'}

pCalculateTransitions:  processing J3_93059.1
    {'> J3_93059.1  6MWN C  610 G  667'}    {'CUUAAAUG*CUC*GG'}

pCalculateTransitions:  processing J3_93637.1
    {'> J3_93637.1  3KTW U  144 A  234'}    {'UAGUC*GUUGAC*GCUA'}

pCalculateTransitions:  processing J3_94515.1
    {'> J3_94515.1  4V88 A  760 U  790'}    {'AGAGCA*GUCG*AAU'}

pCalculateTransitions:  processing J3_94652.1
    {'> J3_94652.1  1G1X C  586 G  755'}    {'CGGC*GCUAG*CG'}

pCalculateTransitions:  processing J3_96170.1
    {'> J3_96170.1  6JQ5 U   70 A   67'}    {'UUAAAACC*GUGGG*CAGA'}

pCalculateTransitions:  processing J3_96372.1
    {'> J3_96372.1  3MXH G   14…'}    {'GCACAGGG*CAAAG*UUACC'}    {'> J3_96372.1  4YAZ G    8…'}    {'GACAAUAC*GAAAG*CUGCC'}

pCalculateTransitions:  processing J3_97609.1
    {'> J3_97609.1  4V9F G 2131 C 2262'}    {'GCUG*CUCAC*GGACACC'}

pCalculateTransitions:  processing J3_98102.1
    {'> J3_98102.1  4V88 C 1215 G 1448'}    {'CCAGAC*GGGUG*UUAGACG'}

pCalculateTransitions:  processing J3_98298.1
    {'> J3_98298.1  5TBW C  113 G  267'}    {'CAAAUUUGAAAU*AAUUU*GGAGCGAAG'}

pCalculateTransitions:  processing J3_98484.1
    {'> J3_98484.1  4R4V C  663 G  710'}    {'CUCC*GUCG*UGUGAUUG'}

pCalculateTransitions:  processing J3_98985.1
    {'> J3_98985.1  6CZR G   47…'}    {'GCGGAAU*CUA*GC'}    {'> J3_98985.1  5J7L G   46…'}    {'GCGGAAU*AUA*GC'}

pCalculateTransitions:  processing J3_99170.1
    {'> J3_99170.1  5TBW U 1479 A 1874'}    {'UGAAGUG*CAA*UCUA'}

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

cWW_M =

    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

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

initial_M =

    0.2906
    0.1437
    0.3000
    0.2656

pCalculateTransitions:  initial transition matrix is

initialTransition_M =

    0.4211    0.2105    0.1842    0.1842
    0.2868    0.0809    0.3676    0.2647
    0.2500    0.2065    0.2391    0.3043
    0.2778    0.1481    0.3148    0.2593

pCalculateTransitions:  interior transition matrix is

transition_M =

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

Timestamp 18-Jul-2025 00:12:37
pMakeSCFGModels: Making JAR3D model for motif group J3_00584.1, number 1 of 88
pMakeSCFGModels: Loaded C:\Users\zirbel\Documents\JAR3D\Motifs\J3_3.48\mat\J3_00584.1.mat, looks like:
Search = 

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

         motif_id: 'J3_00584.1'
       Candidates: [4 5 6 7 8 9 10 11 12 13 14 1 2 3 1]
    consensusEdge: [14×14 double]
     bp_signature: 'cWW-F-F-tWH-cWW-tSS-F-tHS-F-cWW'
        Signature: 'cWW-F-F-tWH-cWW-tSS-F-tHS-F-cWW'
       chainbreak: {2×1 cell}
         loop_ids: {'J3_7A0S_012'}
         Truncate: [2×1 double]
            Query: [1×1 struct]
       MaxDiffMat: [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 0 0 0 0 Inf 0 0 0 0 Inf]
             File: [1×1 struct]
         NumFixed: 0


ans = 

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

         Backbone: [14×14 double]
    BasePhosphate: [14×14 double]
       BaseRibose: [14×14 double]
       BestChains: {{2×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [14×14 double]
         Covalent: [14×14 double]
         Crossing: [14×14 double]
         Distance: []
             Edge: [54×55 double]
         Filename: '7A0S'
            Flank: [14×14 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [1 2699]
         Modified: 0
               NT: [1×14 struct]
            NumNT: 14
      PDBFilename: '7A0S.pdb'
            PDBID: '7A0S'
            Range: [14×14 double]
        Redundant: [14×14 double]


ans = 

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

         Backbone: [14×14 double]
    BasePhosphate: [14×14 double]
       BaseRibose: [14×14 double]
       BestChains: {{2×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [14×14 double]
         Covalent: [14×14 double]
         Crossing: [14×14 double]
         Distance: []
             Edge: [54×55 double]
         Filename: '7A0S'
            Flank: [14×14 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [1 2699]
         Modified: 0
               NT: [1×14 struct]
            NumNT: 14
      PDBFilename: '7A0S.pdb'
            PDBID: '7A0S'
            Range: [14×14 double]
        Redundant: [14×14 double]

pMakeNodes starting loop:     a=7A0S|1|X|G|2781 B=7A0S|1|X|C|2771
  2 Basepair  2781 2771 GC cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|2782 B=7A0S|1|X|A|2770
    Insertion on right 7A0S|1|X|A|2770
pMakeNodes probed for insert:  a=7A0S|1|X|G|2782 B=7A0S|1|X|C|2769
pMakeNodesJunction: a=7A0S|1|X|G|2782 r=7A0S|1|X|G|2782 s=7A0S|1|X|G|2867 t=7A0S|1|X|G|2868 u=B=7A0S|1|X|C|2769
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|G|2782 and 7A0S|1|X|G|2867 and between 7A0S|1|X|G|2868 and 7A0S|1|X|C|2769
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|G|2782 s=7A0S|1|X|G|2867 t=7A0S|1|X|G|2868 B=7A0S|1|X|C|2769
pMakeNodesJunction: first branch starts at   7A0S|1|X|G|2782
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|2867
pMakeNodesJunction: second branch starts at  7A0S|1|X|G|2868
pMakeNodesJunction: junction ends at         7A0S|1|X|C|2769
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|2786
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|C|2864
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|2868
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|2769
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J8147
Actual Branch 1 of junction J8147 - Nucleotides 7A0S|1|X|G|2782 to 7A0S|1|X|G|2867, length   9
Actual Branch 2 of junction J8147 - Nucleotides 7A0S|1|X|G|2868 to 7A0S|1|X|C|2769, length   2
  3 Junction

2B Branch 1 of 2 of junction J8147 - Nucleotides  2782 to  2867, length   9
pMakeNodes starting loop:     a=7A0S|1|X|G|2782 B=7A0S|1|X|G|2867
  5 Basepair  2782 2867 GG tWW 
No need to probe because of interaction between a=7A0S|1|X|U|2783 B=7A0S|1|X|A|2866
  6 Basepair  2783 2866 UA tWH 
pMakeNodes probe for inserts:  a=7A0S|1|X|A|2784 B=7A0S|1|X|G|2865
    Insertion on left  7A0S|1|X|A|2784
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|2785 interacts with 7A0S|1|X|G|2865
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2865 interacts with 7A0S|1|X|A|2785
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2865 interacts with 7A0S|1|X|A|2785
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7A0S|1|X|A|2785 B=7A0S|1|X|G|2865
  7 Basepair  2785 2865 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|G|2786 B=7A0S|1|X|C|2864
  8 Basepair  2786 2864 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J8147 - Nucleotides  2868 to  2769, length   2
pMakeNodes starting loop:     a=7A0S|1|X|G|2868 B=7A0S|1|X|C|2769
 11 Basepair  2868 2769 GC cWW 
 12 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 10
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  10   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|2867
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|2781
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 'G'
           RightLetter: 'AC'
               Comment: ' // Basepair G2781 - 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: 13
             Insertion: []
                    id: 'J8147'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|2867'
              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: 'J8147'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 10]
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: 'J8147'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2782 - C2769 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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 10
             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 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G2782 - G2867 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: 'Basepair'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U2783 - A2866 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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2781'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J8147'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2785 - G2865 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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2786 - C2864 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 11
            RightIndex: 12
             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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             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 G2868 - C2769 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 19
             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  2 Right 12
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  14   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  16   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 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

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 10
             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: 15
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: 'J8147'
        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 J3_00584.1. Nodes 6 and 14 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 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

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 9 and 12
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 9 and 12
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_00584.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7248

Timestamp 18-Jul-2025 00:12:40
pMakeSCFGModels: Making JAR3D model for motif group J3_02067.1, number 2 of 88
pMakeNodes starting loop:     a=4P95|1|A|G|7 B=4P95|1|A|U|260
  2 Basepair     7  260 GU cWW 
No need to probe because of interaction between a=4P95|1|A|U|8 B=4P95|1|A|A|259
  3 Basepair     8  259 UA tSS 
pMakeNodes probe for inserts:  a=4P95|1|A|A|9 B=4P95|1|A|A|258
    Insertion on left  4P95|1|A|A|9
    Insertion on left  4P95|1|A|U|10
    Insertion on right 4P95|1|A|A|258
pMakeNodes probed for insert:  a=4P95|1|A|C|11 B=4P95|1|A|C|257
pMakeNodesJunction: a=4P95|1|A|C|11 r=4P95|1|A|C|11 s=4P95|1|A|G|230 t=4P95|1|A|A|231 u=B=4P95|1|A|C|257
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4P95|1|A|C|11 and 4P95|1|A|G|230 and between 4P95|1|A|A|231 and 4P95|1|A|C|257
pMakeNodesJunction: about to make a junction: a=4P95|1|A|C|11 s=4P95|1|A|G|230 t=4P95|1|A|A|231 B=4P95|1|A|C|257
pMakeNodesJunction: first branch starts at   4P95|1|A|C|11
pMakeNodesJunction: first branch ends around 4P95|1|A|G|230
pMakeNodesJunction: second branch starts at  4P95|1|A|A|231
pMakeNodesJunction: junction ends at         4P95|1|A|C|257
pMakeNodesJunction: first branch strand start goes up to  4P95|1|A|C|11
pMakeNodesJunction: first branch strand end goes down to  4P95|1|A|G|230
pMakeNodesJunction: second branch strand start goes up to 4P95|1|A|G|233
pMakeNodesJunction: last strand of junction goes down to  4P95|1|A|C|257

Junction with 2 loops, call it J9057
Actual Branch 1 of junction J9057 - Nucleotides 4P95|1|A|C|11 to 4P95|1|A|G|230, length   2
Actual Branch 2 of junction J9057 - Nucleotides 4P95|1|A|A|231 to 4P95|1|A|C|257, length   4
  4 Junction

2B Branch 1 of 2 of junction J9057 - Nucleotides    11 to   230, length   2
pMakeNodes starting loop:     a=4P95|1|A|C|11 B=4P95|1|A|G|230
  6 Basepair    11  230 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J9057 - Nucleotides   231 to   257, length   4
pMakeNodes starting loop:     a=4P95|1|A|A|231 B=4P95|1|A|C|257
    Insertion on left  4P95|1|A|A|231
    Insertion on left  4P95|1|A|A|232
pMakeNodesProbeForInsertions:  a 4P95|1|A|G|233 interacts with 4P95|1|A|C|257
pMakeNodesProbeForInsertions:  B 4P95|1|A|C|257 interacts with 4P95|1|A|G|233
pMakeNodesProbeForInsertions:  B 4P95|1|A|C|257 interacts with 4P95|1|A|G|233
  8 Initial    231 (2 insertion) and  257 (0 insertion)
  9 Basepair   233  257 GC cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  10   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4P95|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4P95|1|A|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4P95|1|A|A|258
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4P95|1|A|A|231
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4P95|1|A|A|232
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G7 - U260 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 12
             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: 'UAU'
           RightLetter: 'AA'
               Comment: ' // Basepair U8 - A259 tSS '
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 11
             Insertion: []
                    id: 'J9057'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4P95|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 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J9057'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 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 4P95|1|A|U|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     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: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: 'J9057'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4P95|1|A|A|258'
              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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J9057'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C11 - C257 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 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: '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 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 C11 - G230 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 'J9057'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4P95|1|A|A|231 - 4P95|1|A|C|257 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 4P95|1|A|A|231'
              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 4P95|1|A|A|232'
              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 G233 - C257 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  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 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

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             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: 15
             LeftIndex: 7
            RightIndex: 10
             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: 'AA'
           RightLetter: []
               Comment: ' // Initial node 4P95|1|A|A|231 - 4P95|1|A|C|257 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_02067.1. 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_02067.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5427

Timestamp 18-Jul-2025 00:12:40
pMakeSCFGModels: Making JAR3D model for motif group J3_04858.1, number 3 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|U|1344 B=5J7L|1|DA|A|1403
  2 Basepair  1344 1403 UA cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|1345 B=5J7L|1|DA|U|1402
    Insertion on left  5J7L|1|DA|C|1345
    Insertion on left  5J7L|1|DA|G|1346
    Insertion on left  5J7L|1|DA|A|1347
    Insertion on left  5J7L|1|DA|C|1348
pMakeNodes probed for insert:  a=5J7L|1|DA|C|1349 B=5J7L|1|DA|U|1402
pMakeNodesJunction: a=5J7L|1|DA|C|1349 r=5J7L|1|DA|C|1349 s=5J7L|1|DA|G|1382 t=5J7L|1|DA|A|1383 u=B=5J7L|1|DA|U|1402
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|1349 and 5J7L|1|DA|G|1382 and between 5J7L|1|DA|A|1383 and 5J7L|1|DA|U|1402
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|1349 s=5J7L|1|DA|G|1382 t=5J7L|1|DA|A|1383 B=5J7L|1|DA|U|1402
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|1349
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|1382
pMakeNodesJunction: second branch starts at  5J7L|1|DA|A|1383
pMakeNodesJunction: junction ends at         5J7L|1|DA|U|1402
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|1349
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|1382
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|A|1385
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|U|1402

Junction with 2 loops, call it J1269
Actual Branch 1 of junction J1269 - Nucleotides 5J7L|1|DA|C|1349 to 5J7L|1|DA|G|1382, length   2
Actual Branch 2 of junction J1269 - Nucleotides 5J7L|1|DA|A|1383 to 5J7L|1|DA|U|1402, length   4
  3 Junction

2B Branch 1 of 2 of junction J1269 - Nucleotides  1349 to  1382, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|1349 B=5J7L|1|DA|G|1382
  5 Basepair  1349 1382 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1269 - Nucleotides  1383 to  1402, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|A|1383 B=5J7L|1|DA|U|1402
    Insertion on left  5J7L|1|DA|A|1383
    Insertion on left  5J7L|1|DA|A|1384
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1385 interacts with 5J7L|1|DA|U|1402
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1402 interacts with 5J7L|1|DA|A|1385
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1402 interacts with 5J7L|1|DA|A|1385
  7 Initial   1383 (2 insertion) and 1402 (0 insertion)
  8 Basepair  1385 1402 AU cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 11
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 11
pMakeMotifModelFromSSF:   8  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   9   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|1345
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1346
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1347
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|1348
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1383
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1384
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  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: [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: 'UCGAC'
           RightLetter: 'A'
               Comment: ' // Basepair U1344 - A1403 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J1269'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|1345'
              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: 'J1269'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 5J7L|1|DA|G|1346'
              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: 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: 11
             Insertion: []
                    id: 'J1269'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1347'
              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: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|1348'
              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

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 11
             Insertion: []
                    id: 'J1269'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1349 - U1402 ID J1269'
              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: 'J1269'
        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 C1349 - G1382 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 11
             Insertion: []
                    id: 'J1269'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1383 - 5J7L|1|DA|U|1402 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: 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 5J7L|1|DA|A|1383'
              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: 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 18

ans = 

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

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1384'
              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: 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: 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 A1385 - U1402 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11  Junction Left  6 Right 11
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 11
pMakeMotifModelFromSSF:  16     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  17   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  18     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  20  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  21   Hairpin Left 11 Right 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 21
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: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J1269'
        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: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1269'
        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: 'AA'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1383 - 5J7L|1|DA|U|1402 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_04858.1. 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
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 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_04858.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8890
   -8.5821

Timestamp 18-Jul-2025 00:12:41
pMakeSCFGModels: Making JAR3D model for motif group J3_05170.1, number 4 of 88
pMakeNodes starting loop:     a=7A0S|1|X|G|269 B=7A0S|1|X|C|250
  2 Basepair   269  250 GC cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|270 B=7A0S|1|X|A|248
    Insertion on left  7A0S|1|X|G|270
pMakeNodes probed for insert:  a=7A0S|1|X|G|271 B=7A0S|1|X|A|248
  3 Basepair   271  248 GA tSH 
No need to probe because of interaction between a=7A0S|1|X|U|272 B=7A0S|1|X|A|247
pMakeNodes making a cluster near strand break a=7A0S|1|X|U|272 B=7A0S|1|X|A|247
pMakeNodesCluster: amax is 6 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 11 to 11
aa is 5 bb is 11
  4 Cluster   7A0S|1|X|U|272:7A0S|1|X|U|273 7A0S|1|X|A|247:7A0S|1|X|A|247
    LR Inter  7A0S|1|X|U|272 7A0S|1|X|A|247 tWH 
    LL Inter  7A0S|1|X|U|272 7A0S|1|X|U|273 cSH 
pMakeNodesCluster a=6 B=10 at the end
pMakeNodesCluster a=6 B=10 at the end
pMakeNodes probe for inserts:  a=7A0S|1|X|G|274 B=7A0S|1|X|C|246
    Insertion on left  7A0S|1|X|G|274
  5 Initial    274 (1 insertion) and  246 (0 insertion)
pMakeNodes probed for insert:  a=7A0S|1|X|A|276 B=7A0S|1|X|C|246
pMakeNodesJunction: a=7A0S|1|X|A|276 r=7A0S|1|X|A|276 s=7A0S|1|X|U|382 t=7A0S|1|X|G|383 u=B=7A0S|1|X|C|246
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|A|276 and 7A0S|1|X|U|382 and between 7A0S|1|X|G|383 and 7A0S|1|X|C|246
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|A|276 s=7A0S|1|X|U|382 t=7A0S|1|X|G|383 B=7A0S|1|X|C|246
pMakeNodesJunction: first branch starts at   7A0S|1|X|A|276
pMakeNodesJunction: first branch ends around 7A0S|1|X|U|382
pMakeNodesJunction: second branch starts at  7A0S|1|X|G|383
pMakeNodesJunction: junction ends at         7A0S|1|X|C|246
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|A|276
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|U|382
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|383
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|246

Junction with 2 loops, call it J9133
Actual Branch 1 of junction J9133 - Nucleotides 7A0S|1|X|A|276 to 7A0S|1|X|U|382, length   2
Actual Branch 2 of junction J9133 - Nucleotides 7A0S|1|X|G|383 to 7A0S|1|X|C|246, length   2
  6 Junction

2B Branch 1 of 2 of junction J9133 - Nucleotides   276 to   382, length   2
pMakeNodes starting loop:     a=7A0S|1|X|A|276 B=7A0S|1|X|U|382
  8 Basepair   276  382 AU cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J9133 - Nucleotides   383 to   246, length   2
pMakeNodes starting loop:     a=7A0S|1|X|G|383 B=7A0S|1|X|C|246
 11 Basepair   383  246 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  4  5 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   6  Junction Left  7 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|247
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|269
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 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 G269 - C250 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|A|247'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UU'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2526
           numbranches: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G271 - A248 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 6

ans = 

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

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [4 5]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|X|U|272:7A0S|1|X|U|273 and 7A0S|1|X|A|247:7A0S|1|X|A|247'
              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: 0.2526
           numbranches: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|G|274 - 7A0S|1|X|C|246 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: 'Fixed'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|G|269'
              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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 10

ans = 

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

                  type: 'Junction'
              nextnode: [7 10]
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J9133'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A276 - C246 ID J9133'
              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: 7
            RightIndex: 8
             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: []
          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: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A276 - U382 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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: '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: []
          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: 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 G383 - C246 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   6   Cluster Left  4  5 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  10  Junction Left  7 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  15  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  16   Hairpin Left 10 Right  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

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9133'
        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 J3_05170.1. Nodes 11 and 14 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 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

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 7
pConservedInteractionList: did not find a substitution probability matrix for tWS  between 5 and 8
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 7
pConservedInteractionList: did not find a substitution probability matrix for tWS  between 5 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_05170.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.6924

Timestamp 18-Jul-2025 00:12:42
pMakeSCFGModels: Making JAR3D model for motif group J3_06335.1, number 5 of 88
pMakeNodes starting loop:     a=4V9F|1|0|C|240 B=4V9F|1|0|G|379
  2 Basepair   240  379 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|241 B=4V9F|1|0|A|378
    Insertion on right 4V9F|1|0|A|378
pMakeNodes probed for insert:  a=4V9F|1|0|A|241 B=4V9F|1|0|C|377
pMakeNodesJunction: a=4V9F|1|0|A|241 r=4V9F|1|0|A|241 s=4V9F|1|0|U|270 t=4V9F|1|0|C|271 u=B=4V9F|1|0|C|377
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|A|241 and 4V9F|1|0|U|270 and between 4V9F|1|0|C|271 and 4V9F|1|0|C|377
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|A|241 s=4V9F|1|0|U|270 t=4V9F|1|0|C|271 B=4V9F|1|0|C|377
pMakeNodesJunction: first branch starts at   4V9F|1|0|A|241
pMakeNodesJunction: first branch ends around 4V9F|1|0|U|270
pMakeNodesJunction: second branch starts at  4V9F|1|0|C|271
pMakeNodesJunction: junction ends at         4V9F|1|0|C|377
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|C|244
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|G|267
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|273
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|377
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     0


Junction with 2 loops, call it J6323
Actual Branch 1 of junction J6323 - Nucleotides 4V9F|1|0|A|241 to 4V9F|1|0|U|270, length   8
Actual Branch 2 of junction J6323 - Nucleotides 4V9F|1|0|C|271 to 4V9F|1|0|C|377, length   3
  3 Junction

2B Branch 1 of 2 of junction J6323 - Nucleotides   241 to   270, length   8
pMakeNodes starting loop:     a=4V9F|1|0|A|241 B=4V9F|1|0|U|270
  5 Basepair   241  270 AU tHW 
No need to probe because of interaction between a=4V9F|1|0|A|242 B=4V9F|1|0|G|269
  6 Basepair   242  269 AG tHS 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|243 B=4V9F|1|0|U|268
    Insertion on left  4V9F|1|0|A|243
    Insertion on right 4V9F|1|0|U|268
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|244 interacts with 4V9F|1|0|G|267
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|267 interacts with 4V9F|1|0|C|244
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|267 interacts with 4V9F|1|0|C|244
pMakeNodes probed for insert:  a=4V9F|1|0|C|244 B=4V9F|1|0|G|267
  7 Basepair   244  267 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6323 - Nucleotides   271 to   377, length   3
pMakeNodes starting loop:     a=4V9F|1|0|C|271 B=4V9F|1|0|C|377
    Insertion on left  4V9F|1|0|C|271
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|273 interacts with 4V9F|1|0|C|377
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|377 interacts with 4V9F|1|0|G|273
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|377 interacts with 4V9F|1|0|G|273
  9 Initial    271 (1 insertion) and  377 (0 insertion)
 10 Basepair   273  377 GC cWW 
 11 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  9
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  11   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|C|377
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|243
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|U|268
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|271
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 1 1 1 1 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: 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: 'AG'
               Comment: ' // Basepair C240 - G379 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J6323'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|C|377'
              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: '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: 'Junction'
              nextnode: [4 9]
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: 'J6323'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A241 - C377 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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 9
             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 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A241 - U270 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 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: [0.0826 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: 'UG'
               Comment: ' // Basepair A242 - G269 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: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             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 4V9F|1|0|A|243'
              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: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 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 4V9F|1|0|U|268'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C244 - G267 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: 'J6323'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|C|271 - 4V9F|1|0|C|377 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: 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 4V9F|1|0|C|271'
              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: 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 18

ans = 

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

                  type: 'Basepair'
              nextnode: 19
             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 G273 - C377 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  2 Right 12
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  13  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  14   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  15   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  17   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  18  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  19   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 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
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: 7
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: 'J6323'
        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: 10
            RightIndex: 12
             Insertion: []
                    id: 'J6323'
        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 4V9F|1|0|C|271 - 4V9F|1|0|C|377 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_06335.1. Nodes 6 and 15 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 5
pNextNodeJunction: Found a junction child at node 6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 3 and 12
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 3 and 12
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_06335.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8508

Timestamp 18-Jul-2025 00:12:42
pMakeSCFGModels: Making JAR3D model for motif group J3_06579.1, number 6 of 88
pMakeNodes starting loop:     a=2R8S|1|R|G|175 B=2R8S|1|R|C|165
  2 Basepair   175  165 GC cWW 
pMakeNodes probe for inserts:  a=2R8S|1|R|G|176 B=2R8S|1|R|G|164
    Insertion on left  2R8S|1|R|G|176
    Insertion on left  2R8S|1|R|U|177
    Insertion on left  2R8S|1|R|A|178
pMakeNodes probed for insert:  a=2R8S|1|R|G|180 B=2R8S|1|R|G|164
pMakeNodesJunction: a=2R8S|1|R|G|180 r=2R8S|1|R|G|180 s=2R8S|1|R|C|138 t=2R8S|1|R|A|139 u=B=2R8S|1|R|G|164
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2R8S|1|R|G|180 and 2R8S|1|R|C|138 and between 2R8S|1|R|A|139 and 2R8S|1|R|G|164
pMakeNodesJunction: about to make a junction: a=2R8S|1|R|G|180 s=2R8S|1|R|C|138 t=2R8S|1|R|A|139 B=2R8S|1|R|G|164
pMakeNodesJunction: first branch starts at   2R8S|1|R|G|180
pMakeNodesJunction: first branch ends around 2R8S|1|R|C|138
pMakeNodesJunction: second branch starts at  2R8S|1|R|A|139
pMakeNodesJunction: junction ends at         2R8S|1|R|G|164
pMakeNodesJunction: first branch strand start goes up to  2R8S|1|R|G|180
pMakeNodesJunction: first branch strand end goes down to  2R8S|1|R|C|138
pMakeNodesJunction: second branch strand start goes up to 2R8S|1|R|G|141
pMakeNodesJunction: last strand of junction goes down to  2R8S|1|R|U|162

Junction with 2 loops, call it J975
Actual Branch 1 of junction J975 - Nucleotides 2R8S|1|R|G|180 to 2R8S|1|R|C|138, length   2
Actual Branch 2 of junction J975 - Nucleotides 2R8S|1|R|A|139 to 2R8S|1|R|G|164, length   6
  3 Junction

2B Branch 1 of 2 of junction J975 - Nucleotides   180 to   138, length   2
pMakeNodes starting loop:     a=2R8S|1|R|G|180 B=2R8S|1|R|C|138
  5 Basepair   180  138 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J975 - Nucleotides   139 to   164, length   6
pMakeNodes starting loop:     a=2R8S|1|R|A|139 B=2R8S|1|R|G|164
  8 Basepair   139  164 AG tHS 
No need to probe because of interaction between a=2R8S|1|R|A|140 B=2R8S|1|R|G|163
  9 Basepair   140  163 AG tHS 
No need to probe because of interaction between a=2R8S|1|R|G|141 B=2R8S|1|R|U|162
 10 Basepair   141  162 GU cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  5 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|A|139
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|A|140
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|G|141
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGUA'
           RightLetter: 'C'
               Comment: ' // Basepair G175 - C165 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J975'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|A|139'
              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: 'J975'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 2R8S|1|R|A|140'
              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: 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: 4
            RightIndex: 12
             Insertion: []
                    id: 'J975'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|G|141'
              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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J975'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G180 - G164 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 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: '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 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 G180 - C138 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
            RightIndex: 12
             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 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A139 - G164 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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A140 - G163 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: 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 G141 - U162 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 12
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 12
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   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 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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J975'
        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: 7
            RightIndex: 12
             Insertion: []
                    id: 'J975'
        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 J3_06579.1. 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_06579.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0717

Timestamp 18-Jul-2025 00:12:43
pMakeSCFGModels: Making JAR3D model for motif group J3_08394.2, number 7 of 88
pMakeNodes starting loop:     a=4LFB|1|A|C|1063 B=4LFB|1|A|G|1193
  2 Basepair  1063 1193 CG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|1064 B=4LFB|1|A|C|1192
    Insertion on right 4LFB|1|A|C|1192
pMakeNodes probed for insert:  a=4LFB|1|A|G|1064 B=4LFB|1|A|A|1191
pMakeNodes making a cluster near strand break a=4LFB|1|A|G|1064 B=4LFB|1|A|A|1191
pMakeNodesCluster: amax is 5 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 17 to 18
aa is 4 bb is 17
  3 Cluster   4LFB|1|A|G|1064:4LFB|1|A|C|1066 4LFB|1|A|G|1190:4LFB|1|A|A|1191
    LR Inter  4LFB|1|A|G|1064 4LFB|1|A|G|1190 tSS 
    LR Inter  4LFB|1|A|C|1066 4LFB|1|A|A|1191 tWH 
    Left  strand conserved insertion 4LFB|1|A|U|1065 at position 2
pMakeNodesCluster a=5 B=16 at the end
pMakeNodesCluster a=5 B=16 at the end
pMakeNodes probe for inserts:  a=4LFB|1|A|A|1067 B=4LFB|1|A|C|1189
    Insertion on left  4LFB|1|A|A|1067
    Insertion on right 4LFB|1|A|C|1189
    Insertion on right 4LFB|1|A|A|1188
  4 Initial   1067 (1 insertion) and 1189 (2 insertion)
pMakeNodes probed for insert:  a=4LFB|1|A|G|1068 B=4LFB|1|A|G|1187
pMakeNodesJunction: a=4LFB|1|A|G|1068 r=4LFB|1|A|G|1068 s=4LFB|1|A|C|1107 t=4LFB|1|A|G|1108 u=B=4LFB|1|A|G|1187
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|G|1068 and 4LFB|1|A|C|1107 and between 4LFB|1|A|G|1108 and 4LFB|1|A|G|1187
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|G|1068 s=4LFB|1|A|C|1107 t=4LFB|1|A|G|1108 B=4LFB|1|A|G|1187
pMakeNodesJunction: first branch starts at   4LFB|1|A|G|1068
pMakeNodesJunction: first branch ends around 4LFB|1|A|C|1107
pMakeNodesJunction: second branch starts at  4LFB|1|A|G|1108
pMakeNodesJunction: junction ends at         4LFB|1|A|G|1187
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|G|1068
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|C|1107
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|C|1113
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|G|1187

Junction with 2 loops, call it J2784
Actual Branch 1 of junction J2784 - Nucleotides 4LFB|1|A|G|1068 to 4LFB|1|A|C|1107, length   2
Actual Branch 2 of junction J2784 - Nucleotides 4LFB|1|A|G|1108 to 4LFB|1|A|G|1187, length   7
  5 Junction

2B Branch 1 of 2 of junction J2784 - Nucleotides  1068 to  1107, length   2
pMakeNodes starting loop:     a=4LFB|1|A|G|1068 B=4LFB|1|A|C|1107
  7 Basepair  1068 1107 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J2784 - Nucleotides  1108 to  1187, length   7
pMakeNodes starting loop:     a=4LFB|1|A|G|1108 B=4LFB|1|A|G|1187
    Insertion on left  4LFB|1|A|G|1108
    Insertion on left  4LFB|1|A|C|1109
    Insertion on left  4LFB|1|A|A|1110
    Insertion on left  4LFB|1|A|A|1111
    Insertion on left  4LFB|1|A|C|1112
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|1113 interacts with 4LFB|1|A|G|1187
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1187 interacts with 4LFB|1|A|C|1113
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1187 interacts with 4LFB|1|A|C|1113
  9 Initial   1108 (5 insertion) and 1187 (0 insertion)
 10 Basepair  1113 1187 CG cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 17 18
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  10  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  11   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1192
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1067
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1189
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|1188
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1108
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|1109
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1110
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1111
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|1112
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: [0.9950 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 C1063 - G1193 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            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 4LFB|1|A|C|1192'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            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: 'A'
           RightLetter: 'AC'
               Comment: ' // New 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 5

ans = 

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

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4]
            RightIndex: [17 18]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUC'
           RightLetter: 'GA'
               Comment: ' // Cluster node 4LFB|1|A|G|1064:4LFB|1|A|C|1066 and 4LFB|1|A|G|1190:4LFB|1|A|A|1191'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AC'
               Comment: ' // Initial node 4LFB|1|A|A|1067 - 4LFB|1|A|C|1189 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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|1067'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: '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 4LFB|1|A|C|1189'
              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 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: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 1
        leftLetterDist: [0.2500 0.2500 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|1188'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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: []

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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 13

ans = 

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

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J2784'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1068 - G1187 ID J2784'
              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 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: 'J2784'
        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: 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 G1068 - C1107 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 17

ans = 

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

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J2784'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCAAC'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1108 - 4LFB|1|A|G|1187 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 18

ans = 

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

                  type: 'Fixed'
              nextnode: 19
             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 4LFB|1|A|G|1108'
              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 19

ans = 

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

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 20

ans = 

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

                  type: 'Fixed'
              nextnode: 21
             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 4LFB|1|A|C|1109'
              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 21

ans = 

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

                  type: 'Initial'
              nextnode: 22
             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: []
          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: 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 4LFB|1|A|A|1110'
              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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 24

ans = 

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

                  type: 'Fixed'
              nextnode: 25
             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|A|1111'
              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 25

ans = 

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

                  type: 'Initial'
              nextnode: 26
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 26

ans = 

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

                  type: 'Fixed'
              nextnode: 27
             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|C|1112'
              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 27

ans = 

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

                  type: 'Initial'
              nextnode: 28
             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 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 C1113 - G1187 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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  2 Right 18
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4 Right 17 18
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  13  Junction Left  6 Right 14
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 14
pMakeMotifModelFromSSF:  18     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  20     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  22     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  23   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  24     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  25   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  26     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  27   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  28  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  29   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 hairpin at node 29
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: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J2784'
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J2784'
        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: 'GCAAC'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1108 - 4LFB|1|A|G|1187 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 J3_08394.2. 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 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 29
pNextNodeJunction: Finished at node 29 out of 29, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_08394.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8299
   -8.3407
   -7.8299

Timestamp 18-Jul-2025 00:12:44
pMakeSCFGModels: Making JAR3D model for motif group J3_08465.1, number 8 of 88
pMakeNodes starting loop:     a=4WF9|1|X|G|2249 B=4WF9|1|X|C|2228
  2 Basepair  2249 2228 GC cWW 
No need to probe because of interaction between a=4WF9|1|X|A|2250 B=4WF9|1|X|C|2227
  3 Basepair  2250 2227 AC cWW 
No need to probe because of interaction between a=4WF9|1|X|G|2251 B=4WF9|1|X|A|2226
  4 Basepair  2251 2226 GA tSH 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|2252 B=4WF9|1|X|A|2225
    Insertion on right 4WF9|1|X|A|2225
pMakeNodes probed for insert:  a=4WF9|1|X|A|2252 B=4WF9|1|X|U|2224
  5 Basepair  2252 2224 AU tHW 
pMakeNodes probe for inserts:  a=4WF9|1|X|C|2253 B=4WF9|1|X|C|2223
    Insertion on left  4WF9|1|X|C|2253
pMakeNodes probed for insert:  a=4WF9|1|X|A|2254 B=4WF9|1|X|C|2223
pMakeNodesJunction: a=4WF9|1|X|A|2254 r=4WF9|1|X|A|2254 s=4WF9|1|X|U|2119 t=4WF9|1|X|G|2120 u=B=4WF9|1|X|C|2223
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|A|2254 and 4WF9|1|X|U|2119 and between 4WF9|1|X|G|2120 and 4WF9|1|X|C|2223
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|A|2254 s=4WF9|1|X|U|2119 t=4WF9|1|X|G|2120 B=4WF9|1|X|C|2223
pMakeNodesJunction: first branch starts at   4WF9|1|X|A|2254
pMakeNodesJunction: first branch ends around 4WF9|1|X|U|2119
pMakeNodesJunction: second branch starts at  4WF9|1|X|G|2120
pMakeNodesJunction: junction ends at         4WF9|1|X|C|2223
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|2255
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|U|2118
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|G|2120
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|C|2223

Junction with 2 loops, call it J5468
Actual Branch 1 of junction J5468 - Nucleotides 4WF9|1|X|A|2254 to 4WF9|1|X|U|2119, length   4
Actual Branch 2 of junction J5468 - Nucleotides 4WF9|1|X|G|2120 to 4WF9|1|X|C|2223, length   2
  6 Junction

2B Branch 1 of 2 of junction J5468 - Nucleotides  2254 to  2119, length   4
pMakeNodes starting loop:     a=4WF9|1|X|A|2254 B=4WF9|1|X|U|2119
  8 Basepair  2254 2119 AU tHH 
No need to probe because of interaction between a=4WF9|1|X|G|2255 B=4WF9|1|X|U|2118
  9 Basepair  2255 2118 GU cWW 
 10 Hairpin type *

2B Branch 2 of 2 of junction J5468 - Nucleotides  2120 to  2223, length   2
pMakeNodes starting loop:     a=4WF9|1|X|G|2120 B=4WF9|1|X|C|2223
 12 Basepair  2120 2223 GC cWW 
 13 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  10   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  11   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  13   Hairpin Left 11 Right 10
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 4WF9|1|X|A|2252
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|2224
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 G2249 - C2228 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 A2250 - C2227 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            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: 'G'
           RightLetter: 'AA'
               Comment: ' // Basepair G2251 - A2226 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 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|A|2252'
              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 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: '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 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: 'U'
               Comment: ' // Basepair A2252 - U2224 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 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|2224'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 10

ans = 

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

                  type: 'Junction'
              nextnode: [7 11]
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J5468'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2254 - C2223 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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: '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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2254 - U2119 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: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G2255 - U2118 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
            RightIndex: 11
             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 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: 'C'
               Comment: ' // Basepair G2120 - C2223 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10  Junction Left  6 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  15   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 10
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 17
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: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J5468'
        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: 10
            RightIndex: 11
             Insertion: []
                    id: 'J5468'
        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 J3_08465.1. Nodes 11 and 15 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 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 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_08465.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1363

Timestamp 18-Jul-2025 00:12:45
pMakeSCFGModels: Making JAR3D model for motif group J3_11279.1, number 9 of 88
pMakeNodes starting loop:     a=4V88|1|A6|U|1609 B=4V88|1|A6|A|1587
  2 Basepair  1609 1587 UA cWW 
No need to probe because of interaction between a=4V88|1|A6|G|1610 B=4V88|1|A6|A|1586
  3 Basepair  1610 1586 GA tSH 
No need to probe because of interaction between a=4V88|1|A6|A|1611 B=4V88|1|A6|U|1585
pMakeNodes making a cluster near strand break a=4V88|1|A6|A|1611 B=4V88|1|A6|U|1585
pMakeNodesCluster: amax is 7 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 3 and then 16 to 17
aa is 3 bb is 16
  4 Cluster   4V88|1|A6|A|1611:4V88|1|A6|A|1611 4V88|1|A6|G|1584:4V88|1|A6|U|1585
    LR Inter  4V88|1|A6|A|1611 4V88|1|A6|U|1585 tHW 
    RR Inter  4V88|1|A6|G|1584 4V88|1|A6|U|1585 cSH 
pMakeNodesCluster a=4 B=15 at the end
pMakeNodesCluster a=4 B=15 at the end
No need to probe because of interaction between a=4V88|1|A6|U|1612 B=4V88|1|A6|A|1583
pMakeNodes making a cluster near strand break a=4V88|1|A6|U|1612 B=4V88|1|A6|A|1583
pMakeNodesCluster: amax is 7 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 14 to 15
aa is 5 bb is 14
  5 Cluster   4V88|1|A6|U|1612:4V88|1|A6|U|1613 4V88|1|A6|U|1582:4V88|1|A6|A|1583
    LR Inter  4V88|1|A6|U|1613 4V88|1|A6|U|1582 tWW 
    LR Inter  4V88|1|A6|U|1612 4V88|1|A6|A|1583 tHH 
    LR Inter  4V88|1|A6|U|1613 4V88|1|A6|A|1583 tHH 
pMakeNodesCluster a=6 B=13 at the end
pMakeNodesCluster a=6 B=13 at the end
pMakeNodes probe for inserts:  a=4V88|1|A6|A|1614 B=4V88|1|A6|C|1581
    Insertion on left  4V88|1|A6|A|1614
  6 Initial   1614 (1 insertion) and 1581 (0 insertion)
pMakeNodes probed for insert:  a=4V88|1|A6|C|1615 B=4V88|1|A6|C|1581
pMakeNodesJunction: a=4V88|1|A6|C|1615 r=4V88|1|A6|C|1615 s=4V88|1|A6|C|1162 t=4V88|1|A6|A|1163 u=B=4V88|1|A6|C|1581
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|C|1615 and 4V88|1|A6|C|1162 and between 4V88|1|A6|A|1163 and 4V88|1|A6|C|1581
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|C|1615 s=4V88|1|A6|C|1162 t=4V88|1|A6|A|1163 B=4V88|1|A6|C|1581
pMakeNodesJunction: first branch starts at   4V88|1|A6|C|1615
pMakeNodesJunction: first branch ends around 4V88|1|A6|C|1162
pMakeNodesJunction: second branch starts at  4V88|1|A6|A|1163
pMakeNodesJunction: junction ends at         4V88|1|A6|C|1581
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|G|1616
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|C|1161
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|G|1164
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|C|1581

Junction with 2 loops, call it J9575
Actual Branch 1 of junction J9575 - Nucleotides 4V88|1|A6|C|1615 to 4V88|1|A6|C|1162, length   4
Actual Branch 2 of junction J9575 - Nucleotides 4V88|1|A6|A|1163 to 4V88|1|A6|C|1581, length   3
  7 Junction

2B Branch 1 of 2 of junction J9575 - Nucleotides  1615 to  1162, length   4
pMakeNodes starting loop:     a=4V88|1|A6|C|1615 B=4V88|1|A6|C|1162
  9 Basepair  1615 1162 CC tHS 
No need to probe because of interaction between a=4V88|1|A6|G|1616 B=4V88|1|A6|C|1161
 10 Basepair  1616 1161 GC cWW 
 11 Hairpin type *

2B Branch 2 of 2 of junction J9575 - Nucleotides  1163 to  1581, length   3
pMakeNodes starting loop:     a=4V88|1|A6|A|1163 B=4V88|1|A6|C|1581
    Insertion on left  4V88|1|A6|A|1163
pMakeNodesProbeForInsertions:  a 4V88|1|A6|G|1164 interacts with 4V88|1|A6|C|1581
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1581 interacts with 4V88|1|A6|G|1164
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1581 interacts with 4V88|1|A6|G|1164
 12 Initial   1163 (1 insertion) and 1581 (0 insertion)
 13 Basepair  1164 1581 GC cWW 
 14 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   Cluster Left  3 Right 16 17
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 14 15
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   7  Junction Left  7 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  12   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  13  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  14   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|1582
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1587
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: []
          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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1609 - A1587 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1610 - A1586 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: 'Cluster'
              nextnode: 5
             LeftIndex: 3
            RightIndex: [16 17]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Cluster node 4V88|1|A6|A|1611:4V88|1|A6|A|1611 and 4V88|1|A6|G|1584:4V88|1|A6|U|1585'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971
           numbranches: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              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: [4 5]
            RightIndex: [14 15]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UU'
           RightLetter: 'UA'
               Comment: ' // Cluster node 4V88|1|A6|U|1612:4V88|1|A6|U|1613 and 4V88|1|A6|U|1582:4V88|1|A6|A|1583'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2093
           numbranches: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|A|1614 - 4V88|1|A6|C|1581 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: 'Fixed'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J9575'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1582'
              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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 10

ans = 

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

                  type: 'Junction'
              nextnode: [8 12]
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J9575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1615 - C1581 ID J9575'
              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: 7
            RightIndex: 10
             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: []
          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: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C1615 - C1162 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1616 - C1161 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Hairpin'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J9575'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|A|1163 - 4V88|1|A6|C|1581 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 16

ans = 

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

                  type: 'Fixed'
              nextnode: 17
             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 4V88|1|A6|A|1587'
              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: 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 18

ans = 

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

                  type: 'Basepair'
              nextnode: 19
             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 G1164 - C1581 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 19

ans = 

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

                  type: 'Hairpin'
              nextnode: 20
             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 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 18
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 16 17
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6   Cluster Left  4  5 Right 14 15
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  10  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 10
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 11 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  17   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  18  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  19   Hairpin Left 13 Right 12
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 19
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: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J9575'
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J9575'
        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 4V88|1|A6|A|1163 - 4V88|1|A6|C|1581 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 J3_11279.1. Nodes 11 and 15 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 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 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 12
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 11
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 12
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_11279.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1511
  -10.5670

Timestamp 18-Jul-2025 00:12:46
pMakeSCFGModels: Making JAR3D model for motif group J3_11934.2, number 10 of 88
pMakeNodes starting loop:     a=1G1X|1|J|C|717 B=1G1X|1|I|G|673
  2 Basepair   717  673 CG cWW 
pMakeNodes probe for inserts:  a=1G1X|1|J|G|718 B=1G1X|1|I|U|672
    Insertion on left  1G1X|1|J|G|718
    Insertion on left  1G1X|1|J|C|719
    Insertion on left  1G1X|1|J|C|720
    Insertion on left  1G1X|1|J|G|721
pMakeNodes probed for insert:  a=1G1X|1|J|A|722 B=1G1X|1|I|U|672
pMakeNodesJunction: a=1G1X|1|J|A|722 r=1G1X|1|J|A|722 s=1G1X|1|J|A|733 t=1G1X|1|J|G|734 u=B=1G1X|1|I|U|672
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1G1X|1|J|A|722 and 1G1X|1|J|A|733 and between 1G1X|1|J|G|734 and 1G1X|1|I|U|672
pMakeNodesJunction: about to make a junction: a=1G1X|1|J|A|722 s=1G1X|1|J|A|733 t=1G1X|1|J|G|734 B=1G1X|1|I|U|672
pMakeNodesJunction: first branch starts at   1G1X|1|J|A|722
pMakeNodesJunction: first branch ends around 1G1X|1|J|A|733
pMakeNodesJunction: second branch starts at  1G1X|1|J|G|734
pMakeNodesJunction: junction ends at         1G1X|1|I|U|672
pMakeNodesJunction: first branch strand start goes up to  1G1X|1|J|G|725
pMakeNodesJunction: first branch strand end goes down to  1G1X|1|J|C|732
pMakeNodesJunction: second branch strand start goes up to 1G1X|1|J|G|734
pMakeNodesJunction: last strand of junction goes down to  1G1X|1|I|U|672

Junction with 2 loops, call it J9648
Actual Branch 1 of junction J9648 - Nucleotides 1G1X|1|J|A|722 to 1G1X|1|J|A|733, length   5
Actual Branch 2 of junction J9648 - Nucleotides 1G1X|1|J|G|734 to 1G1X|1|I|U|672, length   2
  3 Junction

2B Branch 1 of 2 of junction J9648 - Nucleotides   722 to   733, length   5
pMakeNodes starting loop:     a=1G1X|1|J|A|722 B=1G1X|1|J|A|733
  5 Basepair   722  733 AA tWW 
pMakeNodes probe for inserts:  a=1G1X|1|J|G|724 B=1G1X|1|J|C|732
    Insertion on left  1G1X|1|J|G|724
pMakeNodesProbeForInsertions:  a 1G1X|1|J|G|725 interacts with 1G1X|1|J|C|732
pMakeNodesProbeForInsertions:  B 1G1X|1|J|C|732 interacts with 1G1X|1|J|G|725
pMakeNodesProbeForInsertions:  B 1G1X|1|J|C|732 interacts with 1G1X|1|J|G|725
pMakeNodes probed for insert:  a=1G1X|1|J|G|725 B=1G1X|1|J|C|732
  6 Basepair   725  732 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J9648 - Nucleotides   734 to   672, length   2
pMakeNodes starting loop:     a=1G1X|1|J|G|734 B=1G1X|1|I|U|672
  9 Basepair   734  672 GU cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|I|G|673
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|J|C|717
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|J|G|718
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|J|C|719
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|J|G|721
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [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: 'CGCCG'
           RightLetter: 'G'
               Comment: ' // Basepair C717 - G673 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J9648'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1G1X|1|I|G|673'
              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: '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: []
              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 1G1X|1|J|C|717'
              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: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 1G1X|1|J|G|718'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J9648'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1G1X|1|J|C|719'
              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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: '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 8]
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J9648'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A722 - U672 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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            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 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'A'
               Comment: ' // Basepair A722 - A733 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 14

ans = 

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

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1G1X|1|J|G|721'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 G725 - C732 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: []
                  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: 12
             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 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: 'U'
               Comment: ' // Basepair G734 - U672 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11  Junction Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  15   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  20   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
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: 13
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9648'
        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: 11
            RightIndex: 12
             Insertion: []
                    id: 'J9648'
        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 J3_11934.2. Nodes 12 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 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_11934.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6474
   -6.6474
   -7.6875
   -6.6474

Timestamp 18-Jul-2025 00:12:46
pMakeSCFGModels: Making JAR3D model for motif group J3_13944.1, number 11 of 88
pMakeNodes starting loop:     a=7A0S|1|Y|C|12 B=7A0S|1|Y|G|113
  2 Basepair    12  113 CG cWW 
No need to probe because of interaction between a=7A0S|1|Y|C|13 B=7A0S|1|Y|A|112
pMakeNodes making a cluster near strand break a=7A0S|1|Y|C|13 B=7A0S|1|Y|A|112
pMakeNodesCluster: amax is 5 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 12 to 12
aa is 5 bb is 12
  3 Cluster   7A0S|1|Y|C|13:7A0S|1|Y|A|17 7A0S|1|Y|A|112:7A0S|1|Y|A|112
    LR Inter  7A0S|1|Y|C|13 7A0S|1|Y|A|112 cWW 
    LL Inter  7A0S|1|Y|C|13 7A0S|1|Y|A|17 tSS 
    Left  strand conserved insertion 7A0S|1|Y|C|14 at position 2
    Left  strand conserved insertion 7A0S|1|Y|A|15 at position 3
pMakeNodesCluster a=6 B=11 at the end
pMakeNodesCluster a=6 B=11 at the end
pMakeNodes probe for inserts:  a=7A0S|1|Y|G|18 B=7A0S|1|Y|U|110
  4 Initial     18 (0 insertion) and  110 (0 insertion)
pMakeNodes probed for insert:  a=7A0S|1|Y|G|18 B=7A0S|1|Y|U|110
pMakeNodesJunction: a=7A0S|1|Y|G|18 r=7A0S|1|Y|G|18 s=7A0S|1|Y|C|70 t=7A0S|1|Y|G|71 u=B=7A0S|1|Y|U|110
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|Y|G|18 and 7A0S|1|Y|C|70 and between 7A0S|1|Y|G|71 and 7A0S|1|Y|U|110
pMakeNodesJunction: about to make a junction: a=7A0S|1|Y|G|18 s=7A0S|1|Y|C|70 t=7A0S|1|Y|G|71 B=7A0S|1|Y|U|110
pMakeNodesJunction: first branch starts at   7A0S|1|Y|G|18
pMakeNodesJunction: first branch ends around 7A0S|1|Y|C|70
pMakeNodesJunction: second branch starts at  7A0S|1|Y|G|71
pMakeNodesJunction: junction ends at         7A0S|1|Y|U|110
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|Y|G|18
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|Y|C|70
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|Y|C|72
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|Y|G|109

Junction with 2 loops, call it J1576
Actual Branch 1 of junction J1576 - Nucleotides 7A0S|1|Y|G|18 to 7A0S|1|Y|C|70, length   2
Actual Branch 2 of junction J1576 - Nucleotides 7A0S|1|Y|G|71 to 7A0S|1|Y|U|110, length   4
  5 Junction

2B Branch 1 of 2 of junction J1576 - Nucleotides    18 to    70, length   2
pMakeNodes starting loop:     a=7A0S|1|Y|G|18 B=7A0S|1|Y|C|70
  7 Basepair    18   70 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J1576 - Nucleotides    71 to   110, length   4
pMakeNodes starting loop:     a=7A0S|1|Y|G|71 B=7A0S|1|Y|U|110
 10 Basepair    71  110 GU tHS 
No need to probe because of interaction between a=7A0S|1|Y|C|72 B=7A0S|1|Y|G|109
 11 Basepair    72  109 CG cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
All nodes in 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C12 - G113 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4 5]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCAA'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|Y|C|13:7A0S|1|Y|A|17 and 7A0S|1|Y|A|112:7A0S|1|Y|A|112'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2500
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 11
             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 7A0S|1|Y|G|18 - 7A0S|1|Y|U|110 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: 6
            RightIndex: 11
             Insertion: []
                    id: 'J1576'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G18 - U110 ID J1576'
              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: 6
            RightIndex: 7
             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: []
          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: 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 G18 - C70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: '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: []
          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: 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: 'U'
               Comment: ' // Basepair G71 - U110 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C72 - G109 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 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: []
          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  3  4  5 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pNextNodeJunction: Found a 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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 7
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1576'
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Motif J3_13944.1. Nodes 6 and 9 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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 4 and 8
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 4 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_13944.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.2143
   -9.9178

Timestamp 18-Jul-2025 00:12:47
pMakeSCFGModels: Making JAR3D model for motif group J3_15893.1, number 12 of 88
pMakeNodes starting loop:     a=6N5P|1|A|U|48 B=6N5P|1|A|A|91
  2 Basepair    48   91 UA cWW 
No need to probe because of interaction between a=6N5P|1|A|U|49 B=6N5P|1|A|C|90
  3 Basepair    49   90 UC tSH 
pMakeNodes probe for inserts:  a=6N5P|1|A|A|50 B=6N5P|1|A|G|89
pMakeNodes probed for insert:  a=6N5P|1|A|A|50 B=6N5P|1|A|G|89
pMakeNodesJunction: a=6N5P|1|A|A|50 r=6N5P|1|A|A|50 s=6N5P|1|A|U|70 t=6N5P|1|A|A|71 u=B=6N5P|1|A|G|89
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6N5P|1|A|A|50 and 6N5P|1|A|U|70 and between 6N5P|1|A|A|71 and 6N5P|1|A|G|89
pMakeNodesJunction: about to make a junction: a=6N5P|1|A|A|50 s=6N5P|1|A|U|70 t=6N5P|1|A|A|71 B=6N5P|1|A|G|89
pMakeNodesJunction: first branch starts at   6N5P|1|A|A|50
pMakeNodesJunction: first branch ends around 6N5P|1|A|U|70
pMakeNodesJunction: second branch starts at  6N5P|1|A|A|71
pMakeNodesJunction: junction ends at         6N5P|1|A|G|89
pMakeNodesJunction: first branch strand start goes up to  6N5P|1|A|C|53
pMakeNodesJunction: first branch strand end goes down to  6N5P|1|A|G|69
pMakeNodesJunction: second branch strand start goes up to 6N5P|1|A|G|72
pMakeNodesJunction: last strand of junction goes down to  6N5P|1|A|C|88
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J9705
Actual Branch 1 of junction J9705 - Nucleotides 6N5P|1|A|A|50 to 6N5P|1|A|U|70, length   6
Actual Branch 2 of junction J9705 - Nucleotides 6N5P|1|A|A|71 to 6N5P|1|A|G|89, length   4
  4 Junction

2B Branch 1 of 2 of junction J9705 - Nucleotides    50 to    70, length   6
pMakeNodes starting loop:     a=6N5P|1|A|A|50 B=6N5P|1|A|U|70
    Insertion on left  6N5P|1|A|A|50
    Insertion on left  6N5P|1|A|A|51
pMakeNodesProbeForInsertions:  a 6N5P|1|A|U|52 interacts with 6N5P|1|A|U|70
pMakeNodesProbeForInsertions:  B 6N5P|1|A|U|70 interacts with 6N5P|1|A|U|52
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6N5P|1|A|U|70 interacts with 6N5P|1|A|U|52
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  5 Initial     50 (2 insertion) and   70 (0 insertion)
  6 Basepair    52   70 UU cWW 
No need to probe because of interaction between a=6N5P|1|A|C|53 B=6N5P|1|A|G|69
  7 Basepair    53   69 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J9705 - Nucleotides    71 to    89, length   4
pMakeNodes starting loop:     a=6N5P|1|A|A|71 B=6N5P|1|A|G|89
 10 Basepair    71   89 AG tHS 
No need to probe because of interaction between a=6N5P|1|A|G|72 B=6N5P|1|A|C|88
 11 Basepair    72   88 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|A|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|A|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U48 - A91 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U49 - C90 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 4

ans = 

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

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J9705'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A50 - G89 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 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J9705'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 6N5P|1|A|A|50 - 6N5P|1|A|U|70 from 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: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|A|50'
              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: 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 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|A|51'
              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 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: '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: []
                  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: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U52 - U70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 C53 - 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 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: []
           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: 12
             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 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A71 - G89 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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G72 - C88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 16

ans = 

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

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [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  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  8
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  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
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: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J9705'
        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 6N5P|1|A|A|50 - 6N5P|1|A|U|70 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: 14
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J9705'
        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 J3_15893.1. Nodes 5 and 13 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 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a junction child at node 13
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 3 and 10
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 3 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_15893.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8207
   -7.7837
   -7.9764
   -7.7837
   -7.8331

Timestamp 18-Jul-2025 00:12:48
pMakeSCFGModels: Making JAR3D model for motif group J3_18709.1, number 13 of 88
pMakeNodes starting loop:     a=4V88|1|A6|U|1079 B=4V88|1|A6|A|1039
  2 Basepair  1079 1039 UA cWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|U|1080 B=4V88|1|A6|U|1038
pMakeNodes probed for insert:  a=4V88|1|A6|U|1080 B=4V88|1|A6|U|1038
pMakeNodesJunction: a=4V88|1|A6|U|1080 r=4V88|1|A6|U|1080 s=4V88|1|A6|A|1091 t=4V88|1|A6|A|1092 u=B=4V88|1|A6|U|1038
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|U|1080 and 4V88|1|A6|A|1091 and between 4V88|1|A6|A|1092 and 4V88|1|A6|U|1038
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|U|1080 s=4V88|1|A6|A|1091 t=4V88|1|A6|A|1092 B=4V88|1|A6|U|1038
pMakeNodesJunction: first branch starts at   4V88|1|A6|U|1080
pMakeNodesJunction: first branch ends around 4V88|1|A6|A|1091
pMakeNodesJunction: second branch starts at  4V88|1|A6|A|1092
pMakeNodesJunction: junction ends at         4V88|1|A6|U|1038
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|G|1083
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|C|1090
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|G|1094
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|C|1037

Junction with 2 loops, call it J9571
Actual Branch 1 of junction J9571 - Nucleotides 4V88|1|A6|U|1080 to 4V88|1|A6|A|1091, length   6
Actual Branch 2 of junction J9571 - Nucleotides 4V88|1|A6|A|1092 to 4V88|1|A6|U|1038, length   4
  3 Junction

2B Branch 1 of 2 of junction J9571 - Nucleotides  1080 to  1091, length   6
pMakeNodes starting loop:     a=4V88|1|A6|U|1080 B=4V88|1|A6|A|1091
  5 Basepair  1080 1091 UA tWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|A|1081 B=4V88|1|A6|C|1090
pMakeNodesProbeForInsertions:  a 4V88|1|A6|A|1081 interacts with 4V88|1|A6|C|1082
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1090 interacts with 4V88|1|A6|G|1083
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1090 interacts with 4V88|1|A6|G|1083
pMakeNodes probed for insert:  a=4V88|1|A6|A|1081 B=4V88|1|A6|C|1090
pMakeNodes making a cluster near strand break a=4V88|1|A6|A|1081 B=4V88|1|A6|C|1090
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 6 to 6
aa is 5 bb is 6
  6 Cluster   4V88|1|A6|A|1081:4V88|1|A6|G|1083 4V88|1|A6|C|1090:4V88|1|A6|C|1090
    LR Inter  4V88|1|A6|G|1083 4V88|1|A6|C|1090 cWW 
    LL Inter  4V88|1|A6|A|1081 4V88|1|A6|C|1082 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  7 Hairpin type *

2B Branch 2 of 2 of junction J9571 - Nucleotides  1092 to  1038, length   4
pMakeNodes starting loop:     a=4V88|1|A6|A|1092 B=4V88|1|A6|U|1038
  9 Basepair  1092 1038 AU tWW 
No need to probe because of interaction between a=4V88|1|A6|G|1094 B=4V88|1|A6|C|1037
 10 Basepair  1094 1037 GC cWW 
 11 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  7
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   6   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  8 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1079 - A1039 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 11
             Insertion: []
                    id: 'J9571'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1080 - U1038 ID J9571'
              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: 7
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1080 - A1091 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [3 4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACG'
           RightLetter: 'C'
               Comment: ' // Cluster node 4V88|1|A6|A|1081:4V88|1|A6|G|1083 and 4V88|1|A6|C|1090:4V88|1|A6|C|1090'
              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: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             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 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1092 - U1038 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1094 - C1037 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 12

ans = 

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

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: [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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   6   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pNextNodeJunction: Found a 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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []


ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            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: []
            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 J3_18709.1. Nodes 4 and 9 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 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_18709.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6198

Timestamp 18-Jul-2025 00:12:49
pMakeSCFGModels: Making JAR3D model for motif group J3_19256.1, number 14 of 88
pMakeNodes starting loop:     a=7KGA|1|B|G|65 B=7KGA|1|B|C|52
  2 Basepair    65   52 GC cWW 
pMakeNodes probe for inserts:  a=7KGA|1|B|A|66 B=7KGA|1|B|A|51
    Insertion on left  7KGA|1|B|A|66
    Insertion on left  7KGA|1|B|A|67
    Insertion on left  7KGA|1|B|A|68
    Insertion on left  7KGA|1|B|C|69
    Insertion on left  7KGA|1|B|C|70
    Insertion on right 7KGA|1|B|A|51
pMakeNodes probed for insert:  a=7KGA|1|B|C|71 B=7KGA|1|B|G|50
pMakeNodesJunction: a=7KGA|1|B|C|71 r=7KGA|1|B|C|71 s=7KGA|1|B|G|5 t=7KGA|1|B|C|6 u=B=7KGA|1|B|G|50
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7KGA|1|B|C|71 and 7KGA|1|B|G|5 and between 7KGA|1|B|C|6 and 7KGA|1|B|G|50
pMakeNodesJunction: about to make a junction: a=7KGA|1|B|C|71 s=7KGA|1|B|G|5 t=7KGA|1|B|C|6 B=7KGA|1|B|G|50
pMakeNodesJunction: first branch starts at   7KGA|1|B|C|71
pMakeNodesJunction: first branch ends around 7KGA|1|B|G|5
pMakeNodesJunction: second branch starts at  7KGA|1|B|C|6
pMakeNodesJunction: junction ends at         7KGA|1|B|G|50
pMakeNodesJunction: first branch strand start goes up to  7KGA|1|B|C|71
pMakeNodesJunction: first branch strand end goes down to  7KGA|1|B|G|5
pMakeNodesJunction: second branch strand start goes up to 7KGA|1|B|C|6
pMakeNodesJunction: last strand of junction goes down to  7KGA|1|B|G|50

Junction with 2 loops, call it J4853
Actual Branch 1 of junction J4853 - Nucleotides 7KGA|1|B|C|71 to 7KGA|1|B|G|5, length   2
Actual Branch 2 of junction J4853 - Nucleotides 7KGA|1|B|C|6 to 7KGA|1|B|G|50, length   2
  3 Junction

2B Branch 1 of 2 of junction J4853 - Nucleotides    71 to     5, length   2
pMakeNodes starting loop:     a=7KGA|1|B|C|71 B=7KGA|1|B|G|5
  5 Basepair    71    5 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J4853 - Nucleotides     6 to    50, length   2
pMakeNodes starting loop:     a=7KGA|1|B|C|6 B=7KGA|1|B|G|50
  8 Basepair     6   50 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  7 Right 10
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 10
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KGA|1|B|C|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KGA|1|B|G|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KGA|1|B|A|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KGA|1|B|C|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KGA|1|B|G|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7KGA|1|B|C|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAAACC'
           RightLetter: 'AC'
               Comment: ' // Basepair G65 - C52 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J4853'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KGA|1|B|C|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: 11
             Insertion: []
                    id: 'J4853'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 7KGA|1|B|G|50'
              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: 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: 11
             Insertion: []
                    id: 'J4853'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KGA|1|B|A|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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KGA|1|B|C|52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 7KGA|1|B|G|65'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7KGA|1|B|C|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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: 'J4853'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C71 - G50 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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: '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 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 C71 - G5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 9
            RightIndex: 10
             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 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 C6 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 21

ans = 

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

                  type: 'Hairpin'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: [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     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  15  Junction Left  7 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  17  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  18   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  19   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  20  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  21   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
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: 17
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J4853'
        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: 9
            RightIndex: 10
             Insertion: []
                    id: 'J4853'
        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 J3_19256.1. Nodes 16 and 19 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 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_19256.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.3909
   -7.3909

Timestamp 18-Jul-2025 00:12:49
pMakeSCFGModels: Making JAR3D model for motif group J3_19286.1, number 15 of 88
pMakeNodes starting loop:     a=5KPY|1|A|C|18 B=5KPY|1|A|G|78
  2 Basepair    18   78 CG cWW 
No need to probe because of interaction between a=5KPY|1|A|U|19 B=5KPY|1|A|C|77
  3 Basepair    19   77 UC tSH 
No need to probe because of interaction between a=5KPY|1|A|G|20 B=5KPY|1|A|A|76
  4 Basepair    20   76 GA tSH 
pMakeNodes probe for inserts:  a=5KPY|1|A|A|21 B=5KPY|1|A|C|75
    Insertion on left  5KPY|1|A|A|21
    Insertion on left  5KPY|1|A|U|22
    Insertion on left  5KPY|1|A|A|24
pMakeNodes probed for insert:  a=5KPY|1|A|U|25 B=5KPY|1|A|C|75
pMakeNodesJunction: a=5KPY|1|A|U|25 r=5KPY|1|A|U|25 s=5KPY|1|A|A|44 t=5KPY|1|A|U|45 u=B=5KPY|1|A|C|75
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5KPY|1|A|U|25 and 5KPY|1|A|A|44 and between 5KPY|1|A|U|45 and 5KPY|1|A|C|75
pMakeNodesJunction: about to make a junction: a=5KPY|1|A|U|25 s=5KPY|1|A|A|44 t=5KPY|1|A|U|45 B=5KPY|1|A|C|75
pMakeNodesJunction: first branch starts at   5KPY|1|A|U|25
pMakeNodesJunction: first branch ends around 5KPY|1|A|A|44
pMakeNodesJunction: second branch starts at  5KPY|1|A|U|45
pMakeNodesJunction: junction ends at         5KPY|1|A|C|75
pMakeNodesJunction: first branch strand start goes up to  5KPY|1|A|U|25
pMakeNodesJunction: first branch strand end goes down to  5KPY|1|A|A|44
pMakeNodesJunction: second branch strand start goes up to 5KPY|1|A|G|47
pMakeNodesJunction: last strand of junction goes down to  5KPY|1|A|C|75

Junction with 2 loops, call it J8002
Actual Branch 1 of junction J8002 - Nucleotides 5KPY|1|A|U|25 to 5KPY|1|A|A|44, length   2
Actual Branch 2 of junction J8002 - Nucleotides 5KPY|1|A|U|45 to 5KPY|1|A|C|75, length   4
  5 Junction

2B Branch 1 of 2 of junction J8002 - Nucleotides    25 to    44, length   2
pMakeNodes starting loop:     a=5KPY|1|A|U|25 B=5KPY|1|A|A|44
  7 Basepair    25   44 UA cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J8002 - Nucleotides    45 to    75, length   4
pMakeNodes starting loop:     a=5KPY|1|A|U|45 B=5KPY|1|A|C|75
    Insertion on left  5KPY|1|A|U|45
    Insertion on left  5KPY|1|A|U|46
pMakeNodesProbeForInsertions:  a 5KPY|1|A|G|47 interacts with 5KPY|1|A|C|75
pMakeNodesProbeForInsertions:  B 5KPY|1|A|C|75 interacts with 5KPY|1|A|G|47
pMakeNodesProbeForInsertions:  B 5KPY|1|A|C|75 interacts with 5KPY|1|A|G|47
  9 Initial     45 (2 insertion) and   75 (0 insertion)
 10 Basepair    47   75 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Junction Left  7 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  11   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|A|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|U|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|G|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|A|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C18 - G78 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U19 - C77 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 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUA'
           RightLetter: 'A'
               Comment: ' // Basepair G20 - A76 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 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J8002'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|A|21'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J8002'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             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 5KPY|1|A|U|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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J8002'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             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: '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: 'Junction'
              nextnode: [6 9]
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: 'J8002'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U25 - C75 ID J8002'
              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: '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: []
           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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U25 - 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 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: 12
             Insertion: []
                    id: 'J8002'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 5KPY|1|A|U|45 - 5KPY|1|A|C|75 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 5KPY|1|A|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: 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 5KPY|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 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 G47 - C75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  11  Junction Left  7 Right 12
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 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 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 21
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: 13
             LeftIndex: 7
            RightIndex: 8
             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: []
           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: '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: 'UU'
           RightLetter: []
               Comment: ' // Initial node 5KPY|1|A|U|45 - 5KPY|1|A|C|75 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_19286.1. 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 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 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_19286.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4085

Timestamp 18-Jul-2025 00:12:50
pMakeSCFGModels: Making JAR3D model for motif group J3_19431.1, number 16 of 88
pMakeNodes starting loop:     a=5TBW|1|AS|C|9 B=5TBW|1|AS|G|112
  2 Basepair     9  112 CG cWW 
pMakeNodes probe for inserts:  a=5TBW|1|AS|C|10 B=5TBW|1|AS|U|111
    Insertion on left  5TBW|1|AS|C|10
pMakeNodes probed for insert:  a=5TBW|1|AS|A|11 B=5TBW|1|AS|U|111
pMakeNodesJunction: a=5TBW|1|AS|A|11 r=5TBW|1|AS|A|11 s=5TBW|1|AS|A|66 t=5TBW|1|AS|G|67 u=B=5TBW|1|AS|U|111
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|AS|A|11 and 5TBW|1|AS|A|66 and between 5TBW|1|AS|G|67 and 5TBW|1|AS|U|111
pMakeNodesJunction: about to make a junction: a=5TBW|1|AS|A|11 s=5TBW|1|AS|A|66 t=5TBW|1|AS|G|67 B=5TBW|1|AS|U|111
pMakeNodesJunction: first branch starts at   5TBW|1|AS|A|11
pMakeNodesJunction: first branch ends around 5TBW|1|AS|A|66
pMakeNodesJunction: second branch starts at  5TBW|1|AS|G|67
pMakeNodesJunction: junction ends at         5TBW|1|AS|U|111
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|AS|U|14
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|AS|A|66
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|AS|G|67
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|AS|U|111
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J1418
Actual Branch 1 of junction J1418 - Nucleotides 5TBW|1|AS|A|11 to 5TBW|1|AS|A|66, length   4
Actual Branch 2 of junction J1418 - Nucleotides 5TBW|1|AS|G|67 to 5TBW|1|AS|U|111, length   2
  3 Junction

2B Branch 1 of 2 of junction J1418 - Nucleotides    11 to    66, length   4
pMakeNodes starting loop:     a=5TBW|1|AS|A|11 B=5TBW|1|AS|A|66
    Insertion on left  5TBW|1|AS|A|11
    Insertion on left  5TBW|1|AS|A|13
pMakeNodesProbeForInsertions:  a 5TBW|1|AS|U|14 interacts with 5TBW|1|AS|A|66
pMakeNodesProbeForInsertions:  B 5TBW|1|AS|A|66 interacts with 5TBW|1|AS|U|14
pMakeNodesProbeForInsertions:  B 5TBW|1|AS|A|66 interacts with 5TBW|1|AS|U|14
  4 Initial     11 (2 insertion) and   66 (0 insertion)
  5 Basepair    14   66 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J1418 - Nucleotides    67 to   111, length   2
pMakeNodes starting loop:     a=5TBW|1|AS|G|67 B=5TBW|1|AS|U|111
  8 Basepair    67  111 GU cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  8
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  8
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|AS|C|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|AS|A|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|AS|U|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 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: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'G'
               Comment: ' // Basepair C9 - 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 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: '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 5TBW|1|AS|C|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
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J1418'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [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: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J1418'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A11 - U111 ID J1418'
              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: 'J1418'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|AS|A|11 - 5TBW|1|AS|A|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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             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 5TBW|1|AS|A|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: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             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 5TBW|1|AS|U|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 U14 - 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 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: 7
            RightIndex: 8
             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: []
           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: 'U'
               Comment: ' // Basepair G67 - U111 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

ans = 

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

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: [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     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  6
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  8
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   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 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

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J1418'
        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: 'AA'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|AS|A|11 - 5TBW|1|AS|A|66 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: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J1418'
        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 J3_19431.1. Nodes 6 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 5
pNextNodeJunction: Found a junction child at node 6
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

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 7
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_19431.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4173

Timestamp 18-Jul-2025 00:12:50
pMakeSCFGModels: Making JAR3D model for motif group J3_20650.1, number 17 of 88
pMakeNodes starting loop:     a=5BJO|1|E|C|5 B=5BJO|1|E|G|32
  2 Basepair     5   32 CG cWW 
pMakeNodes probe for inserts:  a=5BJO|1|E|G|6 B=5BJO|1|E|U|31
    Insertion on left  5BJO|1|E|G|6
    Insertion on left  5BJO|1|E|A|7
    Insertion on right 5BJO|1|E|U|31
    Insertion on right 5BJO|1|E|C|30
pMakeNodes probed for insert:  a=5BJO|1|E|G|8 B=5BJO|1|E|A|29
  3 Basepair     8   29 GA cSS 
pMakeNodes probe for inserts:  a=5BJO|1|E|G|9 B=5BJO|1|E|C|28
pMakeNodes probed for insert:  a=5BJO|1|E|G|9 B=5BJO|1|E|C|28
pMakeNodesJunction: a=5BJO|1|E|G|9 r=5BJO|1|E|G|9 s=5BJO|1|E|C|18 t=5BJO|1|E|U|19 u=B=5BJO|1|E|C|28
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5BJO|1|E|G|9 and 5BJO|1|E|C|18 and between 5BJO|1|E|U|19 and 5BJO|1|E|C|28
pMakeNodesJunction: about to make a junction: a=5BJO|1|E|G|9 s=5BJO|1|E|C|18 t=5BJO|1|E|U|19 B=5BJO|1|E|C|28
pMakeNodesJunction: first branch starts at   5BJO|1|E|G|9
pMakeNodesJunction: first branch ends around 5BJO|1|E|C|18
pMakeNodesJunction: second branch starts at  5BJO|1|E|U|19
pMakeNodesJunction: junction ends at         5BJO|1|E|C|28
pMakeNodesJunction: first branch strand start goes up to  5BJO|1|E|G|9
pMakeNodesJunction: first branch strand end goes down to  5BJO|1|E|C|18
pMakeNodesJunction: second branch strand start goes up to 5BJO|1|E|G|20
pMakeNodesJunction: last strand of junction goes down to  5BJO|1|E|C|28

Junction with 2 loops, call it J4217
Actual Branch 1 of junction J4217 - Nucleotides 5BJO|1|E|G|9 to 5BJO|1|E|C|18, length   2
Actual Branch 2 of junction J4217 - Nucleotides 5BJO|1|E|U|19 to 5BJO|1|E|C|28, length   3
  4 Junction

2B Branch 1 of 2 of junction J4217 - Nucleotides     9 to    18, length   2
pMakeNodes starting loop:     a=5BJO|1|E|G|9 B=5BJO|1|E|C|18
  6 Basepair     9   18 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J4217 - Nucleotides    19 to    28, length   3
pMakeNodes starting loop:     a=5BJO|1|E|U|19 B=5BJO|1|E|C|28
    Insertion on left  5BJO|1|E|U|19
pMakeNodesProbeForInsertions:  a 5BJO|1|E|G|20 interacts with 5BJO|1|E|C|28
pMakeNodesProbeForInsertions:  B 5BJO|1|E|C|28 interacts with 5BJO|1|E|G|20
pMakeNodesProbeForInsertions:  B 5BJO|1|E|C|28 interacts with 5BJO|1|E|G|20
  8 Initial     19 (1 insertion) and   28 (0 insertion)
  9 Basepair    20   28 GC cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   4  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BJO|1|E|G|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BJO|1|E|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5BJO|1|E|U|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5BJO|1|E|C|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BJO|1|E|U|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGA'
           RightLetter: 'CUG'
               Comment: ' // Basepair C5 - G32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BJO|1|E|G|6'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: '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: 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: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BJO|1|E|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 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: '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: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5BJO|1|E|U|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: '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: 'U'
           RightLetter: []
               Comment: ' // New 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: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5BJO|1|E|C|30'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G8 - A29 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: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J4217'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G9 - C28 ID J4217'
              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: 5
            RightIndex: 6
             Insertion: []
                    id: 'J4217'
        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: 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 G9 - C18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
            RightIndex: 9
             Insertion: []
                    id: 'J4217'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5BJO|1|E|U|19 - 5BJO|1|E|C|28 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: 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 5BJO|1|E|U|19'
              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: 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: []
           numbranches: []
              NormCons: []

Node 19

ans = 

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

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G20 - C28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 20

ans = 

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

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: [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     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right 10
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 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

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J4217'
        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: 7
            RightIndex: 9
             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: 'U'
           RightLetter: []
               Comment: ' // Initial node 5BJO|1|E|U|19 - 5BJO|1|E|C|28 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_20650.1. 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_20650.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5675

Timestamp 18-Jul-2025 00:12:51
pMakeSCFGModels: Making JAR3D model for motif group J3_22198.1, number 18 of 88
pMakeNodes starting loop:     a=4RGE|1|C|A|11 B=4RGE|1|C|U|44
  2 Basepair    11   44 AU cWW 
pMakeNodes probe for inserts:  a=4RGE|1|C|G|12 B=4RGE|1|C|A|43
    Insertion on left  4RGE|1|C|G|12
pMakeNodes probed for insert:  a=4RGE|1|C|C|13 B=4RGE|1|C|A|43
  3 Basepair    13   43 CA cSS 
pMakeNodes probe for inserts:  a=4RGE|1|C|C|14 B=4RGE|1|C|A|42
pMakeNodes probed for insert:  a=4RGE|1|C|C|14 B=4RGE|1|C|A|42
pMakeNodesJunction: a=4RGE|1|C|C|14 r=4RGE|1|C|C|14 s=4RGE|1|C|G|25 t=4RGE|1|C|A|26 u=B=4RGE|1|C|A|42
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4RGE|1|C|C|14 and 4RGE|1|C|G|25 and between 4RGE|1|C|A|26 and 4RGE|1|C|A|42
pMakeNodesJunction: about to make a junction: a=4RGE|1|C|C|14 s=4RGE|1|C|G|25 t=4RGE|1|C|A|26 B=4RGE|1|C|A|42
pMakeNodesJunction: first branch starts at   4RGE|1|C|C|14
pMakeNodesJunction: first branch ends around 4RGE|1|C|G|25
pMakeNodesJunction: second branch starts at  4RGE|1|C|A|26
pMakeNodesJunction: junction ends at         4RGE|1|C|A|42
pMakeNodesJunction: first branch strand start goes up to  4RGE|1|C|C|14
pMakeNodesJunction: first branch strand end goes down to  4RGE|1|C|G|25
pMakeNodesJunction: second branch strand start goes up to 4RGE|1|C|G|27
pMakeNodesJunction: last strand of junction goes down to  4RGE|1|C|C|40

Junction with 2 loops, call it J9157
Actual Branch 1 of junction J9157 - Nucleotides 4RGE|1|C|C|14 to 4RGE|1|C|G|25, length   2
Actual Branch 2 of junction J9157 - Nucleotides 4RGE|1|C|A|26 to 4RGE|1|C|A|42, length   5
  4 Junction

2B Branch 1 of 2 of junction J9157 - Nucleotides    14 to    25, length   2
pMakeNodes starting loop:     a=4RGE|1|C|C|14 B=4RGE|1|C|G|25
  6 Basepair    14   25 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J9157 - Nucleotides    26 to    42, length   5
pMakeNodes starting loop:     a=4RGE|1|C|A|26 B=4RGE|1|C|A|42
    Insertion on left  4RGE|1|C|A|26
pMakeNodesProbeForInsertions:  a 4RGE|1|C|G|27 interacts with 4RGE|1|C|C|40
pMakeNodesProbeForInsertions:  B 4RGE|1|C|A|42 interacts with 4RGE|1|C|U|41
pMakeNodesProbeForInsertions:  B 4RGE|1|C|A|42 interacts with 4RGE|1|C|U|41
  8 Initial     26 (1 insertion) and   42 (0 insertion)
pMakeNodes making a cluster near strand break a=4RGE|1|C|G|27 B=4RGE|1|C|A|42
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 7 and then 8 to 10
aa is 7 bb is 8
  9 Cluster   4RGE|1|C|G|27:4RGE|1|C|G|27 4RGE|1|C|C|40:4RGE|1|C|A|42
    LR Inter  4RGE|1|C|G|27 4RGE|1|C|C|40 cWW 
    RR Inter  4RGE|1|C|U|41 4RGE|1|C|A|42 cSH 
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 10
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 10
pMakeMotifModelFromSSF:   9   Cluster Left  7 Right  8  9 10
pMakeMotifModelFromSSF:  10   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4RGE|1|C|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4RGE|1|C|A|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: []
          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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Basepair A11 - U44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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 4RGE|1|C|G|12'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 11
             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: 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: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C13 - A43 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: []
          LeftNotInter: []
         RightNotInter: []

Node 6

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J9157'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C14 - A42 ID J9157'
              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 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: '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: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

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
          LeftNotInter: []
         RightNotInter: []

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9157'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4RGE|1|C|A|26 - 4RGE|1|C|A|42 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4RGE|1|C|A|26'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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
          LeftNotInter: []
         RightNotInter: []

Node 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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
            RightIndex: [8 9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'CUA'
               Comment: ' // Cluster node 4RGE|1|C|G|27:4RGE|1|C|G|27 and 4RGE|1|C|C|40:4RGE|1|C|A|42'
              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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

ans = 

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

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: [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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   6  Junction Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13   Cluster Left  7 Right  8  9 10
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin
pUpdateModelWithSSF: J3_22198.1 allow insertions from initial node 14?
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: 8
             LeftIndex: 4
            RightIndex: 5
             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: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9157'
        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 4RGE|1|C|A|26 - 4RGE|1|C|A|42 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 J3_22198.1. Nodes 7 and 10 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 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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_22198.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4869

Timestamp 18-Jul-2025 00:12:51
pMakeSCFGModels: Making JAR3D model for motif group J3_25217.1, number 19 of 88
pMakeNodes starting loop:     a=2RFK|1|D|C|16 B=2RFK|1|F|G|11
  2 Basepair    16   11 CG cWW 
pMakeNodes probe for inserts:  a=2RFK|1|D|G|17 B=2RFK|1|F|G|9
    Insertion on right 2RFK|1|F|G|9
pMakeNodes probed for insert:  a=2RFK|1|D|G|17 B=2RFK|1|F|C|8
pMakeNodesJunction: a=2RFK|1|D|G|17 r=2RFK|1|D|G|17 s=2RFK|1|E|U|5 t=2RFK|1|E|U|6 u=B=2RFK|1|F|C|8
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 2RFK|1|D|G|17 and 2RFK|1|E|U|5 and between 2RFK|1|E|U|6 and 2RFK|1|F|C|8
pMakeNodesJunction: about to make a junction: a=2RFK|1|D|G|17 s=2RFK|1|E|U|5 t=2RFK|1|E|U|6 B=2RFK|1|F|C|8
pMakeNodesJunction: first branch starts at   2RFK|1|D|G|17
pMakeNodesJunction: first branch ends around 2RFK|1|E|U|5
pMakeNodesJunction: second branch starts at  2RFK|1|E|U|6
pMakeNodesJunction: junction ends at         2RFK|1|F|C|8
pMakeNodesJunction: first branch strand start goes up to  2RFK|1|D|G|17
pMakeNodesJunction: first branch strand end goes down to  2RFK|1|E|U|5
pMakeNodesJunction: second branch strand start goes up to 2RFK|1|E|G|8
pMakeNodesJunction: last strand of junction goes down to  2RFK|1|F|C|8

Junction with 2 loops, call it J7922
Actual Branch 1 of junction J7922 - Nucleotides 2RFK|1|D|G|17 to 2RFK|1|E|U|5, length   2
Actual Branch 2 of junction J7922 - Nucleotides 2RFK|1|E|U|6 to 2RFK|1|F|C|8, length   4
  3 Junction

2B Branch 1 of 2 of junction J7922 - Nucleotides    17 to     5, length   2
pMakeNodes starting loop:     a=2RFK|1|D|G|17 B=2RFK|1|E|U|5
  5 Basepair    17    5 GU cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7922 - Nucleotides     6 to     8, length   4
pMakeNodes starting loop:     a=2RFK|1|E|U|6 B=2RFK|1|F|C|8
    Insertion on left  2RFK|1|E|U|6
    Insertion on left  2RFK|1|E|C|7
pMakeNodesProbeForInsertions:  a 2RFK|1|E|G|8 interacts with 2RFK|1|F|C|8
pMakeNodesProbeForInsertions:  B 2RFK|1|F|C|8 interacts with 2RFK|1|E|G|8
pMakeNodesProbeForInsertions:  B 2RFK|1|F|C|8 interacts with 2RFK|1|E|G|8
  7 Initial      6 (2 insertion) and    8 (0 insertion)
  8 Basepair     8    8 GC cWW 
  9 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  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  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2RFK|1|F|G|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2RFK|1|E|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2RFK|1|E|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'GG'
               Comment: ' // Basepair C16 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 8
             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 2RFK|1|F|G|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: 2
            RightIndex: 7
             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: ''
           RightLetter: ''
               Comment: ' // New 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: 2
            RightIndex: 7
             Insertion: []
                    id: 'J7922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G17 - C8 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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J7922'
        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: 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 G17 - U5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             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 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: 'J7922'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: []
               Comment: ' // Initial node 2RFK|1|E|U|6 - 2RFK|1|F|C|8 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: 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 2RFK|1|E|U|6'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2RFK|1|E|C|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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 G8 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

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: [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     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5  Junction Left  2 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  10     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  12     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pNextNodeJunction: Found a 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 hairpin at node 15
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: 7
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: 'J7922'
        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: 4
            RightIndex: 7
             Insertion: []
                    id: 'J7922'
        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: 'UC'
           RightLetter: []
               Comment: ' // Initial node 2RFK|1|E|U|6 - 2RFK|1|F|C|8 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_25217.1. Nodes 6 and 9 both model an insertion before position 4. 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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_25217.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1782

Timestamp 18-Jul-2025 00:12:52
pMakeSCFGModels: Making JAR3D model for motif group J3_25670.1, number 20 of 88
pMakeNodes starting loop:     a=5TBW|1|1|G|1640 B=5TBW|1|1|C|1633
  2 Basepair  1640 1633 GC cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|U|1641 B=5TBW|1|1|A|1632
    Insertion on left  5TBW|1|1|U|1641
    Insertion on left  5TBW|1|1|A|1642
    Insertion on left  5TBW|1|1|A|1643
    Insertion on left  5TBW|1|1|C|1644
    Insertion on right 5TBW|1|1|A|1632
pMakeNodes probed for insert:  a=5TBW|1|1|U|1645 B=5TBW|1|1|C|1631
pMakeNodesJunction: a=5TBW|1|1|U|1645 r=5TBW|1|1|U|1645 s=5TBW|1|1|A|1810 t=5TBW|1|1|G|1811 u=B=5TBW|1|1|C|1631
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|1645 and 5TBW|1|1|A|1810 and between 5TBW|1|1|G|1811 and 5TBW|1|1|C|1631
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|1645 s=5TBW|1|1|A|1810 t=5TBW|1|1|G|1811 B=5TBW|1|1|C|1631
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|1645
pMakeNodesJunction: first branch ends around 5TBW|1|1|A|1810
pMakeNodesJunction: second branch starts at  5TBW|1|1|G|1811
pMakeNodesJunction: junction ends at         5TBW|1|1|C|1631
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|U|1645
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|A|1810
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|1811
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|1631

Junction with 2 loops, call it J9594
Actual Branch 1 of junction J9594 - Nucleotides 5TBW|1|1|U|1645 to 5TBW|1|1|A|1810, length   2
Actual Branch 2 of junction J9594 - Nucleotides 5TBW|1|1|G|1811 to 5TBW|1|1|C|1631, length   2
  3 Junction

2B Branch 1 of 2 of junction J9594 - Nucleotides  1645 to  1810, length   2
pMakeNodes starting loop:     a=5TBW|1|1|U|1645 B=5TBW|1|1|A|1810
  5 Basepair  1645 1810 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9594 - Nucleotides  1811 to  1631, length   2
pMakeNodes starting loop:     a=5TBW|1|1|G|1811 B=5TBW|1|1|C|1631
  8 Basepair  1811 1631 GC cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  6 Right  9
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  9
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1632
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|1633
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|1640
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|1641
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|A|1810
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [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: 'GUAAC'
           RightLetter: 'AC'
               Comment: ' // Basepair G1640 - C1633 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J9594'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1632'
              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: '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: ''
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 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 5TBW|1|1|C|1633'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
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Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J9594'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1640'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|U|1641'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|A|1810'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 13

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J9594'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U1645 - C1631 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 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: '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 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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1645 - A1810 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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: []
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Node 18

ans = 

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

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 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 G1811 - C1631 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
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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: []
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              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  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 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

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J9594'
        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: 'J9594'
        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 J3_25670.1. 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_25670.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1632

Timestamp 18-Jul-2025 00:12:52
pMakeSCFGModels: Making JAR3D model for motif group J3_28621.2, number 21 of 88
pMakeNodes starting loop:     a=4V9F|1|0|U|1185 B=4V9F|1|0|A|1161
  2 Basepair  1185 1161 UA cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|C|1186 B=4V9F|1|0|G|1160
pMakeNodes probed for insert:  a=4V9F|1|0|C|1186 B=4V9F|1|0|G|1160
pMakeNodesJunction: a=4V9F|1|0|C|1186 r=4V9F|1|0|C|1186 s=4V9F|1|0|U|1206 t=4V9F|1|0|A|1207 u=B=4V9F|1|0|G|1160
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|C|1186 and 4V9F|1|0|U|1206 and between 4V9F|1|0|A|1207 and 4V9F|1|0|G|1160
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|C|1186 s=4V9F|1|0|U|1206 t=4V9F|1|0|A|1207 B=4V9F|1|0|G|1160
pMakeNodesJunction: first branch starts at   4V9F|1|0|C|1186
pMakeNodesJunction: first branch ends around 4V9F|1|0|U|1206
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|1207
pMakeNodesJunction: junction ends at         4V9F|1|0|G|1160
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|A|1191
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|U|1206
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|C|1208
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|G|1159
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     1     0     0


Junction with 2 loops, call it J6557
Actual Branch 1 of junction J6557 - Nucleotides 4V9F|1|0|C|1186 to 4V9F|1|0|U|1206, length   7
Actual Branch 2 of junction J6557 - Nucleotides 4V9F|1|0|A|1207 to 4V9F|1|0|G|1160, length   4
  3 Junction

2B Branch 1 of 2 of junction J6557 - Nucleotides  1186 to  1206, length   7
pMakeNodes starting loop:     a=4V9F|1|0|C|1186 B=4V9F|1|0|U|1206
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|1186 interacts with 4V9F|1|0|G|1190
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|1206 interacts with 4V9F|1|0|A|1191
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|1206 interacts with 4V9F|1|0|A|1191
  4 Initial   1186 (0 insertion) and 1206 (0 insertion)
pMakeNodes making a cluster near strand break a=4V9F|1|0|C|1186 B=4V9F|1|0|U|1206
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 7 and then 8 to 8
aa is 7 bb is 8
  5 Cluster   4V9F|1|0|C|1186:4V9F|1|0|A|1191 4V9F|1|0|U|1206:4V9F|1|0|U|1206
    LR Inter  4V9F|1|0|A|1191 4V9F|1|0|U|1206 cWW 
    LL Inter  4V9F|1|0|U|1187 4V9F|1|0|A|1189 tSH 
    LL Inter  4V9F|1|0|C|1186 4V9F|1|0|G|1190 tWW 
    Left  strand conserved insertion 4V9F|1|0|A|1188 at position 3
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J6557 - Nucleotides  1207 to  1160, length   4
pMakeNodes starting loop:     a=4V9F|1|0|A|1207 B=4V9F|1|0|G|1160
  8 Basepair  1207 1160 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|C|1208 B=4V9F|1|0|G|1159
  9 Basepair  1208 1159 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1185 - A1161 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 12
             Insertion: []
                    id: 'J6557'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1186 - G1160 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 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             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 4V9F|1|0|C|1186 - 4V9F|1|0|U|1206 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]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAAGA'
           RightLetter: 'U'
               Comment: ' // Cluster node 4V9F|1|0|C|1186:4V9F|1|0|A|1191 and 4V9F|1|0|U|1206:4V9F|1|0|U|1206'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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: []
          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: 9
            RightIndex: 12
             Insertion: []
                    id: 'J6557'
        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 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             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 A1207 - G1160 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1208 - G1159 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 11

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   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 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: 'J6557'
        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: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|C|1186 - 4V9F|1|0|U|1206 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: 9
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J6557'
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J3_28621.2. Nodes 4 and 8 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 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 hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 11
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_28621.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4176
   -7.0605
   -7.0605
   -7.0605
   -7.7258
   -7.0605

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J3_30104.1, number 22 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|C|2789 B=5J7L|1|DA|G|2894
  2 Basepair  2789 2894 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|2790 B=5J7L|1|DA|A|2893
    Insertion on left  5J7L|1|DA|U|2790
    Insertion on right 5J7L|1|DA|A|2893
pMakeNodes probed for insert:  a=5J7L|1|DA|G|2791 B=5J7L|1|DA|G|2892
pMakeNodesJunction: a=5J7L|1|DA|G|2791 r=5J7L|1|DA|G|2791 s=5J7L|1|DA|C|2805 t=5J7L|1|DA|C|2806 u=B=5J7L|1|DA|G|2892
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|G|2791 and 5J7L|1|DA|C|2805 and between 5J7L|1|DA|C|2806 and 5J7L|1|DA|G|2892
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|G|2791 s=5J7L|1|DA|C|2805 t=5J7L|1|DA|C|2806 B=5J7L|1|DA|G|2892
pMakeNodesJunction: first branch starts at   5J7L|1|DA|G|2791
pMakeNodesJunction: first branch ends around 5J7L|1|DA|C|2805
pMakeNodesJunction: second branch starts at  5J7L|1|DA|C|2806
pMakeNodesJunction: junction ends at         5J7L|1|DA|G|2892
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|2791
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|C|2805
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|C|2806
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|G|2892

Junction with 2 loops, call it J357
Actual Branch 1 of junction J357 - Nucleotides 5J7L|1|DA|G|2791 to 5J7L|1|DA|C|2805, length   2
Actual Branch 2 of junction J357 - Nucleotides 5J7L|1|DA|C|2806 to 5J7L|1|DA|G|2892, length   2
  3 Junction

2B Branch 1 of 2 of junction J357 - Nucleotides  2791 to  2805, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|G|2791 B=5J7L|1|DA|C|2805
  5 Basepair  2791 2805 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J357 - Nucleotides  2806 to  2892, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|2806 B=5J7L|1|DA|G|2892
  8 Basepair  2806 2892 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  6
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  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2790
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|2893
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CU'
           RightLetter: 'AG'
               Comment: ' // Basepair C2789 - G2894 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
             Insertion: []
                    id: 'J357'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2790'
              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: 7
             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: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|2893'
              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: 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: 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: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J357'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2791 - G2892 ID J357'
              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: 4
             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: []
              NormCons: []

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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2791 - C2805 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 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: '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: []
              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 C2806 - G2892 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: [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     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Junction Left  3 Right  6
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  6
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, 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: '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: []
              NormCons: []


ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J357'
        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 J3_30104.1. 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
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_30104.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5147

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J3_32030.1, number 23 of 88
pMakeNodes starting loop:     a=3NPQ|1|A|C|13 B=3NPQ|1|A|G|48
  2 Basepair    13   48 CG cWW 
pMakeNodes probe for inserts:  a=3NPQ|1|A|U|14 B=3NPQ|1|A|G|47
    Insertion on right 3NPQ|1|A|G|47
pMakeNodes probed for insert:  a=3NPQ|1|A|U|14 B=3NPQ|1|A|C|46
pMakeNodesJunction: a=3NPQ|1|A|U|14 r=3NPQ|1|A|U|14 s=3NPQ|1|A|A|29 t=3NPQ|1|A|G|30 u=B=3NPQ|1|A|C|46
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3NPQ|1|A|U|14 and 3NPQ|1|A|A|29 and between 3NPQ|1|A|G|30 and 3NPQ|1|A|C|46
pMakeNodesJunction: about to make a junction: a=3NPQ|1|A|U|14 s=3NPQ|1|A|A|29 t=3NPQ|1|A|G|30 B=3NPQ|1|A|C|46
pMakeNodesJunction: first branch starts at   3NPQ|1|A|U|14
pMakeNodesJunction: first branch ends around 3NPQ|1|A|A|29
pMakeNodesJunction: second branch starts at  3NPQ|1|A|G|30
pMakeNodesJunction: junction ends at         3NPQ|1|A|C|46
pMakeNodesJunction: first branch strand start goes up to  3NPQ|1|A|G|19
pMakeNodesJunction: first branch strand end goes down to  3NPQ|1|A|C|26
pMakeNodesJunction: second branch strand start goes up to 3NPQ|1|A|G|30
pMakeNodesJunction: last strand of junction goes down to  3NPQ|1|A|C|46

Junction with 2 loops, call it J8491
Actual Branch 1 of junction J8491 - Nucleotides 3NPQ|1|A|U|14 to 3NPQ|1|A|A|29, length  10
Actual Branch 2 of junction J8491 - Nucleotides 3NPQ|1|A|G|30 to 3NPQ|1|A|C|46, length   2
  3 Junction

2B Branch 1 of 2 of junction J8491 - Nucleotides    14 to    29, length  10
pMakeNodes starting loop:     a=3NPQ|1|A|U|14 B=3NPQ|1|A|A|29
  5 Basepair    14   29 UA tWH 
pMakeNodes probe for inserts:  a=3NPQ|1|A|G|15 B=3NPQ|1|A|C|28
    Insertion on left  3NPQ|1|A|G|15
pMakeNodesProbeForInsertions:  a 3NPQ|1|A|C|16 interacts with 3NPQ|1|A|C|28
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|C|28 interacts with 3NPQ|1|A|C|16
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|C|28 interacts with 3NPQ|1|A|A|17
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3NPQ|1|A|C|16 B=3NPQ|1|A|C|28
pMakeNodes making a cluster near strand break a=3NPQ|1|A|C|16 B=3NPQ|1|A|C|28
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  6 Cluster   3NPQ|1|A|C|16:3NPQ|1|A|A|17 3NPQ|1|A|C|28:3NPQ|1|A|C|28
    LR Inter  3NPQ|1|A|C|16 3NPQ|1|A|C|28 tHS 
    LR Inter  3NPQ|1|A|A|17 3NPQ|1|A|C|28 tHS 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=3NPQ|1|A|A|18 B=3NPQ|1|A|C|27
  7 Basepair    18   27 AC bif 
No need to probe because of interaction between a=3NPQ|1|A|G|19 B=3NPQ|1|A|C|26
  8 Basepair    19   26 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J8491 - Nucleotides    30 to    46, length   2
pMakeNodes starting loop:     a=3NPQ|1|A|G|30 B=3NPQ|1|A|C|46
 11 Basepair    30   46 GC cWW 
 12 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 13
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   6   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  12   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3NPQ|1|A|G|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'GG'
               Comment: ' // Basepair C13 - G48 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 14
             Insertion: []
                    id: 'J8491'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3NPQ|1|A|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
          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: 13
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Junction'
              nextnode: [4 10]
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: 'J8491'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U14 - C46 ID J8491'
              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: 11
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            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: 'UG'
           RightLetter: 'A'
               Comment: ' // Basepair U14 - A29 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|15'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'C'
               Comment: ' // Cluster node 3NPQ|1|A|C|16:3NPQ|1|A|A|17 and 3NPQ|1|A|C|28:3NPQ|1|A|C|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: 0.2610

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after 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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A18 - C27 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              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: []
          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: 12
            RightIndex: 13
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

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

                  type: 'Basepair'
              nextnode: 17
             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 G30 - 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

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

                  type: 'Hairpin'
              nextnode: 20
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 13
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  10   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  15   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  16  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  17   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 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
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: 2
            RightIndex: 11
             Insertion: []
                    id: 'J8491'
        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: 16
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: 'J8491'
        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 J3_32030.1. Nodes 6 and 15 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 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_32030.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8308

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J3_32601.2, number 24 of 88
pMakeNodes starting loop:     a=4Y4O|1|2A|A|2561 B=4Y4O|1|2A|U|2547
  2 Basepair  2561 2547 AU cWW 
pMakeNodes probe for inserts:  a=4Y4O|1|2A|U|2562 B=4Y4O|1|2A|U|2546
pMakeNodes probed for insert:  a=4Y4O|1|2A|U|2562 B=4Y4O|1|2A|U|2546
pMakeNodes making a cluster near strand break a=4Y4O|1|2A|U|2562 B=4Y4O|1|2A|U|2546
pMakeNodesCluster: amax is 6 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 11 to 11
aa is 6 bb is 11
  3 Cluster   4Y4O|1|2A|U|2562:4Y4O|1|2A|A|2566 4Y4O|1|2A|U|2546:4Y4O|1|2A|U|2546
    LL Inter  4Y4O|1|2A|U|2563 4Y4O|1|2A|A|2565 tSH 
    LL Inter  4Y4O|1|2A|U|2562 4Y4O|1|2A|A|2566 tWH 
    Left  strand conserved insertion 4Y4O|1|2A|A|2564 at position 3
    Right strand conserved insertion 4Y4O|1|2A|U|2546 at position 1
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
pMakeNodes probe for inserts:  a=4Y4O|1|2A|G|2567 B=4Y4O|1|2A|G|2545
  4 Initial   2567 (0 insertion) and 2545 (0 insertion)
pMakeNodes probed for insert:  a=4Y4O|1|2A|G|2567 B=4Y4O|1|2A|G|2545
pMakeNodesJunction: a=4Y4O|1|2A|G|2567 r=4Y4O|1|2A|G|2567 s=4Y4O|1|2A|C|2517 t=4Y4O|1|2A|C|2520 u=B=4Y4O|1|2A|G|2545
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4Y4O|1|2A|G|2567 and 4Y4O|1|2A|C|2517 and between 4Y4O|1|2A|C|2520 and 4Y4O|1|2A|G|2545
pMakeNodesJunction: about to make a junction: a=4Y4O|1|2A|G|2567 s=4Y4O|1|2A|C|2517 t=4Y4O|1|2A|C|2520 B=4Y4O|1|2A|G|2545
pMakeNodesJunction: first branch starts at   4Y4O|1|2A|G|2567
pMakeNodesJunction: first branch ends around 4Y4O|1|2A|C|2517
pMakeNodesJunction: second branch starts at  4Y4O|1|2A|C|2520
pMakeNodesJunction: junction ends at         4Y4O|1|2A|G|2545
pMakeNodesJunction: first branch strand start goes up to  4Y4O|1|2A|G|2567
pMakeNodesJunction: first branch strand end goes down to  4Y4O|1|2A|C|2517
pMakeNodesJunction: second branch strand start goes up to 4Y4O|1|2A|C|2520
pMakeNodesJunction: last strand of junction goes down to  4Y4O|1|2A|G|2545

Junction with 2 loops, call it J9339
Actual Branch 1 of junction J9339 - Nucleotides 4Y4O|1|2A|G|2567 to 4Y4O|1|2A|C|2517, length   2
Actual Branch 2 of junction J9339 - Nucleotides 4Y4O|1|2A|C|2520 to 4Y4O|1|2A|G|2545, length   2
  5 Junction

2B Branch 1 of 2 of junction J9339 - Nucleotides  2567 to  2517, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|G|2567 B=4Y4O|1|2A|C|2517
  7 Basepair  2567 2517 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J9339 - Nucleotides  2520 to  2545, length   2
pMakeNodes starting loop:     a=4Y4O|1|2A|C|2520 B=4Y4O|1|2A|G|2545
 10 Basepair  2520 2545 CG cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  7 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2561 - U2547 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4 5 6]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 4Y4O|1|2A|U|2562:4Y4O|1|2A|A|2566 and 4Y4O|1|2A|U|2546:4Y4O|1|2A|U|2546'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 1
              NormCons: 1.0000
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 7
            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 4Y4O|1|2A|G|2567 - 4Y4O|1|2A|G|2545 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: 7
            RightIndex: 10
             Insertion: []
                    id: 'J9339'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2567 - G2545 ID J9339'
              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: 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: []
          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: 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 G2567 - C2517 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 9
            RightIndex: 10
             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: []
          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: 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 C2520 - G2545 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J9339'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0 0.0122 0.9750 0.0122 6.0938e-04]
       rightLetterDist: [0.4500 0.0500 0.0500 0.4500 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: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9339'
        leftLengthDist: [0 0.0122 0.9750 0.0122 6.0938e-04]
        leftLetterDist: [0.4500 0.0500 0.0500 0.4500 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 J3_32601.2. Nodes 6 and 9 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 hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 9
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 7 and 11
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 9
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 7 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_32601.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6711
   -8.8847
   -7.6711
   -7.6711

Timestamp 18-Jul-2025 00:12:53
pMakeSCFGModels: Making JAR3D model for motif group J3_32852.2, number 25 of 88
pMakeNodes starting loop:     a=7A0S|1|X|C|1311 B=7A0S|1|X|G|1659
  2 Basepair  1311 1659 CG cWW 
No need to probe because of interaction between a=7A0S|1|X|G|1312 B=7A0S|1|X|A|1658
pMakeNodes making a cluster near strand break a=7A0S|1|X|G|1312 B=7A0S|1|X|A|1658
pMakeNodesCluster: amax is 4 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 11
aa is 4 bb is 11
  3 Cluster   7A0S|1|X|G|1312:7A0S|1|X|A|1314 7A0S|1|X|A|1658:7A0S|1|X|A|1658
    LR Inter  7A0S|1|X|G|1312 7A0S|1|X|A|1658 tSH 
    LR Inter  7A0S|1|X|A|1314 7A0S|1|X|A|1658 tHW 
    Left  strand conserved insertion 7A0S|1|X|U|1313 at position 2
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
pMakeNodes probe for inserts:  a=7A0S|1|X|G|1316 B=7A0S|1|X|A|1657
    Insertion on right 7A0S|1|X|A|1657
  4 Initial   1316 (0 insertion) and 1657 (1 insertion)
pMakeNodes probed for insert:  a=7A0S|1|X|G|1316 B=7A0S|1|X|U|1656
pMakeNodesJunction: a=7A0S|1|X|G|1316 r=7A0S|1|X|G|1316 s=7A0S|1|X|C|1641 t=7A0S|1|X|G|1642 u=B=7A0S|1|X|U|1656
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|G|1316 and 7A0S|1|X|C|1641 and between 7A0S|1|X|G|1642 and 7A0S|1|X|U|1656
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|G|1316 s=7A0S|1|X|C|1641 t=7A0S|1|X|G|1642 B=7A0S|1|X|U|1656
pMakeNodesJunction: first branch starts at   7A0S|1|X|G|1316
pMakeNodesJunction: first branch ends around 7A0S|1|X|C|1641
pMakeNodesJunction: second branch starts at  7A0S|1|X|G|1642
pMakeNodesJunction: junction ends at         7A0S|1|X|U|1656
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|G|1316
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|C|1641
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|A|1643
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|U|1656

Junction with 2 loops, call it J6787
Actual Branch 1 of junction J6787 - Nucleotides 7A0S|1|X|G|1316 to 7A0S|1|X|C|1641, length   2
Actual Branch 2 of junction J6787 - Nucleotides 7A0S|1|X|G|1642 to 7A0S|1|X|U|1656, length   3
  5 Junction

2B Branch 1 of 2 of junction J6787 - Nucleotides  1316 to  1641, length   2
pMakeNodes starting loop:     a=7A0S|1|X|G|1316 B=7A0S|1|X|C|1641
  7 Basepair  1316 1641 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6787 - Nucleotides  1642 to  1656, length   3
pMakeNodes starting loop:     a=7A0S|1|X|G|1642 B=7A0S|1|X|U|1656
    Insertion on left  7A0S|1|X|G|1642
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|1643 interacts with 7A0S|1|X|U|1656
pMakeNodesProbeForInsertions:  B 7A0S|1|X|U|1656 interacts with 7A0S|1|X|A|1643
pMakeNodesProbeForInsertions:  B 7A0S|1|X|U|1656 interacts with 7A0S|1|X|A|1643
  9 Initial   1642 (1 insertion) and 1656 (0 insertion)
 10 Basepair  1643 1656 AU cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|U|1656
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|C|1641
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: []
          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: 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 C1311 - G1659 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUA'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|X|G|1312:7A0S|1|X|A|1314 and 7A0S|1|X|A|1658:7A0S|1|X|A|1658'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.3779
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'A'
               Comment: ' // Initial node 7A0S|1|X|G|1316 - 7A0S|1|X|A|1657 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: 5
            RightIndex: 10
             Insertion: []
                    id: 'J6787'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|1656'
              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: 5
            RightIndex: 9
             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: []
          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: 5
            RightIndex: 9
             Insertion: []
                    id: 'J6787'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1316 - U1656 ID J6787'
              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: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6787'
        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: 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 G1316 - C1641 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J6787'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|G|1642 - 7A0S|1|X|U|1656 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: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|C|1641'
              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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          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: 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 A1643 - U1656 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   7  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a 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 hairpin at node 15
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: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J6787'
        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: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J6787'
        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: 'G'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|G|1642 - 7A0S|1|X|U|1656 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 J3_32852.2. Nodes 8 and 11 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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, 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\J3\3.48\lib\J3_32852.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4398
   -8.9173
  -10.9312
   -8.0737

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J3_32857.1, number 26 of 88
pMakeNodes starting loop:     a=4LFB|1|A|G|1003|||A B=4LFB|1|A|C|1038
  2 Basepair  1003A 1038 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|1004 B=4LFB|1|A|C|1037
    Insertion on left  4LFB|1|A|A|1004
    Insertion on left  4LFB|1|A|A|1005
    Insertion on right 4LFB|1|A|C|1037
    Insertion on right 4LFB|1|A|G|1036
    Insertion on right 4LFB|1|A|A|1035
    Insertion on right 4LFB|1|A|G|1034
pMakeNodes probed for insert:  a=4LFB|1|A|C|1006 B=4LFB|1|A|G|1033
pMakeNodesJunction: a=4LFB|1|A|C|1006 r=4LFB|1|A|C|1006 s=4LFB|1|A|G|1023 t=4LFB|1|A|G|1024 u=B=4LFB|1|A|G|1033
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|C|1006 and 4LFB|1|A|G|1023 and between 4LFB|1|A|G|1024 and 4LFB|1|A|G|1033
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|C|1006 s=4LFB|1|A|G|1023 t=4LFB|1|A|G|1024 B=4LFB|1|A|G|1033
pMakeNodesJunction: first branch starts at   4LFB|1|A|C|1006
pMakeNodesJunction: first branch ends around 4LFB|1|A|G|1023
pMakeNodesJunction: second branch starts at  4LFB|1|A|G|1024
pMakeNodesJunction: junction ends at         4LFB|1|A|G|1033
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|C|1006
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|G|1023
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|C|1028
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|G|1033

Junction with 2 loops, call it J7577
Actual Branch 1 of junction J7577 - Nucleotides 4LFB|1|A|C|1006 to 4LFB|1|A|G|1023, length   2
Actual Branch 2 of junction J7577 - Nucleotides 4LFB|1|A|G|1024 to 4LFB|1|A|G|1033, length   5
  3 Junction

2B Branch 1 of 2 of junction J7577 - Nucleotides  1006 to  1023, length   2
pMakeNodes starting loop:     a=4LFB|1|A|C|1006 B=4LFB|1|A|G|1023
  5 Basepair  1006 1023 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7577 - Nucleotides  1024 to  1033, length   5
pMakeNodes starting loop:     a=4LFB|1|A|G|1024 B=4LFB|1|A|G|1033
    Insertion on left  4LFB|1|A|G|1024
    Insertion on left  4LFB|1|A|U|1025
    Insertion on left  4LFB|1|A|G|1026
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|1028 interacts with 4LFB|1|A|G|1033
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1033 interacts with 4LFB|1|A|C|1028
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1033 interacts with 4LFB|1|A|C|1028
  7 Initial   1024 (3 insertion) and 1033 (0 insertion)
  8 Basepair  1028 1033 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 10
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 10
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1004
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1005
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|1036
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|1035
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|1034
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|1033
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1024
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|1025
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1026
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'GAGCC'
               Comment: ' // Basepair G1003A - C1038 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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 4LFB|1|A|A|1004'
              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: 'J7577'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 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|A|1005'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 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: []
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Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J7577'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|1036'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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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: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|1035'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      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: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|1034'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|1033'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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Node 15

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J7577'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1006 - G1033 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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 4
            RightIndex: 5
             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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1006 - G1023 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 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: 'J7577'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUG'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1024 - 4LFB|1|A|G|1033 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: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|1024'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  rpar: []
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Node 21

ans = 

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

                  type: 'Initial'
              nextnode: 22
             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: []
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                IBases: []
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Node 22

ans = 

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

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|1025'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
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Node 23

ans = 

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

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 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: []
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                IBases: []
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Node 24

ans = 

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

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 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 4LFB|1|A|G|1026'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
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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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed 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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1028 - G1033 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 29
             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     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     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  4 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  4 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  15  Junction Left  4 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  4 Right  5
pMakeMotifModelFromSSF:  17  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  18   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  19   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  20     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  21   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  22     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  23   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  24     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  25   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  26  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  27   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Finished at node 27 out of 27, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 4
            RightIndex: 5
             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: 20
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J7577'
        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: 'GUG'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1024 - 4LFB|1|A|G|1033 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_32857.1. Nodes 16 and 19 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 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Finished at node 27 out of 27, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_32857.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.2450

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J3_33851.1, number 27 of 88
pMakeNodes starting loop:     a=5TBW|1|1|C|863 B=5TBW|1|1|G|831
  2 Basepair   863  831 CG cWW 
No need to probe because of interaction between a=5TBW|1|1|G|864 B=5TBW|1|1|A|830
  3 Basepair   864  830 GA tSH 
pMakeNodes probe for inserts:  a=5TBW|1|1|U|865 B=5TBW|1|1|U|829
    Insertion on left  5TBW|1|1|U|865
pMakeNodes probed for insert:  a=5TBW|1|1|A|866 B=5TBW|1|1|U|829
pMakeNodesJunction: a=5TBW|1|1|A|866 r=5TBW|1|1|A|866 s=5TBW|1|1|C|893 t=5TBW|1|1|G|894 u=B=5TBW|1|1|U|829
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|A|866 and 5TBW|1|1|C|893 and between 5TBW|1|1|G|894 and 5TBW|1|1|U|829
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|A|866 s=5TBW|1|1|C|893 t=5TBW|1|1|G|894 B=5TBW|1|1|U|829
pMakeNodesJunction: first branch starts at   5TBW|1|1|A|866
pMakeNodesJunction: first branch ends around 5TBW|1|1|C|893
pMakeNodesJunction: second branch starts at  5TBW|1|1|G|894
pMakeNodesJunction: junction ends at         5TBW|1|1|U|829
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|867
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|U|892
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|U|897
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|828

Junction with 2 loops, call it J7431
Actual Branch 1 of junction J7431 - Nucleotides 5TBW|1|1|A|866 to 5TBW|1|1|C|893, length   4
Actual Branch 2 of junction J7431 - Nucleotides 5TBW|1|1|G|894 to 5TBW|1|1|U|829, length   5
  4 Junction

2B Branch 1 of 2 of junction J7431 - Nucleotides   866 to   893, length   4
pMakeNodes starting loop:     a=5TBW|1|1|A|866 B=5TBW|1|1|C|893
  6 Basepair   866  893 AC tHS 
No need to probe because of interaction between a=5TBW|1|1|G|867 B=5TBW|1|1|U|892
  7 Basepair   867  892 GU cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J7431 - Nucleotides   894 to   829, length   5
pMakeNodes starting loop:     a=5TBW|1|1|G|894 B=5TBW|1|1|U|829
    Insertion on left  5TBW|1|1|G|894
pMakeNodesProbeForInsertions:  a 5TBW|1|1|A|895 interacts with 5TBW|1|1|U|829
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|829 interacts with 5TBW|1|1|A|895
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|829 interacts with 5TBW|1|1|A|895
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  9 Initial    894 (1 insertion) and  829 (0 insertion)
 10 Basepair   895  829 AU cHW 
No need to probe because of interaction between a=5TBW|1|1|U|897 B=5TBW|1|1|A|828
 11 Basepair   897  828 UA cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   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|830
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|866
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C863 - G831 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: 'GU'
           RightLetter: 'A'
               Comment: ' // Basepair G864 - A830 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: 'J7431'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|830'
              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: 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 6

ans = 

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

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J7431'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A866 - U829 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 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: '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 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A866 - C893 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: 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 G867 - U892 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            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 5TBW|1|1|G|894 - 5TBW|1|1|U|829 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: 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 5TBW|1|1|A|866'
              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

Node 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A895 - U829 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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U897 - A828 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   6  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  11   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  12     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 16
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: 8
             LeftIndex: 4
            RightIndex: 7
             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: 12
             LeftIndex: 8
            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 5TBW|1|1|G|894 - 5TBW|1|1|U|829 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_33851.1. Nodes 7 and 11 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 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_33851.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9609

Timestamp 18-Jul-2025 00:12:54
pMakeSCFGModels: Making JAR3D model for motif group J3_35321.1, number 28 of 88
pMakeNodes starting loop:     a=5TBW|1|1|C|1092 B=5TBW|1|1|G|1066
pMakeNodes making a cluster near strand break a=5TBW|1|1|C|1092 B=5TBW|1|1|G|1066
pMakeNodesCluster: amax is 5 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 1 and then 10 to 12
aa is 1 bb is 10
  2 Cluster   5TBW|1|1|C|1092:5TBW|1|1|C|1092 5TBW|1|1|G|1063:5TBW|1|1|G|1066
    LR Inter  5TBW|1|1|C|1092 5TBW|1|1|G|1066 cWW 
    RR Inter  5TBW|1|1|G|1063 5TBW|1|1|G|1066 cSS 
    Right strand conserved insertion 5TBW|1|1|A|1064 at position 2
pMakeNodesCluster a=2 B=9 at the end
pMakeNodesCluster a=2 B=9 at the end
pMakeNodes probe for inserts:  a=5TBW|1|1|A|1093 B=5TBW|1|1|A|1062
    Insertion on left  5TBW|1|1|A|1093
    Insertion on left  5TBW|1|1|U|1094
    Insertion on left  5TBW|1|1|U|1096
    Insertion on left  5TBW|1|1|G|1097
  3 Initial   1093 (4 insertion) and 1062 (0 insertion)
pMakeNodes probed for insert:  a=5TBW|1|1|A|1098 B=5TBW|1|1|A|1062
pMakeNodesJunction: a=5TBW|1|1|A|1098 r=5TBW|1|1|A|1098 s=5TBW|1|1|U|986 t=5TBW|1|1|U|987 u=B=5TBW|1|1|A|1062
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|A|1098 and 5TBW|1|1|U|986 and between 5TBW|1|1|U|987 and 5TBW|1|1|A|1062
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|A|1098 s=5TBW|1|1|U|986 t=5TBW|1|1|U|987 B=5TBW|1|1|A|1062
pMakeNodesJunction: first branch starts at   5TBW|1|1|A|1098
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|986
pMakeNodesJunction: second branch starts at  5TBW|1|1|U|987
pMakeNodesJunction: junction ends at         5TBW|1|1|A|1062
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|A|1098
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|U|986
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|U|987
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|A|1062

Junction with 2 loops, call it J3922
Actual Branch 1 of junction J3922 - Nucleotides 5TBW|1|1|A|1098 to 5TBW|1|1|U|986, length   2
Actual Branch 2 of junction J3922 - Nucleotides 5TBW|1|1|U|987 to 5TBW|1|1|A|1062, length   2
  4 Junction

2B Branch 1 of 2 of junction J3922 - Nucleotides  1098 to   986, length   2
pMakeNodes starting loop:     a=5TBW|1|1|A|1098 B=5TBW|1|1|U|986
  6 Basepair  1098  986 AU cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J3922 - Nucleotides   987 to  1062, length   2
pMakeNodes starting loop:     a=5TBW|1|1|U|987 B=5TBW|1|1|A|1062
  9 Basepair   987 1062 UA cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   4  Junction Left  6 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|987
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1062
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|1063
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|1064
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 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
            RightIndex: [10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 5TBW|1|1|C|1092:5TBW|1|1|C|1092 and 5TBW|1|1|G|1063:5TBW|1|1|G|1066'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2515
           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: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AUUG'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|A|1093 - 5TBW|1|1|A|1062 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: 9
             Insertion: []
                    id: 'J3922'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|987'
              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: 9
             Insertion: []
                    id: 'J3922'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: 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 5TBW|1|1|A|1062'
              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: 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: []
          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: 9
             Insertion: []
                    id: 'J3922'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1063'
              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: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             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 5TBW|1|1|A|1064'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      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: 'Junction'
              nextnode: [5 8]
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J3922'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1098 - A1062 ID J3922'
              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: 6
            RightIndex: 7
             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: []
          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: 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 A1098 - U986 cWW '
              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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 9
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             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 U987 - A1062 cWW '
              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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  12  Junction Left  6 Right  9
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  9
pMakeMotifModelFromSSF:  17  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  18   Hairpin Left  9 Right  8
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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 9
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J3_35321.1. 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 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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_35321.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3308

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J3_36387.1, number 29 of 88
pMakeNodes starting loop:     a=4WFL|1|A|C|10 B=4WFL|1|A|G|102
  2 Basepair    10  102 CG cWW 
pMakeNodes probe for inserts:  a=4WFL|1|A|U|11 B=4WFL|1|A|U|101
pMakeNodes probed for insert:  a=4WFL|1|A|U|11 B=4WFL|1|A|U|101
pMakeNodesJunction: a=4WFL|1|A|U|11 r=4WFL|1|A|U|11 s=4WFL|1|A|A|64 t=4WFL|1|A|U|65 u=B=4WFL|1|A|U|101
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WFL|1|A|U|11 and 4WFL|1|A|A|64 and between 4WFL|1|A|U|65 and 4WFL|1|A|U|101
pMakeNodesJunction: about to make a junction: a=4WFL|1|A|U|11 s=4WFL|1|A|A|64 t=4WFL|1|A|U|65 B=4WFL|1|A|U|101
pMakeNodesJunction: first branch starts at   4WFL|1|A|U|11
pMakeNodesJunction: first branch ends around 4WFL|1|A|A|64
pMakeNodesJunction: second branch starts at  4WFL|1|A|U|65
pMakeNodesJunction: junction ends at         4WFL|1|A|U|101
pMakeNodesJunction: first branch strand start goes up to  4WFL|1|A|G|14
pMakeNodesJunction: first branch strand end goes down to  4WFL|1|A|C|60
pMakeNodesJunction: second branch strand start goes up to 4WFL|1|A|C|67
pMakeNodesJunction: last strand of junction goes down to  4WFL|1|A|G|100
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J6554
Actual Branch 1 of junction J6554 - Nucleotides 4WFL|1|A|U|11 to 4WFL|1|A|A|64, length   9
Actual Branch 2 of junction J6554 - Nucleotides 4WFL|1|A|U|65 to 4WFL|1|A|U|101, length   5
  3 Junction

2B Branch 1 of 2 of junction J6554 - Nucleotides    11 to    64, length   9
pMakeNodes starting loop:     a=4WFL|1|A|U|11 B=4WFL|1|A|A|64
pMakeNodesProbeForInsertions:  a 4WFL|1|A|U|11 interacts with 4WFL|1|A|A|63
pMakeNodesProbeForInsertions:  B 4WFL|1|A|A|64 interacts with 4WFL|1|A|A|12
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WFL|1|A|A|64 interacts with 4WFL|1|A|A|12
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial     11 (0 insertion) and   64 (0 insertion)
pMakeNodes making a cluster near strand break a=4WFL|1|A|U|11 B=4WFL|1|A|A|64
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 8 to 10
aa is 3 bb is 8
  5 Cluster   4WFL|1|A|U|11:4WFL|1|A|A|12 4WFL|1|A|G|62:4WFL|1|A|A|64
    LR Inter  4WFL|1|A|A|12 4WFL|1|A|G|62 tHS 
    LR Inter  4WFL|1|A|U|11 4WFL|1|A|A|63 tWH 
    LR Inter  4WFL|1|A|A|12 4WFL|1|A|A|64 tWW 
pMakeNodesCluster a=4 B=7 at the end
pMakeNodesCluster a=4 B=7 at the end
No need to probe because of interaction between a=4WFL|1|A|A|13 B=4WFL|1|A|C|61
  6 Basepair    13   61 AC bif 
No need to probe because of interaction between a=4WFL|1|A|G|14 B=4WFL|1|A|C|60
  7 Basepair    14   60 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6554 - Nucleotides    65 to   101, length   5
pMakeNodes starting loop:     a=4WFL|1|A|U|65 B=4WFL|1|A|U|101
    Insertion on left  4WFL|1|A|U|65
    Insertion on left  4WFL|1|A|C|66
    Insertion on right 4WFL|1|A|U|101
pMakeNodesProbeForInsertions:  a 4WFL|1|A|C|67 interacts with 4WFL|1|A|G|100
pMakeNodesProbeForInsertions:  B 4WFL|1|A|G|100 interacts with 4WFL|1|A|C|67
pMakeNodesProbeForInsertions:  B 4WFL|1|A|G|100 interacts with 4WFL|1|A|C|67
  9 Initial     65 (2 insertion) and  101 (1 insertion)
 10 Basepair    67  100 CG cWW 
 11 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 15
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  2  3 Right  8  9 10
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  10  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  11   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WFL|1|A|U|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WFL|1|A|C|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WFL|1|A|U|101
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 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: 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C10 - G102 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Junction'
              nextnode: [4 9]
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: 'J6554'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U11 - U101 ID J6554'
              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: 10
             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 4WFL|1|A|U|11 - 4WFL|1|A|A|64 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]
            RightIndex: [8 9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UA'
           RightLetter: 'GAA'
               Comment: ' // Cluster node 4WFL|1|A|U|11:4WFL|1|A|A|12 and 4WFL|1|A|G|62:4WFL|1|A|A|64'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2635

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after 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: 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 A13 - C61 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G14 - 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 11
            RightIndex: 15
             Insertion: []
                    id: 'J6554'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: 'U'
               Comment: ' // Initial node 4WFL|1|A|U|65 - 4WFL|1|A|U|101 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             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 4WFL|1|A|U|65'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          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: 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: 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

Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             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 4WFL|1|A|C|66'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

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

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

Node 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 13
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WFL|1|A|U|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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             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 C67 - 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

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

                  type: 'Hairpin'
              nextnode: 19
             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 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  2  3 Right  8  9 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  12   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left 12 Right 15
pMakeMotifModelFromSSF:  14   Initial Left 13 Right 15
pMakeMotifModelFromSSF:  15     Fixed Left 13 Right 15
pMakeMotifModelFromSSF:  16   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  17  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  18   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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: 'J6554'
        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 4WFL|1|A|U|11 - 4WFL|1|A|A|64 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: 11
             LeftIndex: 11
            RightIndex: 15
             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: 'UC'
           RightLetter: 'U'
               Comment: ' // Initial node 4WFL|1|A|U|65 - 4WFL|1|A|U|101 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 J3_36387.1. Nodes 4 and 10 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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 10 and 15
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 10 and 15
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_36387.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0468

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J3_36499.1, number 30 of 88
pMakeNodes starting loop:     a=4UYK|1|R|C|10 B=4UYK|1|R|G|135
  2 Basepair    10  135 CG cWW 
pMakeNodes probe for inserts:  a=4UYK|1|R|U|11 B=4UYK|1|R|U|134
    Insertion on right 4UYK|1|R|U|134
pMakeNodes probed for insert:  a=4UYK|1|R|U|11 B=4UYK|1|R|G|133
pMakeNodesJunction: a=4UYK|1|R|U|11 r=4UYK|1|R|U|11 s=4UYK|1|R|A|68 t=4UYK|1|R|G|69 u=B=4UYK|1|R|G|133
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4UYK|1|R|U|11 and 4UYK|1|R|A|68 and between 4UYK|1|R|G|69 and 4UYK|1|R|G|133
pMakeNodesJunction: about to make a junction: a=4UYK|1|R|U|11 s=4UYK|1|R|A|68 t=4UYK|1|R|G|69 B=4UYK|1|R|G|133
pMakeNodesJunction: first branch starts at   4UYK|1|R|U|11
pMakeNodesJunction: first branch ends around 4UYK|1|R|A|68
pMakeNodesJunction: second branch starts at  4UYK|1|R|G|69
pMakeNodesJunction: junction ends at         4UYK|1|R|G|133
pMakeNodesJunction: first branch strand start goes up to  4UYK|1|R|G|13
pMakeNodesJunction: first branch strand end goes down to  4UYK|1|R|C|65
pMakeNodesJunction: second branch strand start goes up to 4UYK|1|R|G|69
pMakeNodesJunction: last strand of junction goes down to  4UYK|1|R|C|132
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J1711
Actual Branch 1 of junction J1711 - Nucleotides 4UYK|1|R|U|11 to 4UYK|1|R|A|68, length   7
Actual Branch 2 of junction J1711 - Nucleotides 4UYK|1|R|G|69 to 4UYK|1|R|G|133, length   3
  3 Junction

2B Branch 1 of 2 of junction J1711 - Nucleotides    11 to    68, length   7
pMakeNodes starting loop:     a=4UYK|1|R|U|11 B=4UYK|1|R|A|68
pMakeNodesProbeForInsertions:  a 4UYK|1|R|U|11 interacts with 4UYK|1|R|A|67
pMakeNodesProbeForInsertions:  B 4UYK|1|R|A|68 interacts with 4UYK|1|R|G|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4UYK|1|R|A|68 interacts with 4UYK|1|R|G|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial     11 (0 insertion) and   68 (0 insertion)
pMakeNodes making a cluster near strand break a=4UYK|1|R|U|11 B=4UYK|1|R|A|68
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 5 to 8
aa is 4 bb is 5
  5 Cluster   4UYK|1|R|U|11:4UYK|1|R|G|13 4UYK|1|R|C|65:4UYK|1|R|A|68
    LR Inter  4UYK|1|R|G|13 4UYK|1|R|C|65 cWW 
    LR Inter  4UYK|1|R|A|12 4UYK|1|R|G|66 tHS 
    LR Inter  4UYK|1|R|U|11 4UYK|1|R|A|67 tWH 
    LR Inter  4UYK|1|R|G|13 4UYK|1|R|A|68 tSS 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J1711 - Nucleotides    69 to   133, length   3
pMakeNodes starting loop:     a=4UYK|1|R|G|69 B=4UYK|1|R|G|133
    Insertion on right 4UYK|1|R|G|133
pMakeNodesProbeForInsertions:  a 4UYK|1|R|G|69 interacts with 4UYK|1|R|C|132
pMakeNodesProbeForInsertions:  B 4UYK|1|R|C|132 interacts with 4UYK|1|R|G|69
pMakeNodesProbeForInsertions:  B 4UYK|1|R|C|132 interacts with 4UYK|1|R|G|69
  7 Initial     69 (0 insertion) and  133 (1 insertion)
  8 Basepair    69  132 GC cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4 Right  5  6  7  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4UYK|1|R|U|134
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4UYK|1|R|G|133
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'UG'
               Comment: ' // Basepair C10 - G135 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 12
             Insertion: []
                    id: 'J1711'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4UYK|1|R|U|134'
              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: 11
             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: []
                  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 7]
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: 'J1711'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U11 - G133 ID J1711'
              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: 8
             Insertion: []
                    id: 'J1711'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4UYK|1|R|U|11 - 4UYK|1|R|A|68 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]
            RightIndex: [5 6 7 8]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAG'
           RightLetter: 'CGAA'
               Comment: ' // Cluster node 4UYK|1|R|U|11:4UYK|1|R|G|13 and 4UYK|1|R|C|65:4UYK|1|R|A|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2518

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              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: []
          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: 9
            RightIndex: 11
             Insertion: []
                    id: 'J1711'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'G'
               Comment: ' // Initial node 4UYK|1|R|G|69 - 4UYK|1|R|G|133 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4UYK|1|R|G|133'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G69 - C132 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: '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: [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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   7   Cluster Left  2  3  4 Right  5  6  7  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 14
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: 7
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: 'J1711'
        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 4UYK|1|R|U|11 - 4UYK|1|R|A|68 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: 11
             LeftIndex: 9
            RightIndex: 11
             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: []
           RightLetter: 'G'
               Comment: ' // Initial node 4UYK|1|R|G|69 - 4UYK|1|R|G|133 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 J3_36499.1. Nodes 6 and 10 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 hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHS  between 8 and 11
pConservedInteractionList: did not find a substitution probability matrix for tHS  between 8 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_36499.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2279

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J3_37047.2, number 31 of 88
pMakeNodes starting loop:     a=4LFB|1|A|C|1296 B=4LFB|1|A|G|1241
pMakeNodes making a cluster near strand break a=4LFB|1|A|C|1296 B=4LFB|1|A|G|1241
pMakeNodesCluster: amax is 6 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 6 and then 13 to 15
aa is 6 bb is 13
  2 Cluster   4LFB|1|A|C|1296:4LFB|1|A|U|1301 4LFB|1|A|A|1238:4LFB|1|A|G|1241
    LR Inter  4LFB|1|A|U|1301 4LFB|1|A|A|1238 tWH 
    LR Inter  4LFB|1|A|C|1296 4LFB|1|A|G|1241 cWW 
    LL Inter  4LFB|1|A|C|1297 4LFB|1|A|C|1298 cSH 
    LL Inter  4LFB|1|A|G|1300 4LFB|1|A|U|1301 cSH 
    RR Inter  4LFB|1|A|A|1238 4LFB|1|A|G|1241 cSS 
    Left  strand conserved insertion 4LFB|1|A|A|1299 at position 4
    Right strand conserved insertion 4LFB|1|A|A|1239 at position 2
pMakeNodesCluster a=7 B=12 at the end
pMakeNodesCluster a=7 B=12 at the end
pMakeNodes probe for inserts:  a=4LFB|1|A|C|1303 B=4LFB|1|A|C|1237
  3 Initial   1303 (0 insertion) and 1237 (0 insertion)
pMakeNodes probed for insert:  a=4LFB|1|A|C|1303 B=4LFB|1|A|C|1237
pMakeNodesJunction: a=4LFB|1|A|C|1303 r=4LFB|1|A|C|1303 s=4LFB|1|A|G|1334 t=4LFB|1|A|C|1335 u=B=4LFB|1|A|C|1237
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|C|1303 and 4LFB|1|A|G|1334 and between 4LFB|1|A|C|1335 and 4LFB|1|A|C|1237
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|C|1303 s=4LFB|1|A|G|1334 t=4LFB|1|A|C|1335 B=4LFB|1|A|C|1237
pMakeNodesJunction: first branch starts at   4LFB|1|A|C|1303
pMakeNodesJunction: first branch ends around 4LFB|1|A|G|1334
pMakeNodesJunction: second branch starts at  4LFB|1|A|C|1335
pMakeNodesJunction: junction ends at         4LFB|1|A|C|1237
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|C|1303
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|G|1334
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|G|1337
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|1237

Junction with 2 loops, call it J7060
Actual Branch 1 of junction J7060 - Nucleotides 4LFB|1|A|C|1303 to 4LFB|1|A|G|1334, length   2
Actual Branch 2 of junction J7060 - Nucleotides 4LFB|1|A|C|1335 to 4LFB|1|A|C|1237, length   4
  4 Junction

2B Branch 1 of 2 of junction J7060 - Nucleotides  1303 to  1334, length   2
pMakeNodes starting loop:     a=4LFB|1|A|C|1303 B=4LFB|1|A|G|1334
  6 Basepair  1303 1334 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7060 - Nucleotides  1335 to  1237, length   4
pMakeNodes starting loop:     a=4LFB|1|A|C|1335 B=4LFB|1|A|C|1237
    Insertion on left  4LFB|1|A|C|1335
    Insertion on left  4LFB|1|A|C|1336
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|1337 interacts with 4LFB|1|A|C|1237
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1237 interacts with 4LFB|1|A|G|1337
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1237 interacts with 4LFB|1|A|G|1337
  8 Initial   1335 (2 insertion) and 1237 (0 insertion)
  9 Basepair  1337 1237 GC cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right 13 14 15
pMakeMotifModelFromSSF:   3   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  7 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1299
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1300
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           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 3 4 5 6]
            RightIndex: [13 14 15]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCAGU'
           RightLetter: 'AAG'
               Comment: ' // Cluster node 4LFB|1|A|C|1296:4LFB|1|A|U|1301 and 4LFB|1|A|A|1238:4LFB|1|A|G|1241'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
          LeftNotInter: 4
         RightNotInter: 2
              NormCons: 0.0221
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|1303 - 4LFB|1|A|C|1237 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: 7
            RightIndex: 12
             Insertion: []
                    id: 'J7060'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1303 - C1237 ID J7060'
              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: 7
            RightIndex: 8
             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: []
          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: 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 C1303 - G1334 cWW '
              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: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J7060'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|1335 - 4LFB|1|A|C|1237 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: 'Fixed'
              nextnode: 10
             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 4LFB|1|A|A|1299'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             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: [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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             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 4LFB|1|A|G|1300'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             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 G1337 - C1237 cWW '
              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 14

ans = 

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

                  type: 'Hairpin'
              nextnode: 15
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right 13 14 15
pMakeMotifModelFromSSF:   3   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  7 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  10   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  12   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  14   Hairpin Left 12 Right 11
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 hairpin at node 14
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: 6
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J7060'
        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: 9
            RightIndex: 12
             Insertion: []
                    id: 'J7060'
        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: 'CC'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|C|1335 - 4LFB|1|A|C|1237 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 J3_37047.2. Nodes 5 and 8 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 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 hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_37047.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5525
   -9.3390
  -15.4820
   -8.5525

Timestamp 18-Jul-2025 00:12:55
pMakeSCFGModels: Making JAR3D model for motif group J3_37410.1, number 32 of 88
pMakeNodes starting loop:     a=5TBW|1|1|A|2590 B=5TBW|1|1|U|2517
  2 Basepair  2590 2517 AU cWW 
No need to probe because of interaction between a=5TBW|1|1|A|2591 B=5TBW|1|1|U|2516
  3 Basepair  2591 2516 AU cWW 
No need to probe because of interaction between a=5TBW|1|1|G|2592 B=5TBW|1|1|A|2515
  4 Basepair  2592 2515 GA tSH 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|2593 B=5TBW|1|1|U|2514
    Insertion on right 5TBW|1|1|U|2514
pMakeNodes probed for insert:  a=5TBW|1|1|A|2593 B=5TBW|1|1|U|2513
  5 Basepair  2593 2513 AU tHW 
pMakeNodes probe for inserts:  a=5TBW|1|1|C|2594 B=5TBW|1|1|C|2512
    Insertion on left  5TBW|1|1|C|2594
    Insertion on left  5TBW|1|1|A|2595
pMakeNodes probed for insert:  a=5TBW|1|1|U|2596 B=5TBW|1|1|C|2512
pMakeNodesJunction: a=5TBW|1|1|U|2596 r=5TBW|1|1|U|2596 s=5TBW|1|1|U|2433 t=5TBW|1|1|U|2434 u=B=5TBW|1|1|C|2512
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|2596 and 5TBW|1|1|U|2433 and between 5TBW|1|1|U|2434 and 5TBW|1|1|C|2512
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|2596 s=5TBW|1|1|U|2433 t=5TBW|1|1|U|2434 B=5TBW|1|1|C|2512
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|2596
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|2433
pMakeNodesJunction: second branch starts at  5TBW|1|1|U|2434
pMakeNodesJunction: junction ends at         5TBW|1|1|C|2512
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|U|2597
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|A|2432
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|2435
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|2512

Junction with 2 loops, call it J318
Actual Branch 1 of junction J318 - Nucleotides 5TBW|1|1|U|2596 to 5TBW|1|1|U|2433, length   4
Actual Branch 2 of junction J318 - Nucleotides 5TBW|1|1|U|2434 to 5TBW|1|1|C|2512, length   3
  6 Junction

2B Branch 1 of 2 of junction J318 - Nucleotides  2596 to  2433, length   4
pMakeNodes starting loop:     a=5TBW|1|1|U|2596 B=5TBW|1|1|U|2433
  8 Basepair  2596 2433 UU cWW 
No need to probe because of interaction between a=5TBW|1|1|U|2597 B=5TBW|1|1|A|2432
  9 Basepair  2597 2432 UA cWW 
 10 Hairpin type *

2B Branch 2 of 2 of junction J318 - Nucleotides  2434 to  2512, length   3
pMakeNodes starting loop:     a=5TBW|1|1|U|2434 B=5TBW|1|1|C|2512
    Insertion on left  5TBW|1|1|U|2434
pMakeNodesProbeForInsertions:  a 5TBW|1|1|G|2435 interacts with 5TBW|1|1|C|2512
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|2512 interacts with 5TBW|1|1|G|2435
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|2512 interacts with 5TBW|1|1|G|2435
 11 Initial   2434 (1 insertion) and 2512 (0 insertion)
 12 Basepair  2435 2512 GC cWW 
 13 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6  Junction Left  7 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  11   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  13   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|C|2594
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|2512
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|2513
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|2590
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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2590 - U2517 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 A2591 - U2516 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            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 G2592 - A2515 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 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5TBW|1|1|C|2594'
              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 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: '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: []
                  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: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACA'
           RightLetter: 'U'
               Comment: ' // Basepair A2593 - U2513 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 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|C|2512'
              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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|U|2513'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: '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: 'U'
           RightLetter: []
               Comment: ' // New 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 12

ans = 

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

                  type: 'Junction'
              nextnode: [7 11]
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J318'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U2596 - C2512 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 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: '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 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U2596 - U2433 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 U2597 - A2432 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 17

ans = 

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

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J318'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|U|2434 - 5TBW|1|1|C|2512 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: 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|2590'
              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: 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 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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2435 - C2512 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  12  Junction Left  7 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  17   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  18     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  19   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  20  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  21   Hairpin Left 13 Right 12
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 21
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: 14
             LeftIndex: 7
            RightIndex: 10
             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: 18
             LeftIndex: 11
            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: 'U'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|U|2434 - 5TBW|1|1|C|2512 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_37410.1. Nodes 13 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 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 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_37410.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8837

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J3_38151.1, number 33 of 88
pMakeNodes starting loop:     a=6ZDP|1|B|A|1294 B=6ZDP|1|B|U|1343
  2 Basepair  1294 1343 AU cWW 
pMakeNodes probe for inserts:  a=6ZDP|1|B|A|1295 B=6ZDP|1|B|C|1342
    Insertion on left  6ZDP|1|B|A|1295
    Insertion on right 6ZDP|1|B|C|1342
    Insertion on right 6ZDP|1|B|G|1341
pMakeNodes probed for insert:  a=6ZDP|1|B|G|1296 B=6ZDP|1|B|U|1340
pMakeNodesJunction: a=6ZDP|1|B|G|1296 r=6ZDP|1|B|G|1296 s=6ZDP|1|B|C|1322 t=6ZDP|1|B|A|1323 u=B=6ZDP|1|B|U|1340
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6ZDP|1|B|G|1296 and 6ZDP|1|B|C|1322 and between 6ZDP|1|B|A|1323 and 6ZDP|1|B|U|1340
pMakeNodesJunction: about to make a junction: a=6ZDP|1|B|G|1296 s=6ZDP|1|B|C|1322 t=6ZDP|1|B|A|1323 B=6ZDP|1|B|U|1340
pMakeNodesJunction: first branch starts at   6ZDP|1|B|G|1296
pMakeNodesJunction: first branch ends around 6ZDP|1|B|C|1322
pMakeNodesJunction: second branch starts at  6ZDP|1|B|A|1323
pMakeNodesJunction: junction ends at         6ZDP|1|B|U|1340
pMakeNodesJunction: first branch strand start goes up to  6ZDP|1|B|G|1296
pMakeNodesJunction: first branch strand end goes down to  6ZDP|1|B|C|1322
pMakeNodesJunction: second branch strand start goes up to 6ZDP|1|B|A|1324
pMakeNodesJunction: last strand of junction goes down to  6ZDP|1|B|U|1340

Junction with 2 loops, call it J2769
Actual Branch 1 of junction J2769 - Nucleotides 6ZDP|1|B|G|1296 to 6ZDP|1|B|C|1322, length   2
Actual Branch 2 of junction J2769 - Nucleotides 6ZDP|1|B|A|1323 to 6ZDP|1|B|U|1340, length   3
  3 Junction

2B Branch 1 of 2 of junction J2769 - Nucleotides  1296 to  1322, length   2
pMakeNodes starting loop:     a=6ZDP|1|B|G|1296 B=6ZDP|1|B|C|1322
  5 Basepair  1296 1322 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J2769 - Nucleotides  1323 to  1340, length   3
pMakeNodes starting loop:     a=6ZDP|1|B|A|1323 B=6ZDP|1|B|U|1340
    Insertion on left  6ZDP|1|B|A|1323
pMakeNodesProbeForInsertions:  a 6ZDP|1|B|A|1324 interacts with 6ZDP|1|B|U|1340
pMakeNodesProbeForInsertions:  B 6ZDP|1|B|U|1340 interacts with 6ZDP|1|B|A|1324
pMakeNodesProbeForInsertions:  B 6ZDP|1|B|U|1340 interacts with 6ZDP|1|B|A|1324
  7 Initial   1323 (1 insertion) and 1340 (0 insertion)
  8 Basepair  1324 1340 AU cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  7
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  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ZDP|1|B|A|1295
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6ZDP|1|B|C|1342
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6ZDP|1|B|G|1341
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6ZDP|1|B|A|1323
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 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: 'AA'
           RightLetter: 'GCU'
               Comment: ' // Basepair A1294 - U1343 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
             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 6ZDP|1|B|A|1295'
              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: 9
             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: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6ZDP|1|B|C|1342'
              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: 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: 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: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: 'J2769'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6ZDP|1|B|G|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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 9

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: 'J2769'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1296 - U1340 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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 4
             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 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             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 G1296 - C1322 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: 'J2769'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 6ZDP|1|B|A|1323 - 6ZDP|1|B|U|1340 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: 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 6ZDP|1|B|A|1323'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1324 - U1340 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   9  Junction Left  3 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  3 Right  4
pMakeMotifModelFromSSF:  11  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:  12   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  13   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  14     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  15   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  16  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  17   Hairpin Left  7 Right  6
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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 4
             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: 14
             LeftIndex: 5
            RightIndex: 7
             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: 'A'
           RightLetter: []
               Comment: ' // Initial node 6ZDP|1|B|A|1323 - 6ZDP|1|B|U|1340 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_38151.1. Nodes 10 and 13 both model an insertion before position 5. 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 hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_38151.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0266

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J3_38446.1, number 34 of 88
pMakeNodes starting loop:     a=5TBW|1|1|G|588 B=5TBW|1|1|C|503
  2 Basepair   588  503 GC cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|589 B=5TBW|1|1|U|502
    Insertion on left  5TBW|1|1|A|589
    Insertion on left  5TBW|1|1|G|590
    Insertion on left  5TBW|1|1|G|591
    Insertion on left  5TBW|1|1|A|592
    Insertion on left  5TBW|1|1|C|593
    Insertion on left  5TBW|1|1|U|594
    Insertion on left  5TBW|1|1|G|595
pMakeNodes probed for insert:  a=5TBW|1|1|C|596 B=5TBW|1|1|U|502
pMakeNodesJunction: a=5TBW|1|1|C|596 r=5TBW|1|1|C|596 s=5TBW|1|1|A|608 t=5TBW|1|1|G|609 u=B=5TBW|1|1|U|502
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|C|596 and 5TBW|1|1|A|608 and between 5TBW|1|1|G|609 and 5TBW|1|1|U|502
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|C|596 s=5TBW|1|1|A|608 t=5TBW|1|1|G|609 B=5TBW|1|1|U|502
pMakeNodesJunction: first branch starts at   5TBW|1|1|C|596
pMakeNodesJunction: first branch ends around 5TBW|1|1|A|608
pMakeNodesJunction: second branch starts at  5TBW|1|1|G|609
pMakeNodesJunction: junction ends at         5TBW|1|1|U|502
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|597
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|606
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|A|611
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|U|502

Junction with 2 loops, call it J461
Actual Branch 1 of junction J461 - Nucleotides 5TBW|1|1|C|596 to 5TBW|1|1|A|608, length   4
Actual Branch 2 of junction J461 - Nucleotides 5TBW|1|1|G|609 to 5TBW|1|1|U|502, length   4
  3 Junction

2B Branch 1 of 2 of junction J461 - Nucleotides   596 to   608, length   4
pMakeNodes starting loop:     a=5TBW|1|1|C|596 B=5TBW|1|1|A|608
  5 Basepair   596  608 CA cWS 
No need to probe because of interaction between a=5TBW|1|1|G|597 B=5TBW|1|1|C|606
  6 Basepair   597  606 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J461 - Nucleotides   609 to   502, length   4
pMakeNodes starting loop:     a=5TBW|1|1|G|609 B=5TBW|1|1|U|502
    Insertion on left  5TBW|1|1|G|609
    Insertion on left  5TBW|1|1|G|610
pMakeNodesProbeForInsertions:  a 5TBW|1|1|A|611 interacts with 5TBW|1|1|U|502
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|502 interacts with 5TBW|1|1|A|611
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|502 interacts with 5TBW|1|1|A|611
  8 Initial    609 (2 insertion) and  502 (0 insertion)
  9 Basepair   611  502 AU cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Junction Left  9 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   7   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:   8   Initial Left 13 Right 16
pMakeMotifModelFromSSF:   9  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  10   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|503
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|588
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|589
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|590
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|591
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|592
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|593
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|606
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|607
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAGGACUG'
           RightLetter: 'C'
               Comment: ' // Basepair G588 - C503 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J461'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|C|503'
              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: 'J461'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 5TBW|1|1|G|588'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: '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: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|A|589'
              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 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: 'J461'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // New 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: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|G|590'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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

Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|G|591'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 5TBW|1|1|A|592'
              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: 8
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 5TBW|1|1|C|593'
              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: 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 17

ans = 

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

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: 'J461'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C596 - U502 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 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: '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 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 C596 - A608 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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 G597 - C606 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

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: []
           numbranches: []
              NormCons: 1

Node 22

ans = 

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

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J461'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|609 - 5TBW|1|1|U|502 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: 13
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|C|606'
              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: 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: []
                  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: 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 5TBW|1|1|A|607'
              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: 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 27

ans = 

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

                  type: 'Basepair'
              nextnode: 28
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A611 - U502 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 16
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 16
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  17  Junction Left  9 Right 16
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
pMakeMotifModelFromSSF:  22   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  23     Fixed Left 13 Right 16
pMakeMotifModelFromSSF:  24   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  25     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  26   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  27  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  28   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 17
pNextNodeJunction: Found a junction child at node 18
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

ans = 

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

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 12
             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: 23
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J461'
        leftLengthDist: [0.0454 0.9070 0.0454 0.0023]
        leftLetterDist: [0.5000 0.1667 0.1667 0.1667 0]
       rightLengthDist: 1
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|G|609 - 5TBW|1|1|U|502 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_38446.1. Nodes 18 and 22 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 17
pNextNodeJunction: Found a junction child at node 18
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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_38446.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.6326

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J3_38616.1, number 35 of 88
pMakeNodes starting loop:     a=4V88|1|A6|U|928 B=4V88|1|A6|A|884
  2 Basepair   928  884 UA cWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|A|929 B=4V88|1|A6|C|883
    Insertion on left  4V88|1|A6|A|929
    Insertion on left  4V88|1|A6|A|930
    Insertion on left  4V88|1|A6|C|931
    Insertion on left  4V88|1|A6|U|932
pMakeNodes probed for insert:  a=4V88|1|A6|A|933 B=4V88|1|A6|C|883
pMakeNodesJunction: a=4V88|1|A6|A|933 r=4V88|1|A6|A|933 s=4V88|1|A6|A|944 t=4V88|1|A6|U|945 u=B=4V88|1|A6|C|883
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|A|933 and 4V88|1|A6|A|944 and between 4V88|1|A6|U|945 and 4V88|1|A6|C|883
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|A|933 s=4V88|1|A6|A|944 t=4V88|1|A6|U|945 B=4V88|1|A6|C|883
pMakeNodesJunction: first branch starts at   4V88|1|A6|A|933
pMakeNodesJunction: first branch ends around 4V88|1|A6|A|944
pMakeNodesJunction: second branch starts at  4V88|1|A6|U|945
pMakeNodesJunction: junction ends at         4V88|1|A6|C|883
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|G|936
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|C|943
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|U|947
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|A|881

Junction with 2 loops, call it J971
Actual Branch 1 of junction J971 - Nucleotides 4V88|1|A6|A|933 to 4V88|1|A6|A|944, length   5
Actual Branch 2 of junction J971 - Nucleotides 4V88|1|A6|U|945 to 4V88|1|A6|C|883, length   6
  3 Junction

2B Branch 1 of 2 of junction J971 - Nucleotides   933 to   944, length   5
pMakeNodes starting loop:     a=4V88|1|A6|A|933 B=4V88|1|A6|A|944
  5 Basepair   933  944 AA tWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|U|935 B=4V88|1|A6|C|943
    Insertion on left  4V88|1|A6|U|935
pMakeNodesProbeForInsertions:  a 4V88|1|A6|G|936 interacts with 4V88|1|A6|C|943
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|943 interacts with 4V88|1|A6|G|936
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|943 interacts with 4V88|1|A6|G|936
pMakeNodes probed for insert:  a=4V88|1|A6|G|936 B=4V88|1|A6|C|943
  6 Basepair   936  943 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J971 - Nucleotides   945 to   883, length   6
pMakeNodes starting loop:     a=4V88|1|A6|U|945 B=4V88|1|A6|C|883
  9 Basepair   945  883 UC cWW 
No need to probe because of interaction between a=4V88|1|A6|U|946 B=4V88|1|A6|U|882
 10 Basepair   946  882 UU cWW 
No need to probe because of interaction between a=4V88|1|A6|U|947 B=4V88|1|A6|A|881
 11 Basepair   947  881 UA cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 16
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 16
pMakeMotifModelFromSSF:  10  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  11  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  12   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|882
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|C|883
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|884
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|928
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|930
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [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: 'UAACU'
           RightLetter: 'A'
               Comment: ' // Basepair U928 - A884 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J971'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|882'
              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: '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: []
                  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 4V88|1|A6|C|883'
              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: 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: 9
                     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: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|884'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: 'J971'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|928'
              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: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: '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: 'Junction'
              nextnode: [4 8]
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: 'J971'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A933 - C883 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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 10
             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 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'A'
               Comment: ' // Basepair A933 - A944 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 14

ans = 

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

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|930'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 G936 - C943 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: []
                  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: 16
             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 19

ans = 

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

                  type: 'Basepair'
              nextnode: 20
             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: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U945 - C883 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U946 - U882 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 U947 - A881 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  5 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  11  Junction Left  6 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  15   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 16
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 16
pMakeMotifModelFromSSF:  20  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  21  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  22   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 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

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J971'
        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: 16
             Insertion: []
                    id: 'J971'
        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 J3_38616.1. Nodes 12 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 11
pNextNodeJunction: Found a junction child at node 12
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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_38616.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.1986

Timestamp 18-Jul-2025 00:12:56
pMakeSCFGModels: Making JAR3D model for motif group J3_39238.2, number 36 of 88
pMakeNodes starting loop:     a=4V9F|1|0|C|774 B=4V9F|1|0|G|887
  2 Basepair   774  887 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|G|775 B=4V9F|1|0|C|884
pMakeNodes probed for insert:  a=4V9F|1|0|G|775 B=4V9F|1|0|C|884
pMakeNodesJunction: a=4V9F|1|0|G|775 r=4V9F|1|0|G|775 s=4V9F|1|0|U|866 t=4V9F|1|0|A|867 u=B=4V9F|1|0|C|884
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|775 and 4V9F|1|0|U|866 and between 4V9F|1|0|A|867 and 4V9F|1|0|C|884
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|775 s=4V9F|1|0|U|866 t=4V9F|1|0|A|867 B=4V9F|1|0|C|884
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|775
pMakeNodesJunction: first branch ends around 4V9F|1|0|U|866
pMakeNodesJunction: second branch starts at  4V9F|1|0|A|867
pMakeNodesJunction: junction ends at         4V9F|1|0|C|884
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|A|780
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|U|866
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|G|868
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|C|884
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     1     0     0     0


Junction with 2 loops, call it J8234
Actual Branch 1 of junction J8234 - Nucleotides 4V9F|1|0|G|775 to 4V9F|1|0|U|866, length   6
Actual Branch 2 of junction J8234 - Nucleotides 4V9F|1|0|A|867 to 4V9F|1|0|C|884, length   3
  3 Junction

2B Branch 1 of 2 of junction J8234 - Nucleotides   775 to   866, length   6
pMakeNodes starting loop:     a=4V9F|1|0|G|775 B=4V9F|1|0|U|866
    Insertion on left  4V9F|1|0|G|775
pMakeNodesProbeForInsertions:  a 4V9F|1|0|A|776 interacts with 4V9F|1|0|U|779
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|866 interacts with 4V9F|1|0|A|780
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|866 interacts with 4V9F|1|0|A|780
  4 Initial    775 (1 insertion) and  866 (0 insertion)
pMakeNodes making a cluster near strand break a=4V9F|1|0|A|776 B=4V9F|1|0|U|866
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 6 and then 7 to 7
aa is 6 bb is 7
  5 Cluster   4V9F|1|0|A|776:4V9F|1|0|A|780 4V9F|1|0|U|866:4V9F|1|0|U|866
    LR Inter  4V9F|1|0|A|780 4V9F|1|0|U|866 cWW 
    LL Inter  4V9F|1|0|A|776 4V9F|1|0|U|779 tSW 
    Left  strand conserved insertion 4V9F|1|0|C|778 at position 2
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J8234 - Nucleotides   867 to   884, length   3
pMakeNodes starting loop:     a=4V9F|1|0|A|867 B=4V9F|1|0|C|884
    Insertion on left  4V9F|1|0|A|867
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|868 interacts with 4V9F|1|0|C|884
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|884 interacts with 4V9F|1|0|G|868
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|884 interacts with 4V9F|1|0|G|868
  7 Initial    867 (1 insertion) and  884 (0 insertion)
  8 Basepair   868  884 GC cWW 
  9 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  7
pMakeMotifModelFromSSF:   5   Cluster Left  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  8 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|775
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|866
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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C774 - G887 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 10
             Insertion: []
                    id: 'J8234'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G775 - C884 ID J8234'
              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: 7
             Insertion: []
                    id: 'J8234'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|775 - 4V9F|1|0|U|866 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: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|775'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [3 4 5 6]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACUA'
           RightLetter: 'U'
               Comment: ' // Cluster node 4V9F|1|0|A|776:4V9F|1|0|A|780 and 4V9F|1|0|U|866:4V9F|1|0|U|866'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  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: 8
            RightIndex: 10
             Insertion: []
                    id: 'J8234'
        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|867 - 4V9F|1|0|C|884 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|866'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G868 - C884 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 'Hairpin'
              nextnode: 15
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: [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 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7   Cluster Left  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 14
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: 7
             Insertion: []
                    id: 'J8234'
        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: 'G'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|G|775 - 4V9F|1|0|U|866 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: 11
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J8234'
        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: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|0|A|867 - 4V9F|1|0|C|884 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 J3_39238.2. Nodes 4 and 10 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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWH  between 2 and 9
pConservedInteractionList: did not find a substitution probability matrix for tWH  between 2 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_39238.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.4540
   -8.3588
   -8.6953
   -9.2061
   -9.3479
   -8.7905

Timestamp 18-Jul-2025 00:12:57
pMakeSCFGModels: Making JAR3D model for motif group J3_41097.1, number 37 of 88
pMakeNodes starting loop:     a=4KZ2|1|A|G|8 B=4KZ2|1|C|C|9
  2 Basepair     8    9 GC cWW 
pMakeNodes probe for inserts:  a=4KZ2|1|A|U|9 B=4KZ2|1|C|U|8
pMakeNodes probed for insert:  a=4KZ2|1|A|U|9 B=4KZ2|1|C|U|8
pMakeNodesJunction: a=4KZ2|1|A|U|9 r=4KZ2|1|A|U|9 s=4KZ2|1|B|U|10 t=4KZ2|1|B|U|12 u=B=4KZ2|1|C|U|8
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4KZ2|1|A|U|9 and 4KZ2|1|B|U|10 and between 4KZ2|1|B|U|12 and 4KZ2|1|C|U|8
pMakeNodesJunction: about to make a junction: a=4KZ2|1|A|U|9 s=4KZ2|1|B|U|10 t=4KZ2|1|B|U|12 B=4KZ2|1|C|U|8
pMakeNodesJunction: first branch starts at   4KZ2|1|A|U|9
pMakeNodesJunction: first branch ends around 4KZ2|1|B|U|10
pMakeNodesJunction: second branch starts at  4KZ2|1|B|U|12
pMakeNodesJunction: junction ends at         4KZ2|1|C|U|8
pMakeNodesJunction: first branch strand start goes up to  4KZ2|1|A|G|10
pMakeNodesJunction: first branch strand end goes down to  4KZ2|1|B|C|9
pMakeNodesJunction: second branch strand start goes up to 4KZ2|1|B|G|13
pMakeNodesJunction: last strand of junction goes down to  4KZ2|1|C|U|8

Junction with 2 loops, call it J6948
Actual Branch 1 of junction J6948 - Nucleotides 4KZ2|1|A|U|9 to 4KZ2|1|B|U|10, length   4
Actual Branch 2 of junction J6948 - Nucleotides 4KZ2|1|B|U|12 to 4KZ2|1|C|U|8, length   3
  3 Junction

2B Branch 1 of 2 of junction J6948 - Nucleotides     9 to    10, length   4
pMakeNodes starting loop:     a=4KZ2|1|A|U|9 B=4KZ2|1|B|U|10
  5 Basepair     9   10 UU cWW 
No need to probe because of interaction between a=4KZ2|1|A|G|10 B=4KZ2|1|B|C|9
  6 Basepair    10    9 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J6948 - Nucleotides    12 to     8, length   3
pMakeNodes starting loop:     a=4KZ2|1|B|U|12 B=4KZ2|1|C|U|8
    Insertion on left  4KZ2|1|B|U|12
pMakeNodesProbeForInsertions:  a 4KZ2|1|B|G|13 interacts with 4KZ2|1|C|U|8
pMakeNodesProbeForInsertions:  B 4KZ2|1|C|U|8 interacts with 4KZ2|1|B|G|13
pMakeNodesProbeForInsertions:  B 4KZ2|1|C|U|8 interacts with 4KZ2|1|B|G|13
  8 Initial     12 (1 insertion) and    8 (0 insertion)
  9 Basepair    13    8 GU cWW 
 10 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  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  8
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  10   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KZ2|1|B|U|11
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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 8
             Insertion: []
                    id: 'J6948'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U9 - U8 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 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 5
             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 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U9 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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 G10 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 6
            RightIndex: 8
             Insertion: []
                    id: 'J6948'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 4KZ2|1|B|U|12 - 4KZ2|1|C|U|8 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: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KZ2|1|B|U|11'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G13 - U8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: [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  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  8
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a 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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: 'J6948'
        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: 9
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: 'J6948'
        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: 'U'
           RightLetter: []
               Comment: ' // Initial node 4KZ2|1|B|U|12 - 4KZ2|1|C|U|8 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_41097.1. Nodes 4 and 8 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 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_41097.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9049
   -5.9049

Timestamp 18-Jul-2025 00:12:57
pMakeSCFGModels: Making JAR3D model for motif group J3_42157.1, number 38 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|C|1605 B=5J7L|1|DA|G|1309
  2 Basepair  1605 1309 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|1606 B=5J7L|1|DA|A|1308
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1606 B=5J7L|1|DA|A|1308
pMakeNodesCluster: amax is 4 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 11 to 11
aa is 3 bb is 11
  3 Cluster   5J7L|1|DA|C|1606:5J7L|1|DA|A|1608 5J7L|1|DA|A|1308:5J7L|1|DA|A|1308
    LR Inter  5J7L|1|DA|C|1606 5J7L|1|DA|A|1308 tSH 
    LR Inter  5J7L|1|DA|A|1608 5J7L|1|DA|A|1308 tWW 
pMakeNodesCluster a=4 B=10 at the end
pMakeNodesCluster a=4 B=10 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1610 B=5J7L|1|DA|A|1307
    Insertion on left  5J7L|1|DA|A|1610
    Insertion on right 5J7L|1|DA|A|1307
  4 Initial   1610 (1 insertion) and 1307 (1 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|C|1611 B=5J7L|1|DA|C|1306
pMakeNodesJunction: a=5J7L|1|DA|C|1611 r=5J7L|1|DA|C|1611 s=5J7L|1|DA|G|1620 t=5J7L|1|DA|U|1621 u=B=5J7L|1|DA|C|1306
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|1611 and 5J7L|1|DA|G|1620 and between 5J7L|1|DA|U|1621 and 5J7L|1|DA|C|1306
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|1611 s=5J7L|1|DA|G|1620 t=5J7L|1|DA|U|1621 B=5J7L|1|DA|C|1306
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|1611
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|1620
pMakeNodesJunction: second branch starts at  5J7L|1|DA|U|1621
pMakeNodesJunction: junction ends at         5J7L|1|DA|C|1306
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|1611
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|1620
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|1622
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|C|1306

Junction with 2 loops, call it J3170
Actual Branch 1 of junction J3170 - Nucleotides 5J7L|1|DA|C|1611 to 5J7L|1|DA|G|1620, length   2
Actual Branch 2 of junction J3170 - Nucleotides 5J7L|1|DA|U|1621 to 5J7L|1|DA|C|1306, length   3
  5 Junction

2B Branch 1 of 2 of junction J3170 - Nucleotides  1611 to  1620, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|1611 B=5J7L|1|DA|G|1620
  7 Basepair  1611 1620 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J3170 - Nucleotides  1621 to  1306, length   3
pMakeNodes starting loop:     a=5J7L|1|DA|U|1621 B=5J7L|1|DA|C|1306
    Insertion on left  5J7L|1|DA|U|1621
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|1622 interacts with 5J7L|1|DA|C|1306
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1306 interacts with 5J7L|1|DA|G|1622
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1306 interacts with 5J7L|1|DA|G|1622
  9 Initial   1621 (1 insertion) and 1306 (0 insertion)
 10 Basepair  1622 1306 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1309
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|1610
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|1607
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: []
          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: 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 C1605 - G1309 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'A'
               Comment: ' // Cluster node 5J7L|1|DA|C|1606:5J7L|1|DA|A|1608 and 5J7L|1|DA|A|1308:5J7L|1|DA|A|1308'
              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: 0.3211
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Initial node 5J7L|1|DA|A|1610 - 5J7L|1|DA|A|1307 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: 4
            RightIndex: 10
             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 5J7L|1|DA|G|1309'
              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: 5
            RightIndex: 10
             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: []
                  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: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|1610'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 9

ans = 

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

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J3170'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1611 - C1306 ID J3170'
              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: 5
            RightIndex: 6
             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: []
          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: 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 C1611 - G1620 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J3170'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|1621 - 5J7L|1|DA|C|1306 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: 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 5J7L|1|DA|C|1607'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 G1622 - C1306 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9  Junction Left  5 Right  9
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  9
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  15   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             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: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|1621 - 5J7L|1|DA|C|1306 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 J3_42157.1. 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 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

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 3 and 7
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 3 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_42157.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3238
   -9.4977
   -8.5731

Timestamp 18-Jul-2025 00:12:58
pMakeSCFGModels: Making JAR3D model for motif group J3_44724.2, number 39 of 88
pMakeNodes starting loop:     a=7A0S|1|X|C|745 B=7A0S|1|X|G|713
  2 Basepair   745  713 CG cWW 
No need to probe because of interaction between a=7A0S|1|X|G|746 B=7A0S|1|X|A|712
  3 Basepair   746  712 GA tSH 
pMakeNodes probe for inserts:  a=7A0S|1|X|A|747 B=7A0S|1|X|C|711
    Insertion on left  7A0S|1|X|A|747
pMakeNodes probed for insert:  a=7A0S|1|X|A|748 B=7A0S|1|X|C|711
pMakeNodesJunction: a=7A0S|1|X|A|748 r=7A0S|1|X|A|748 s=7A0S|1|X|A|774 t=7A0S|1|X|U|775 u=B=7A0S|1|X|C|711
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|A|748 and 7A0S|1|X|A|774 and between 7A0S|1|X|U|775 and 7A0S|1|X|C|711
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|A|748 s=7A0S|1|X|A|774 t=7A0S|1|X|U|775 B=7A0S|1|X|C|711
pMakeNodesJunction: first branch starts at   7A0S|1|X|A|748
pMakeNodesJunction: first branch ends around 7A0S|1|X|A|774
pMakeNodesJunction: second branch starts at  7A0S|1|X|U|775
pMakeNodesJunction: junction ends at         7A0S|1|X|C|711
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|C|749
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|G|773
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|776
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|711

Junction with 2 loops, call it J9502
Actual Branch 1 of junction J9502 - Nucleotides 7A0S|1|X|A|748 to 7A0S|1|X|A|774, length   4
Actual Branch 2 of junction J9502 - Nucleotides 7A0S|1|X|U|775 to 7A0S|1|X|C|711, length   3
  4 Junction

2B Branch 1 of 2 of junction J9502 - Nucleotides   748 to   774, length   4
pMakeNodes starting loop:     a=7A0S|1|X|A|748 B=7A0S|1|X|A|774
  6 Basepair   748  774 AA tHS 
No need to probe because of interaction between a=7A0S|1|X|C|749 B=7A0S|1|X|G|773
  7 Basepair   749  773 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J9502 - Nucleotides   775 to   711, length   3
pMakeNodes starting loop:     a=7A0S|1|X|U|775 B=7A0S|1|X|C|711
    Insertion on left  7A0S|1|X|U|775
pMakeNodesProbeForInsertions:  a 7A0S|1|X|G|776 interacts with 7A0S|1|X|C|711
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|711 interacts with 7A0S|1|X|G|776
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|711 interacts with 7A0S|1|X|G|776
  9 Initial    775 (1 insertion) and  711 (0 insertion)
 10 Basepair   776  711 GC cWW 
 11 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 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|713
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|C|749
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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 C745 - G713 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'A'
               Comment: ' // Basepair G746 - A712 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 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: '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 7A0S|1|X|G|713'
              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: '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 6

ans = 

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

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J9502'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A748 - C711 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 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: '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 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A748 - A774 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: 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 C749 - G773 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J9502'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|775 - 7A0S|1|X|C|711 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: 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 7A0S|1|X|C|749'
              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: 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 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             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 G776 - C711 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Junction Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  11   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  15   Hairpin Left 10 Right  9
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 15
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: 8
             LeftIndex: 4
            RightIndex: 7
             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: 12
             LeftIndex: 8
            RightIndex: 10
             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: 'U'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|775 - 7A0S|1|X|C|711 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_44724.2. Nodes 7 and 11 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 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_44724.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7443
   -6.7443
   -6.7443
  -13.0857
   -6.7443

Timestamp 18-Jul-2025 00:12:58
pMakeSCFGModels: Making JAR3D model for motif group J3_45941.1, number 40 of 88
pMakeNodes starting loop:     a=4O26|1|E|A|173 B=4O26|1|E|U|217
pMakeNodes making a cluster near strand break a=4O26|1|E|A|173 B=4O26|1|E|U|217
pMakeNodesCluster: amax is 4 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 13 to 13
aa is 4 bb is 13
  2 Cluster   4O26|1|E|A|173:4O26|1|E|C|176 4O26|1|E|U|217:4O26|1|E|U|217
    LR Inter  4O26|1|E|A|173 4O26|1|E|U|217 cWW 
    LR Inter  4O26|1|E|C|176 4O26|1|E|U|217 cWS 
    LL Inter  4O26|1|E|C|174 4O26|1|E|C|176 cSH 
    Left  strand conserved insertion 4O26|1|E|G|175 at position 3
pMakeNodesCluster a=5 B=12 at the end
pMakeNodesCluster a=5 B=12 at the end
pMakeNodes probe for inserts:  a=4O26|1|E|C|177 B=4O26|1|E|G|216
    Insertion on right 4O26|1|E|G|216
    Insertion on right 4O26|1|E|U|215
    Insertion on right 4O26|1|E|G|213
  3 Initial    177 (0 insertion) and  216 (3 insertion)
pMakeNodes probed for insert:  a=4O26|1|E|C|177 B=4O26|1|E|U|212
pMakeNodesJunction: a=4O26|1|E|C|177 r=4O26|1|E|C|177 s=4O26|1|E|G|198 t=4O26|1|E|A|199 u=B=4O26|1|E|U|212
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4O26|1|E|C|177 and 4O26|1|E|G|198 and between 4O26|1|E|A|199 and 4O26|1|E|U|212
pMakeNodesJunction: about to make a junction: a=4O26|1|E|C|177 s=4O26|1|E|G|198 t=4O26|1|E|A|199 B=4O26|1|E|U|212
pMakeNodesJunction: first branch starts at   4O26|1|E|C|177
pMakeNodesJunction: first branch ends around 4O26|1|E|G|198
pMakeNodesJunction: second branch starts at  4O26|1|E|A|199
pMakeNodesJunction: junction ends at         4O26|1|E|U|212
pMakeNodesJunction: first branch strand start goes up to  4O26|1|E|C|177
pMakeNodesJunction: first branch strand end goes down to  4O26|1|E|G|198
pMakeNodesJunction: second branch strand start goes up to 4O26|1|E|A|200
pMakeNodesJunction: last strand of junction goes down to  4O26|1|E|U|212

Junction with 2 loops, call it J344
Actual Branch 1 of junction J344 - Nucleotides 4O26|1|E|C|177 to 4O26|1|E|G|198, length   2
Actual Branch 2 of junction J344 - Nucleotides 4O26|1|E|A|199 to 4O26|1|E|U|212, length   3
  4 Junction

2B Branch 1 of 2 of junction J344 - Nucleotides   177 to   198, length   2
pMakeNodes starting loop:     a=4O26|1|E|C|177 B=4O26|1|E|G|198
  6 Basepair   177  198 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J344 - Nucleotides   199 to   212, length   3
pMakeNodes starting loop:     a=4O26|1|E|A|199 B=4O26|1|E|U|212
    Insertion on left  4O26|1|E|A|199
pMakeNodesProbeForInsertions:  a 4O26|1|E|A|200 interacts with 4O26|1|E|U|212
pMakeNodesProbeForInsertions:  B 4O26|1|E|U|212 interacts with 4O26|1|E|A|200
pMakeNodesProbeForInsertions:  B 4O26|1|E|U|212 interacts with 4O26|1|E|A|200
  8 Initial    199 (1 insertion) and  212 (0 insertion)
  9 Basepair   200  212 AU cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 13
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4O26|1|E|U|215
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4O26|1|E|U|214
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4O26|1|E|G|213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4O26|1|E|A|199
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 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 3 4]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACGC'
           RightLetter: 'U'
               Comment: ' // Cluster node 4O26|1|E|A|173:4O26|1|E|C|176 and 4O26|1|E|U|217:4O26|1|E|U|217'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0666
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'GUG'
               Comment: ' // Initial node 4O26|1|E|C|177 - 4O26|1|E|G|216 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: 5
            RightIndex: 12
             Insertion: []
                    id: 'J344'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4O26|1|E|U|215'
              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: 5
            RightIndex: 11
             Insertion: []
                    id: 'J344'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4O26|1|E|U|214'
              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: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     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: 5
            RightIndex: 10
             Insertion: []
                    id: 'J344'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4O26|1|E|G|213'
              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: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J344'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C177 - U212 ID J344'
              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 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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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 C177 - G198 cWW '
              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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J344'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4O26|1|E|A|199 - 4O26|1|E|U|212 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 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4O26|1|E|A|199'
              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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             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 A200 - U212 cWW '
              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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 13
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
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     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  16   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  17  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  18   Hairpin Left  9 Right  8
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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J344'
        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: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: 'J344'
        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 4O26|1|E|A|199 - 4O26|1|E|U|212 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 J3_45941.1. 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 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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSH  between 2 and 5
pConservedInteractionList: did not find a substitution probability matrix for tWH  between 2 and 6
pConservedInteractionList: did not find a substitution probability matrix for cSH  between 2 and 5
pConservedInteractionList: did not find a substitution probability matrix for tWH  between 2 and 6
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_45941.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8072

Timestamp 18-Jul-2025 00:12:58
pMakeSCFGModels: Making JAR3D model for motif group J3_47248.1, number 41 of 88
pMakeNodes starting loop:     a=4V88|1|A6|C|1327 B=4V88|1|A6|G|1288
  2 Basepair  1327 1288 CG cWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|G|1328 B=4V88|1|A6|A|1287
    Insertion on left  4V88|1|A6|G|1328
    Insertion on left  4V88|1|A6|A|1329
    Insertion on left  4V88|1|A6|G|1330
    Insertion on left  4V88|1|A6|A|1331
    Insertion on right 4V88|1|A6|A|1287
    Insertion on right 4V88|1|A6|U|1286
pMakeNodes probed for insert:  a=4V88|1|A6|C|1332 B=4V88|1|A6|C|1284
pMakeNodesJunction: a=4V88|1|A6|C|1332 r=4V88|1|A6|C|1332 s=4V88|1|A6|G|1419 t=4V88|1|A6|C|1420 u=B=4V88|1|A6|C|1284
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|C|1332 and 4V88|1|A6|G|1419 and between 4V88|1|A6|C|1420 and 4V88|1|A6|C|1284
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|C|1332 s=4V88|1|A6|G|1419 t=4V88|1|A6|C|1420 B=4V88|1|A6|C|1284
pMakeNodesJunction: first branch starts at   4V88|1|A6|C|1332
pMakeNodesJunction: first branch ends around 4V88|1|A6|G|1419
pMakeNodesJunction: second branch starts at  4V88|1|A6|C|1420
pMakeNodesJunction: junction ends at         4V88|1|A6|C|1284
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|C|1332
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|G|1419
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|A|1424
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|U|1283

Junction with 2 loops, call it J4387
Actual Branch 1 of junction J4387 - Nucleotides 4V88|1|A6|C|1332 to 4V88|1|A6|G|1419, length   2
Actual Branch 2 of junction J4387 - Nucleotides 4V88|1|A6|C|1420 to 4V88|1|A6|C|1284, length   7
  3 Junction

2B Branch 1 of 2 of junction J4387 - Nucleotides  1332 to  1419, length   2
pMakeNodes starting loop:     a=4V88|1|A6|C|1332 B=4V88|1|A6|G|1419
  5 Basepair  1332 1419 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J4387 - Nucleotides  1420 to  1284, length   7
pMakeNodes starting loop:     a=4V88|1|A6|C|1420 B=4V88|1|A6|C|1284
    Insertion on left  4V88|1|A6|C|1420
    Insertion on left  4V88|1|A6|A|1421
    Insertion on left  4V88|1|A6|A|1422
pMakeNodesProbeForInsertions:  a 4V88|1|A6|U|1423 interacts with 4V88|1|A6|C|1284
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1284 interacts with 4V88|1|A6|U|1423
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|1284 interacts with 4V88|1|A6|U|1423
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  7 Initial   1420 (3 insertion) and 1284 (0 insertion)
  8 Basepair  1423 1284 UC tHH 
No need to probe because of interaction between a=4V88|1|A6|A|1424 B=4V88|1|A6|U|1283
  9 Basepair  1424 1283 AU cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
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  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:   9  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  10   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|C|1284
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|1285
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|U|1286
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1287
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V88|1|A6|A|1422
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V88|1|A6|A|1421
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|G|1328
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1329
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|G|1330
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAGA'
           RightLetter: 'UAG'
               Comment: ' // Basepair C1327 - G1288 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J4387'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|C|1284'
              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: 'J4387'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 4V88|1|A6|U|1285'
              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: 'J4387'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1286'
              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: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 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 4V88|1|A6|A|1287'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V88|1|A6|A|1422'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 4V88|1|A6|A|1421'
              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: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

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: 'J4387'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1332 - C1284 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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: '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 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1332 - G1419 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 19

ans = 

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

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: 'J4387'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|C|1420 - 4V88|1|A6|C|1284 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: 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 4V88|1|A6|G|1328'
              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: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 22

ans = 

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

                  type: 'Fixed'
              nextnode: 23
             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 4V88|1|A6|A|1329'
              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: [0 1]
        leftLetterDist: [0.2500 0.2500 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|G|1330'
              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: 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 26

ans = 

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

                  type: 'Basepair'
              nextnode: 27
             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: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U1423 - C1284 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: []

Node 27

ans = 

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

                  type: 'Basepair'
              nextnode: 28
             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 A1424 - U1283 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  15  Junction Left  6 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  17  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  18   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  19   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  20     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  21   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  22     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  23   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  24     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  25   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  26  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:  27  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  28   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 28
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: 17
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J4387'
        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: 8
            RightIndex: 14
             Insertion: []
                    id: 'J4387'
        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: 'CAA'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|C|1420 - 4V88|1|A6|C|1284 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_47248.1. Nodes 16 and 19 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 15
pNextNodeJunction: Found a junction child at node 16
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a junction child at node 19
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Finished at node 28 out of 28, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_47248.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.0999

Timestamp 18-Jul-2025 00:12:58
pMakeSCFGModels: Making JAR3D model for motif group J3_47376.1, number 42 of 88
pMakeNodes starting loop:     a=6P2H|1|A|G|21 B=6P2H|1|A|C|79
  2 Basepair    21   79 GC cWW 
pMakeNodes probe for inserts:  a=6P2H|1|A|U|22 B=6P2H|1|A|C|78
    Insertion on right 6P2H|1|A|C|78
pMakeNodes probed for insert:  a=6P2H|1|A|U|22 B=6P2H|1|A|A|77
pMakeNodesJunction: a=6P2H|1|A|U|22 r=6P2H|1|A|U|22 s=6P2H|1|A|A|52 t=6P2H|1|A|C|53 u=B=6P2H|1|A|A|77
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6P2H|1|A|U|22 and 6P2H|1|A|A|52 and between 6P2H|1|A|C|53 and 6P2H|1|A|A|77
pMakeNodesJunction: about to make a junction: a=6P2H|1|A|U|22 s=6P2H|1|A|A|52 t=6P2H|1|A|C|53 B=6P2H|1|A|A|77
pMakeNodesJunction: first branch starts at   6P2H|1|A|U|22
pMakeNodesJunction: first branch ends around 6P2H|1|A|A|52
pMakeNodesJunction: second branch starts at  6P2H|1|A|C|53
pMakeNodesJunction: junction ends at         6P2H|1|A|A|77
pMakeNodesJunction: first branch strand start goes up to  6P2H|1|A|U|22
pMakeNodesJunction: first branch strand end goes down to  6P2H|1|A|A|52
pMakeNodesJunction: second branch strand start goes up to 6P2H|1|A|C|54
pMakeNodesJunction: last strand of junction goes down to  6P2H|1|A|G|74
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J3815
Actual Branch 1 of junction J3815 - Nucleotides 6P2H|1|A|U|22 to 6P2H|1|A|A|52, length   2
Actual Branch 2 of junction J3815 - Nucleotides 6P2H|1|A|C|53 to 6P2H|1|A|A|77, length   5
  3 Junction

2B Branch 1 of 2 of junction J3815 - Nucleotides    22 to    52, length   2
pMakeNodes starting loop:     a=6P2H|1|A|U|22 B=6P2H|1|A|A|52
  5 Basepair    22   52 UA cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J3815 - Nucleotides    53 to    77, length   5
pMakeNodes starting loop:     a=6P2H|1|A|C|53 B=6P2H|1|A|A|77
    Insertion on left  6P2H|1|A|C|53
    Insertion on right 6P2H|1|A|A|77
    Insertion on right 6P2H|1|A|U|75
pMakeNodesProbeForInsertions:  a 6P2H|1|A|C|54 interacts with 6P2H|1|A|G|74
pMakeNodesProbeForInsertions:  B 6P2H|1|A|G|74 interacts with 6P2H|1|A|C|54
pMakeNodesProbeForInsertions:  B 6P2H|1|A|G|74 interacts with 6P2H|1|A|C|54
  7 Initial     53 (1 insertion) and   77 (2 insertion)
  8 Basepair    54   74 CG cWW 
  9 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  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  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6P2H|1|A|A|77
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|C|53
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6P2H|1|A|C|76
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6P2H|1|A|U|75
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'CC'
               Comment: ' // Basepair G21 - C79 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 9
             Insertion: []
                    id: 'J3815'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6P2H|1|A|A|77'
              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: 8
             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 5

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: 'J3815'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U22 - A77 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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 3
             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 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U22 - A52 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: 'J3815'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'UA'
               Comment: ' // Initial node 6P2H|1|A|C|53 - 6P2H|1|A|A|77 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: 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 6P2H|1|A|C|53'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6P2H|1|A|C|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: []

Node 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 14

ans = 

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

                  type: 'Fixed'
              nextnode: 15
             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 6P2H|1|A|U|75'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

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

                  type: 'Basepair'
              nextnode: 17
             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 C54 - G74 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   5  Junction Left  2 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  2
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  8
pMakeMotifModelFromSSF:  10     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  12     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  13   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  14     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  15   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  16  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  17   Hairpin Left  6 Right  5
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 hairpin at node 17
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: 2
            RightIndex: 3
             Insertion: []
                    id: 'J3815'
        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: 4
            RightIndex: 8
             Insertion: []
                    id: 'J3815'
        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: 'UA'
               Comment: ' // Initial node 6P2H|1|A|C|53 - 6P2H|1|A|A|77 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_47376.1. Nodes 6 and 9 both model an insertion before position 4. 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 hairpin at node 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSW  between 3 and 8
pConservedInteractionList: did not find a substitution probability matrix for cSW  between 3 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_47376.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7245

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J3_47707.1, number 43 of 88
pMakeNodes starting loop:     a=4WF9|1|X|A|56 B=4WF9|1|X|U|113
  2 Basepair    56  113 AU cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|C|57 B=4WF9|1|X|U|112
    Insertion on left  4WF9|1|X|C|57
    Insertion on left  4WF9|1|X|G|58
    Insertion on left  4WF9|1|X|U|59
    Insertion on left  4WF9|1|X|U|60
    Insertion on left  4WF9|1|X|A|61
    Insertion on left  4WF9|1|X|C|62
    Insertion on right 4WF9|1|X|U|112
    Insertion on right 4WF9|1|X|U|111
pMakeNodes probed for insert:  a=4WF9|1|X|U|63 B=4WF9|1|X|A|110
pMakeNodesJunction: a=4WF9|1|X|U|63 r=4WF9|1|X|U|63 s=4WF9|1|X|U|74 t=4WF9|1|X|G|75 u=B=4WF9|1|X|A|110
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|U|63 and 4WF9|1|X|U|74 and between 4WF9|1|X|G|75 and 4WF9|1|X|A|110
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|U|63 s=4WF9|1|X|U|74 t=4WF9|1|X|G|75 B=4WF9|1|X|A|110
pMakeNodesJunction: first branch starts at   4WF9|1|X|U|63
pMakeNodesJunction: first branch ends around 4WF9|1|X|U|74
pMakeNodesJunction: second branch starts at  4WF9|1|X|G|75
pMakeNodesJunction: junction ends at         4WF9|1|X|A|110
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|67
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|U|74
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|C|76
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|G|109

Junction with 2 loops, call it J7655
Actual Branch 1 of junction J7655 - Nucleotides 4WF9|1|X|U|63 to 4WF9|1|X|U|74, length   6
Actual Branch 2 of junction J7655 - Nucleotides 4WF9|1|X|G|75 to 4WF9|1|X|A|110, length   4
  3 Junction

2B Branch 1 of 2 of junction J7655 - Nucleotides    63 to    74, length   6
pMakeNodes starting loop:     a=4WF9|1|X|U|63 B=4WF9|1|X|U|74
pMakeNodesProbeForInsertions:  a 4WF9|1|X|U|63 interacts with 4WF9|1|X|A|65
pMakeNodesProbeForInsertions:  B 4WF9|1|X|U|74 interacts with 4WF9|1|X|G|67
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WF9|1|X|U|74 interacts with 4WF9|1|X|G|67
  4 Initial     63 (0 insertion) and   74 (0 insertion)
pMakeNodes making a cluster near strand break a=4WF9|1|X|U|63 B=4WF9|1|X|U|74
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 8 to 12 and then 13 to 13
aa is 12 bb is 13
  5 Cluster   4WF9|1|X|U|63:4WF9|1|X|G|67 4WF9|1|X|U|74:4WF9|1|X|U|74
    LR Inter  4WF9|1|X|G|67 4WF9|1|X|U|74 cWW 
    LL Inter  4WF9|1|X|U|63 4WF9|1|X|A|64 cSH 
    LL Inter  4WF9|1|X|U|63 4WF9|1|X|A|65 cSH 
    Left  strand conserved insertion 4WF9|1|X|C|66 at position 4
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J7655 - Nucleotides    75 to   110, length   4
pMakeNodes starting loop:     a=4WF9|1|X|G|75 B=4WF9|1|X|A|110
  8 Basepair    75  110 GA cWW 
No need to probe because of interaction between a=4WF9|1|X|C|76 B=4WF9|1|X|G|109
  9 Basepair    76  109 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Junction Left  8 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  8 Right 13
pMakeMotifModelFromSSF:   5   Cluster Left  8  9 10 11 12 Right 13
pMakeMotifModelFromSSF:   6   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:   7   Initial Left 14 Right 17
pMakeMotifModelFromSSF:   8  Basepair Left 14 Right 17
pMakeMotifModelFromSSF:   9  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  10   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|G|58
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|59
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|62
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|U|112
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|U|111
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACGUUAC'
           RightLetter: 'UUU'
               Comment: ' // Basepair A56 - U113 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 19
             Insertion: []
                    id: 'J7655'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|C|57'
              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: 3
            RightIndex: 19
             Insertion: []
                    id: 'J7655'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|G|58'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.2571

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|59'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 5
            RightIndex: 19
             Insertion: []
                    id: 'J7655'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|60'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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: []
          LeftNotInter: []
         RightNotInter: []
              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: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|C|62'
              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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 8
            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|112'
              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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  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: 8
            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|111'
              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: 8
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: 'J7655'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U63 - A110 ID J7655'
              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: 8
            RightIndex: 13
             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 4WF9|1|X|U|63 - 4WF9|1|X|U|74 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 21

ans = 

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

                  type: 'Cluster'
              nextnode: 22
             LeftIndex: [8 9 10 11 12]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAACG'
           RightLetter: 'U'
               Comment: ' // Cluster node 4WF9|1|X|U|63:4WF9|1|X|G|67 and 4WF9|1|X|U|74:4WF9|1|X|U|74'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.2571

Node 22

ans = 

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

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 14
            RightIndex: 17
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

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

                  type: 'Basepair'
              nextnode: 26
             LeftIndex: 14
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G75 - A110 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 26

ans = 

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

                  type: 'Basepair'
              nextnode: 27
             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 C76 - G109 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 27

ans = 

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

                  type: 'Hairpin'
              nextnode: 29
             LeftIndex: 16
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: [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 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 19
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 19
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 19
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 19
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 19
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 19
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 19
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 19
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 19
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 19
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 19
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 19
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 19
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 18
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 18
pMakeMotifModelFromSSF:  18   Initial Left  8 Right 17
pMakeMotifModelFromSSF:  19  Junction Left  8 Right 17
pMakeMotifModelFromSSF:  20   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  21   Cluster Left  8  9 10 11 12 Right 13
pMakeMotifModelFromSSF:  22   Initial Left 13 Right 12
pMakeMotifModelFromSSF:  23   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  24   Initial Left 14 Right 17
pMakeMotifModelFromSSF:  25  Basepair Left 14 Right 17
pMakeMotifModelFromSSF:  26  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  27   Hairpin Left 16 Right 15
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Finished at node 27 out of 27, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J7655'
        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 4WF9|1|X|U|63 - 4WF9|1|X|U|74 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: 14
            RightIndex: 17
             Insertion: []
                    id: 'J7655'
        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 J3_47707.1. Nodes 20 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 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Finished at node 27 out of 27, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_47707.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.3222

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J3_48314.1, number 44 of 88
pMakeNodes starting loop:     a=5TBW|1|1|A|3314 B=5TBW|1|1|U|3300
  2 Basepair  3314 3300 AU cWW 
No need to probe because of interaction between a=5TBW|1|1|G|3315 B=5TBW|1|1|A|3299
  3 Basepair  3315 3299 GA cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|3316 B=5TBW|1|1|C|3298
    Insertion on left  5TBW|1|1|A|3316
    Insertion on left  5TBW|1|1|U|3317
pMakeNodes probed for insert:  a=5TBW|1|1|G|3318 B=5TBW|1|1|C|3298
pMakeNodesJunction: a=5TBW|1|1|G|3318 r=5TBW|1|1|G|3318 s=5TBW|1|1|C|3388 t=5TBW|1|1|U|3389 u=B=5TBW|1|1|C|3298
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|G|3318 and 5TBW|1|1|C|3388 and between 5TBW|1|1|U|3389 and 5TBW|1|1|C|3298
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|G|3318 s=5TBW|1|1|C|3388 t=5TBW|1|1|U|3389 B=5TBW|1|1|C|3298
pMakeNodesJunction: first branch starts at   5TBW|1|1|G|3318
pMakeNodesJunction: first branch ends around 5TBW|1|1|C|3388
pMakeNodesJunction: second branch starts at  5TBW|1|1|U|3389
pMakeNodesJunction: junction ends at         5TBW|1|1|C|3298
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|3318
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|3388
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|3390
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|3298

Junction with 2 loops, call it J7951
Actual Branch 1 of junction J7951 - Nucleotides 5TBW|1|1|G|3318 to 5TBW|1|1|C|3388, length   2
Actual Branch 2 of junction J7951 - Nucleotides 5TBW|1|1|U|3389 to 5TBW|1|1|C|3298, length   3
  4 Junction

2B Branch 1 of 2 of junction J7951 - Nucleotides  3318 to  3388, length   2
pMakeNodes starting loop:     a=5TBW|1|1|G|3318 B=5TBW|1|1|C|3388
  6 Basepair  3318 3388 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7951 - Nucleotides  3389 to  3298, length   3
pMakeNodes starting loop:     a=5TBW|1|1|U|3389 B=5TBW|1|1|C|3298
    Insertion on left  5TBW|1|1|U|3389
pMakeNodesProbeForInsertions:  a 5TBW|1|1|G|3390 interacts with 5TBW|1|1|C|3298
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|3298 interacts with 5TBW|1|1|G|3390
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|3298 interacts with 5TBW|1|1|G|3390
  8 Initial   3389 (1 insertion) and 3298 (0 insertion)
  9 Basepair  3390 3298 GC cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|3300
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|3314
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|3317
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 A3314 - U3300 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'A'
               Comment: ' // Basepair G3315 - A3299 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
             Insertion: []
                    id: 'J7951'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|3300'
              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: 9
             Insertion: []
                    id: 'J7951'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 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 5TBW|1|1|A|3314'
              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: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 8

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J7951'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G3318 - C3298 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: []

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: '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: []

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 G3318 - C3388 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
            RightIndex: 9
             Insertion: []
                    id: 'J7951'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|U|3389 - 5TBW|1|1|C|3298 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: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|U|3317'
              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: 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: []
           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: 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 G3390 - C3298 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8  Junction Left  5 Right  9
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  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pNextNodeJunction: Found a 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 16
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: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J7951'
        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: 7
            RightIndex: 9
             Insertion: []
                    id: 'J7951'
        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 5TBW|1|1|U|3389 - 5TBW|1|1|C|3298 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_48314.1. 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
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 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_48314.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7472

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J3_51910.1, number 45 of 88
pMakeNodes starting loop:     a=4R4V|1|A|G|655 B=4R4V|1|A|C|764
  2 Basepair   655  764 GC cWW 
No need to probe because of interaction between a=4R4V|1|A|A|656 B=4R4V|1|A|G|763
  3 Basepair   656  763 AG cWW 
pMakeNodes probe for inserts:  a=4R4V|1|A|C|658 B=4R4V|1|A|A|762
pMakeNodes probed for insert:  a=4R4V|1|A|C|658 B=4R4V|1|A|A|762
pMakeNodesJunction: a=4R4V|1|A|C|658 r=4R4V|1|A|C|658 s=4R4V|1|A|G|716 t=4R4V|1|A|G|717 u=B=4R4V|1|A|A|762
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4R4V|1|A|C|658 and 4R4V|1|A|G|716 and between 4R4V|1|A|G|717 and 4R4V|1|A|A|762
pMakeNodesJunction: about to make a junction: a=4R4V|1|A|C|658 s=4R4V|1|A|G|716 t=4R4V|1|A|G|717 B=4R4V|1|A|A|762
pMakeNodesJunction: first branch starts at   4R4V|1|A|C|658
pMakeNodesJunction: first branch ends around 4R4V|1|A|G|716
pMakeNodesJunction: second branch starts at  4R4V|1|A|G|717
pMakeNodesJunction: junction ends at         4R4V|1|A|A|762
pMakeNodesJunction: first branch strand start goes up to  4R4V|1|A|C|658
pMakeNodesJunction: first branch strand end goes down to  4R4V|1|A|G|716
pMakeNodesJunction: second branch strand start goes up to 4R4V|1|A|G|717
pMakeNodesJunction: last strand of junction goes down to  4R4V|1|A|C|758
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J1868
Actual Branch 1 of junction J1868 - Nucleotides 4R4V|1|A|C|658 to 4R4V|1|A|G|716, length   2
Actual Branch 2 of junction J1868 - Nucleotides 4R4V|1|A|G|717 to 4R4V|1|A|A|762, length   6
  4 Junction

2B Branch 1 of 2 of junction J1868 - Nucleotides   658 to   716, length   2
pMakeNodes starting loop:     a=4R4V|1|A|C|658 B=4R4V|1|A|G|716
  6 Basepair   658  716 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1868 - Nucleotides   717 to   762, length   6
pMakeNodes starting loop:     a=4R4V|1|A|G|717 B=4R4V|1|A|A|762
    Insertion on right 4R4V|1|A|A|762
    Insertion on right 4R4V|1|A|A|761
    Insertion on right 4R4V|1|A|C|760
    Insertion on right 4R4V|1|A|A|759
pMakeNodesProbeForInsertions:  a 4R4V|1|A|G|717 interacts with 4R4V|1|A|C|758
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|758 interacts with 4R4V|1|A|G|717
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|758 interacts with 4R4V|1|A|G|717
  8 Initial    717 (0 insertion) and  762 (4 insertion)
  9 Basepair   717  758 GC cWW 
 10 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 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  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4R4V|1|A|A|761
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4R4V|1|A|C|760
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4R4V|1|A|A|759
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4R4V|1|A|C|758
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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G655 - 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 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: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A656 - G763 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: 'J1868'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C658 - A762 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 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: '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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C658 - G716 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: 'J1868'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'ACAA'
               Comment: ' // Initial node 4R4V|1|A|G|717 - 4R4V|1|A|A|762 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: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4R4V|1|A|A|761'
              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 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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-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: [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 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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4R4V|1|A|C|760'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4R4V|1|A|A|759'
              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: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             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 4R4V|1|A|C|758'
              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: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             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 G717 - C758 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 18

ans = 

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

                  type: 'Hairpin'
              nextnode: 19
             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: [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  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     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  14   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  15     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  16   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  17  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  18   Hairpin Left  6 Right  5
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 hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, 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: 'J1868'
        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: 10
             Insertion: []
                    id: 'J1868'
        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: 'ACAA'
               Comment: ' // Initial node 4R4V|1|A|G|717 - 4R4V|1|A|A|762 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_51910.1. 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
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 hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSW  between 4 and 10
pConservedInteractionList: did not find a substitution probability matrix for tSW  between 4 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_51910.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7685

Timestamp 18-Jul-2025 00:12:59
pMakeSCFGModels: Making JAR3D model for motif group J3_52655.1, number 46 of 88
pMakeNodes starting loop:     a=4V88|1|A6|U|1168 B=4V88|1|A6|A|1577
  2 Basepair  1168 1577 UA cWW 
No need to probe because of interaction between a=4V88|1|A6|G|1169 B=4V88|1|A6|A|1576
  3 Basepair  1169 1576 GA tSH 
pMakeNodes probe for inserts:  a=4V88|1|A6|G|1170 B=4V88|1|A6|G|1575
    Insertion on right 4V88|1|A6|G|1575
pMakeNodes probed for insert:  a=4V88|1|A6|G|1170 B=4V88|1|A6|G|1574
pMakeNodesJunction: a=4V88|1|A6|G|1170 r=4V88|1|A6|G|1170 s=4V88|1|A6|A|1469 t=4V88|1|A6|C|1470 u=B=4V88|1|A6|G|1574
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|G|1170 and 4V88|1|A6|A|1469 and between 4V88|1|A6|C|1470 and 4V88|1|A6|G|1574
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|G|1170 s=4V88|1|A6|A|1469 t=4V88|1|A6|C|1470 B=4V88|1|A6|G|1574
pMakeNodesJunction: first branch starts at   4V88|1|A6|G|1170
pMakeNodesJunction: first branch ends around 4V88|1|A6|A|1469
pMakeNodesJunction: second branch starts at  4V88|1|A6|C|1470
pMakeNodesJunction: junction ends at         4V88|1|A6|G|1574
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|A|1171
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|U|1468
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|C|1470
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|G|1574

Junction with 2 loops, call it J4897
Actual Branch 1 of junction J4897 - Nucleotides 4V88|1|A6|G|1170 to 4V88|1|A6|A|1469, length   4
Actual Branch 2 of junction J4897 - Nucleotides 4V88|1|A6|C|1470 to 4V88|1|A6|G|1574, length   2
  4 Junction

2B Branch 1 of 2 of junction J4897 - Nucleotides  1170 to  1469, length   4
pMakeNodes starting loop:     a=4V88|1|A6|G|1170 B=4V88|1|A6|A|1469
  6 Basepair  1170 1469 GA cWW 
No need to probe because of interaction between a=4V88|1|A6|A|1171 B=4V88|1|A6|U|1468
  7 Basepair  1171 1468 AU cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J4897 - Nucleotides  1470 to  1574, length   2
pMakeNodes starting loop:     a=4V88|1|A6|C|1470 B=4V88|1|A6|G|1574
 10 Basepair  1470 1574 CG cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Junction Left  3 Right  8
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  8
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V88|1|A6|G|1575
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U1168 - A1577 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'GA'
               Comment: ' // Basepair G1169 - A1576 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: 'J4897'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V88|1|A6|G|1575'
              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: 8
             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: []
                  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: 3
            RightIndex: 8
             Insertion: []
                    id: 'J4897'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1170 - G1574 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 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             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 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1170 - A1469 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 A1171 - U1468 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
            RightIndex: 8
             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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1470 - G1574 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6  Junction Left  3 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             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: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J4897'
        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 J3_52655.1. Nodes 7 and 11 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 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_52655.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7028
   -6.7028
   -6.7028

Timestamp 18-Jul-2025 00:13:00
pMakeSCFGModels: Making JAR3D model for motif group J3_52842.1, number 47 of 88
pMakeNodes starting loop:     a=7A0S|1|X|C|2857 B=7A0S|1|X|G|2811
  2 Basepair  2857 2811 CG cWW 
No need to probe because of interaction between a=7A0S|1|X|A|2858 B=7A0S|1|X|A|2809
  3 Basepair  2858 2809 AA tHS 
pMakeNodes probe for inserts:  a=7A0S|1|X|U|2859 B=7A0S|1|X|U|2807
    Insertion on left  7A0S|1|X|U|2859
    Insertion on left  7A0S|1|X|C|2860
    Insertion on right 7A0S|1|X|U|2807
pMakeNodes probed for insert:  a=7A0S|1|X|A|2861 B=7A0S|1|X|G|2806
pMakeNodesJunction: a=7A0S|1|X|A|2861 r=7A0S|1|X|A|2861 s=7A0S|1|X|U|2789 t=7A0S|1|X|C|2790 u=B=7A0S|1|X|G|2806
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|A|2861 and 7A0S|1|X|U|2789 and between 7A0S|1|X|C|2790 and 7A0S|1|X|G|2806
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|A|2861 s=7A0S|1|X|U|2789 t=7A0S|1|X|C|2790 B=7A0S|1|X|G|2806
pMakeNodesJunction: first branch starts at   7A0S|1|X|A|2861
pMakeNodesJunction: first branch ends around 7A0S|1|X|U|2789
pMakeNodesJunction: second branch starts at  7A0S|1|X|C|2790
pMakeNodesJunction: junction ends at         7A0S|1|X|G|2806
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|A|2861
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|U|2789
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|C|2790
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|G|2806

Junction with 2 loops, call it J4455
Actual Branch 1 of junction J4455 - Nucleotides 7A0S|1|X|A|2861 to 7A0S|1|X|U|2789, length   2
Actual Branch 2 of junction J4455 - Nucleotides 7A0S|1|X|C|2790 to 7A0S|1|X|G|2806, length   2
  4 Junction

2B Branch 1 of 2 of junction J4455 - Nucleotides  2861 to  2789, length   2
pMakeNodes starting loop:     a=7A0S|1|X|A|2861 B=7A0S|1|X|U|2789
  6 Basepair  2861 2789 AU cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J4455 - Nucleotides  2790 to  2806, length   2
pMakeNodes starting loop:     a=7A0S|1|X|C|2790 B=7A0S|1|X|G|2806
  9 Basepair  2790 2806 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Junction Left  5 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  10   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|2806
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|U|2807
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|2857
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C2857 - G2811 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AUC'
           RightLetter: 'UA'
               Comment: ' // Basepair A2858 - A2809 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2806'
              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: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 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 7A0S|1|X|U|2807'
              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: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J4455'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|2857'
              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: 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 10

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J4455'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2861 - G2806 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 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: '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 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 A2861 - U2789 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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 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 C2790 - G2806 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  10  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 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

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J4455'
        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: 8
             Insertion: []
                    id: 'J4455'
        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 J3_52842.1. 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_52842.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5454

Timestamp 18-Jul-2025 00:13:00
pMakeSCFGModels: Making JAR3D model for motif group J3_52917.1, number 48 of 88
pMakeNodes starting loop:     a=5TBW|1|1|A|2930 B=5TBW|1|1|U|2916
  2 Basepair  2930 2916 AU cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|C|2931 B=5TBW|1|1|U|2915
pMakeNodes probed for insert:  a=5TBW|1|1|C|2931 B=5TBW|1|1|U|2915
pMakeNodes making a cluster near strand break a=5TBW|1|1|C|2931 B=5TBW|1|1|U|2915
pMakeNodesCluster: amax is 6 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 11 to 11
aa is 6 bb is 11
  3 Cluster   5TBW|1|1|C|2931:5TBW|1|1|U|2935 5TBW|1|1|U|2915:5TBW|1|1|U|2915
    LL Inter  5TBW|1|1|U|2932 5TBW|1|1|A|2934 tSH 
    LL Inter  5TBW|1|1|C|2931 5TBW|1|1|U|2935 tWW 
    Left  strand conserved insertion 5TBW|1|1|A|2933 at position 3
    Right strand conserved insertion 5TBW|1|1|U|2915 at position 1
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
pMakeNodes probe for inserts:  a=5TBW|1|1|A|2936 B=5TBW|1|1|G|2914
  4 Initial   2936 (0 insertion) and 2914 (0 insertion)
pMakeNodes probed for insert:  a=5TBW|1|1|A|2936 B=5TBW|1|1|G|2914
pMakeNodesJunction: a=5TBW|1|1|A|2936 r=5TBW|1|1|A|2936 s=5TBW|1|1|U|2886 t=5TBW|1|1|C|2889 u=B=5TBW|1|1|G|2914
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|A|2936 and 5TBW|1|1|U|2886 and between 5TBW|1|1|C|2889 and 5TBW|1|1|G|2914
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|A|2936 s=5TBW|1|1|U|2886 t=5TBW|1|1|C|2889 B=5TBW|1|1|G|2914
pMakeNodesJunction: first branch starts at   5TBW|1|1|A|2936
pMakeNodesJunction: first branch ends around 5TBW|1|1|U|2886
pMakeNodesJunction: second branch starts at  5TBW|1|1|C|2889
pMakeNodesJunction: junction ends at         5TBW|1|1|G|2914
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|A|2936
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|U|2886
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|C|2889
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|G|2914

Junction with 2 loops, call it J6463
Actual Branch 1 of junction J6463 - Nucleotides 5TBW|1|1|A|2936 to 5TBW|1|1|U|2886, length   2
Actual Branch 2 of junction J6463 - Nucleotides 5TBW|1|1|C|2889 to 5TBW|1|1|G|2914, length   2
  5 Junction

2B Branch 1 of 2 of junction J6463 - Nucleotides  2936 to  2886, length   2
pMakeNodes starting loop:     a=5TBW|1|1|A|2936 B=5TBW|1|1|U|2886
  7 Basepair  2936 2886 AU cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6463 - Nucleotides  2889 to  2914, length   2
pMakeNodes starting loop:     a=5TBW|1|1|C|2889 B=5TBW|1|1|G|2914
 10 Basepair  2889 2914 CG cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  7 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2930 - U2916 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4 5 6]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAAU'
           RightLetter: 'U'
               Comment: ' // Cluster node 5TBW|1|1|C|2931:5TBW|1|1|U|2935 and 5TBW|1|1|U|2915:5TBW|1|1|U|2915'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 1
              NormCons: 1
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 7
            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 5TBW|1|1|A|2936 - 5TBW|1|1|G|2914 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: 7
            RightIndex: 10
             Insertion: []
                    id: 'J6463'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2936 - G2914 ID J6463'
              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: 7
            RightIndex: 8
             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: []
          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: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2936 - U2886 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 9
            RightIndex: 10
             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: []
          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: 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 C2889 - G2914 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []

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

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J6463'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0 0.0454 0.9070 0.0454 0.0023]
       rightLetterDist: [0.3750 0.1250 0.1250 0.3750 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: 9
            RightIndex: 10
             Insertion: []
                    id: 'J6463'
        leftLengthDist: [0 0.0454 0.9070 0.0454 0.0023]
        leftLetterDist: [0.3750 0.1250 0.1250 0.3750 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 J3_52917.1. Nodes 6 and 9 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 hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 9
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 7 and 11
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 5 and 9
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 10
pConservedInteractionList: did not find a substitution probability matrix for cHW  between 7 and 11
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_52917.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3210

Timestamp 18-Jul-2025 00:13:00
pMakeSCFGModels: Making JAR3D model for motif group J3_56052.2, number 49 of 88
pMakeNodes starting loop:     a=5J7L|1|AA|C|586 B=5J7L|1|AA|G|755
  2 Basepair   586  755 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|G|587 B=5J7L|1|AA|C|754
    Insertion on left  5J7L|1|AA|G|587
pMakeNodes probed for insert:  a=5J7L|1|AA|G|588 B=5J7L|1|AA|C|754
pMakeNodesJunction: a=5J7L|1|AA|G|588 r=5J7L|1|AA|G|588 s=5J7L|1|AA|C|651 t=5J7L|1|AA|U|652 u=B=5J7L|1|AA|C|754
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|AA|G|588 and 5J7L|1|AA|C|651 and between 5J7L|1|AA|U|652 and 5J7L|1|AA|C|754
pMakeNodesJunction: about to make a junction: a=5J7L|1|AA|G|588 s=5J7L|1|AA|C|651 t=5J7L|1|AA|U|652 B=5J7L|1|AA|C|754
pMakeNodesJunction: first branch starts at   5J7L|1|AA|G|588
pMakeNodesJunction: first branch ends around 5J7L|1|AA|C|651
pMakeNodesJunction: second branch starts at  5J7L|1|AA|U|652
pMakeNodesJunction: junction ends at         5J7L|1|AA|C|754
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|AA|G|588
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|AA|C|651
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|AA|G|654
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|AA|C|754

Junction with 2 loops, call it J7093
Actual Branch 1 of junction J7093 - Nucleotides 5J7L|1|AA|G|588 to 5J7L|1|AA|C|651, length   2
Actual Branch 2 of junction J7093 - Nucleotides 5J7L|1|AA|U|652 to 5J7L|1|AA|C|754, length   3
  3 Junction

2B Branch 1 of 2 of junction J7093 - Nucleotides   588 to   651, length   2
pMakeNodes starting loop:     a=5J7L|1|AA|G|588 B=5J7L|1|AA|C|651
  5 Basepair   588  651 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J7093 - Nucleotides   652 to   754, length   3
pMakeNodes starting loop:     a=5J7L|1|AA|U|652 B=5J7L|1|AA|C|754
    Insertion on left  5J7L|1|AA|U|652
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|G|654 interacts with 5J7L|1|AA|C|754
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|C|754 interacts with 5J7L|1|AA|G|654
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|C|754 interacts with 5J7L|1|AA|G|654
  7 Initial    652 (1 insertion) and  754 (0 insertion)
  8 Basepair   654  754 GC cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  7
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  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|587
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|U|652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 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 C586 - G755 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
             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 5J7L|1|AA|G|587'
              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: 7
             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 5

ans = 

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

                  type: 'Junction'
              nextnode: [4 7]
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: 'J7093'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G588 - C754 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 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: '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 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 G588 - C651 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
             Insertion: []
                    id: 'J7093'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|AA|U|652 - 5J7L|1|AA|C|754 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: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|U|652'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 G654 - C754 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  7
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  7
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
pNextNodeJunction: Found a 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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, 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: 'J7093'
        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: 7
             Insertion: []
                    id: 'J7093'
        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: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|AA|U|652 - 5J7L|1|AA|C|754 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_56052.2. 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
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_56052.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2465
   -4.3992
   -4.3992
   -4.3992

Timestamp 18-Jul-2025 00:13:00
pMakeSCFGModels: Making JAR3D model for motif group J3_56708.1, number 50 of 88
pMakeNodes starting loop:     a=3EGZ|1|B|A|53 B=3EGZ|1|B|U|28
  2 Basepair    53   28 AU cWW 
pMakeNodes probe for inserts:  a=3EGZ|1|B|A|54 B=3EGZ|1|B|C|27
    Insertion on left  3EGZ|1|B|A|54
    Insertion on left  3EGZ|1|B|A|55
pMakeNodes probed for insert:  a=3EGZ|1|B|A|56 B=3EGZ|1|B|C|27
pMakeNodesJunction: a=3EGZ|1|B|A|56 r=3EGZ|1|B|A|56 s=3EGZ|1|B|A|8 t=3EGZ|1|B|G|9 u=B=3EGZ|1|B|C|27
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3EGZ|1|B|A|56 and 3EGZ|1|B|A|8 and between 3EGZ|1|B|G|9 and 3EGZ|1|B|C|27
pMakeNodesJunction: about to make a junction: a=3EGZ|1|B|A|56 s=3EGZ|1|B|A|8 t=3EGZ|1|B|G|9 B=3EGZ|1|B|C|27
pMakeNodesJunction: first branch starts at   3EGZ|1|B|A|56
pMakeNodesJunction: first branch ends around 3EGZ|1|B|A|8
pMakeNodesJunction: second branch starts at  3EGZ|1|B|G|9
pMakeNodesJunction: junction ends at         3EGZ|1|B|C|27
pMakeNodesJunction: first branch strand start goes up to  3EGZ|1|B|C|61
pMakeNodesJunction: first branch strand end goes down to  3EGZ|1|B|G|5
pMakeNodesJunction: second branch strand start goes up to 3EGZ|1|B|G|9
pMakeNodesJunction: last strand of junction goes down to  3EGZ|1|B|C|27

Junction with 2 loops, call it J7546
Actual Branch 1 of junction J7546 - Nucleotides 3EGZ|1|B|A|56 to 3EGZ|1|B|A|8, length  10
Actual Branch 2 of junction J7546 - Nucleotides 3EGZ|1|B|G|9 to 3EGZ|1|B|C|27, length   2
  3 Junction

2B Branch 1 of 2 of junction J7546 - Nucleotides    56 to     8, length  10
pMakeNodes starting loop:     a=3EGZ|1|B|A|56 B=3EGZ|1|B|A|8
  5 Basepair    56    8 AA tHW 
pMakeNodes probe for inserts:  a=3EGZ|1|B|C|57 B=3EGZ|1|B|G|7
    Insertion on left  3EGZ|1|B|C|57
    Insertion on left  3EGZ|1|B|A|58
pMakeNodesProbeForInsertions:  a 3EGZ|1|B|U|59 interacts with 3EGZ|1|B|G|7
pMakeNodesProbeForInsertions:  B 3EGZ|1|B|G|7 interacts with 3EGZ|1|B|U|59
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3EGZ|1|B|G|7 interacts with 3EGZ|1|B|U|59
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3EGZ|1|B|U|59 B=3EGZ|1|B|G|7
  6 Basepair    59    7 UG bif 
No need to probe because of interaction between a=3EGZ|1|B|A|60 B=3EGZ|1|B|A|6
  7 Basepair    60    6 AA cWW 
No need to probe because of interaction between a=3EGZ|1|B|C|61 B=3EGZ|1|B|G|5
  8 Basepair    61    5 CG cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J7546 - Nucleotides     9 to    27, length   2
pMakeNodes starting loop:     a=3EGZ|1|B|G|9 B=3EGZ|1|B|C|27
 11 Basepair     9   27 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Junction Left  4 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  10   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  11  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  12   Hairpin Left 15 Right 14
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 3EGZ|1|B|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3EGZ|1|B|G|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3EGZ|1|B|G|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3EGZ|1|B|C|27
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: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Basepair A53 - U28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'J7546'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3EGZ|1|B|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: 15
             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: []
                  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 3EGZ|1|B|G|7'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 'A'
           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 7

ans = 

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

                  type: 'Junction'
              nextnode: [4 10]
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: 'J7546'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A56 - C27 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 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: '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 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            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: 'ACA'
           RightLetter: 'A'
               Comment: ' // Basepair A56 - A8 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 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: 'J7546'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3EGZ|1|B|G|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 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: '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 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: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3EGZ|1|B|C|27'
              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: []
                  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: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U59 - G7 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 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: 'A'
               Comment: ' // Basepair A60 - A6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 C61 - G5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 15
             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: 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 G9 - 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: []
              NormCons: []

Node 20

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 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  Junction Left  4 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right 13
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  Basepair Left  7 Right 12
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 15
pMakeMotifModelFromSSF:  19  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  20   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
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: 4
            RightIndex: 13
             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: 14
            RightIndex: 15
             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 J3_56708.1. Nodes 8 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 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_56708.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.6465

Timestamp 18-Jul-2025 00:13:01
pMakeSCFGModels: Making JAR3D model for motif group J3_58090.1, number 51 of 88
pMakeNodes starting loop:     a=6LAX|1|A|C|6 B=6LAX|1|A|G|50
  2 Basepair     6   50 CG cWW 
pMakeNodes probe for inserts:  a=6LAX|1|A|G|7 B=6LAX|1|A|G|49
pMakeNodes probed for insert:  a=6LAX|1|A|G|7 B=6LAX|1|A|G|49
pMakeNodesJunction: a=6LAX|1|A|G|7 r=6LAX|1|A|G|7 s=6LAX|1|A|G|33 t=6LAX|1|A|A|34 u=B=6LAX|1|A|G|49
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6LAX|1|A|G|7 and 6LAX|1|A|G|33 and between 6LAX|1|A|A|34 and 6LAX|1|A|G|49
pMakeNodesJunction: about to make a junction: a=6LAX|1|A|G|7 s=6LAX|1|A|G|33 t=6LAX|1|A|A|34 B=6LAX|1|A|G|49
pMakeNodesJunction: first branch starts at   6LAX|1|A|G|7
pMakeNodesJunction: first branch ends around 6LAX|1|A|G|33
pMakeNodesJunction: second branch starts at  6LAX|1|A|A|34
pMakeNodesJunction: junction ends at         6LAX|1|A|G|49
pMakeNodesJunction: first branch strand start goes up to  6LAX|1|A|G|9
pMakeNodesJunction: first branch strand end goes down to  6LAX|1|A|C|32
pMakeNodesJunction: second branch strand start goes up to 6LAX|1|A|C|40
pMakeNodesJunction: last strand of junction goes down to  6LAX|1|A|G|49

Junction with 2 loops, call it J2760
Actual Branch 1 of junction J2760 - Nucleotides 6LAX|1|A|G|7 to 6LAX|1|A|G|33, length   5
Actual Branch 2 of junction J2760 - Nucleotides 6LAX|1|A|A|34 to 6LAX|1|A|G|49, length   6
  3 Junction

2B Branch 1 of 2 of junction J2760 - Nucleotides     7 to    33, length   5
pMakeNodes starting loop:     a=6LAX|1|A|G|7 B=6LAX|1|A|G|33
  5 Basepair     7   33 GG tWW 
pMakeNodes probe for inserts:  a=6LAX|1|A|U|8 B=6LAX|1|A|C|32
    Insertion on left  6LAX|1|A|U|8
pMakeNodesProbeForInsertions:  a 6LAX|1|A|G|9 interacts with 6LAX|1|A|C|32
pMakeNodesProbeForInsertions:  B 6LAX|1|A|C|32 interacts with 6LAX|1|A|G|9
pMakeNodesProbeForInsertions:  B 6LAX|1|A|C|32 interacts with 6LAX|1|A|G|9
pMakeNodes probed for insert:  a=6LAX|1|A|G|9 B=6LAX|1|A|C|32
  6 Basepair     9   32 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2760 - Nucleotides    34 to    49, length   6
pMakeNodes starting loop:     a=6LAX|1|A|A|34 B=6LAX|1|A|G|49
    Insertion on left  6LAX|1|A|A|34
    Insertion on left  6LAX|1|A|A|36
    Insertion on left  6LAX|1|A|A|37
    Insertion on left  6LAX|1|A|G|38
pMakeNodesProbeForInsertions:  a 6LAX|1|A|C|40 interacts with 6LAX|1|A|G|49
pMakeNodesProbeForInsertions:  B 6LAX|1|A|G|49 interacts with 6LAX|1|A|C|40
pMakeNodesProbeForInsertions:  B 6LAX|1|A|G|49 interacts with 6LAX|1|A|C|40
  8 Initial     34 (4 insertion) and   49 (0 insertion)
  9 Basepair    40   49 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LAX|1|A|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LAX|1|A|A|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LAX|1|A|U|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LAX|1|A|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LAX|1|A|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [0.9950 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 C6 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 12
             Insertion: []
                    id: 'J2760'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G7 - G49 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 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: '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 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'G'
               Comment: ' // Basepair G7 - G33 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 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6LAX|1|A|U|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    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: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 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 G9 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 12
             Insertion: []
                    id: 'J2760'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAAG'
           RightLetter: []
               Comment: ' // Initial node 6LAX|1|A|A|34 - 6LAX|1|A|G|49 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: 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 6LAX|1|A|A|34'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             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 6LAX|1|A|U|35'
              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: 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 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             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 6LAX|1|A|A|36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             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 17

ans = 

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

                  type: 'Fixed'
              nextnode: 18
             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 6LAX|1|A|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 18

ans = 

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

                  type: 'Initial'
              nextnode: 19
             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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C40 - G49 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  13     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  16   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  20   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 3
pNextNodeJunction: Found a junction child at node 4
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 20
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: 6
             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: 11
             LeftIndex: 7
            RightIndex: 12
             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: 'AAAG'
           RightLetter: []
               Comment: ' // Initial node 6LAX|1|A|A|34 - 6LAX|1|A|G|49 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_58090.1. Nodes 4 and 10 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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_58090.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2033

Timestamp 18-Jul-2025 00:13:01
pMakeSCFGModels: Making JAR3D model for motif group J3_58453.1, number 52 of 88
pMakeNodes starting loop:     a=6JQ5|1|B|U|70 B=6JQ5|1|A|A|67
  2 Basepair    70   67 UA cWW 
No need to probe because of interaction between a=6JQ5|1|B|U|71 B=6JQ5|1|A|A|65
  3 Basepair    71   65 UA cWH 
pMakeNodes probe for inserts:  a=6JQ5|1|B|A|73 B=6JQ5|1|A|C|64
    Insertion on left  6JQ5|1|B|A|73
pMakeNodes probed for insert:  a=6JQ5|1|B|A|74 B=6JQ5|1|A|C|64
pMakeNodesJunction: a=6JQ5|1|B|A|74 r=6JQ5|1|B|A|74 s=6JQ5|1|A|G|29 t=6JQ5|1|A|G|30 u=B=6JQ5|1|A|C|64
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6JQ5|1|B|A|74 and 6JQ5|1|A|G|29 and between 6JQ5|1|A|G|30 and 6JQ5|1|A|C|64
pMakeNodesJunction: about to make a junction: a=6JQ5|1|B|A|74 s=6JQ5|1|A|G|29 t=6JQ5|1|A|G|30 B=6JQ5|1|A|C|64
pMakeNodesJunction: first branch starts at   6JQ5|1|B|A|74
pMakeNodesJunction: first branch ends around 6JQ5|1|A|G|29
pMakeNodesJunction: second branch starts at  6JQ5|1|A|G|30
pMakeNodesJunction: junction ends at         6JQ5|1|A|C|64
pMakeNodesJunction: first branch strand start goes up to  6JQ5|1|B|C|77
pMakeNodesJunction: first branch strand end goes down to  6JQ5|1|A|G|27
pMakeNodesJunction: second branch strand start goes up to 6JQ5|1|A|G|31
pMakeNodesJunction: last strand of junction goes down to  6JQ5|1|A|C|64

Junction with 2 loops, call it J6797
Actual Branch 1 of junction J6797 - Nucleotides 6JQ5|1|B|A|74 to 6JQ5|1|A|G|29, length   6
Actual Branch 2 of junction J6797 - Nucleotides 6JQ5|1|A|G|30 to 6JQ5|1|A|C|64, length   3
  4 Junction

2B Branch 1 of 2 of junction J6797 - Nucleotides    74 to    29, length   6
pMakeNodes starting loop:     a=6JQ5|1|B|A|74 B=6JQ5|1|A|G|29
  6 Basepair    74   29 AG tWS 
pMakeNodes probe for inserts:  a=6JQ5|1|B|A|75 B=6JQ5|1|A|U|28
    Insertion on left  6JQ5|1|B|A|75
    Insertion on right 6JQ5|1|A|U|28
pMakeNodesProbeForInsertions:  a 6JQ5|1|B|C|77 interacts with 6JQ5|1|A|G|27
pMakeNodesProbeForInsertions:  B 6JQ5|1|A|G|27 interacts with 6JQ5|1|B|C|77
pMakeNodesProbeForInsertions:  B 6JQ5|1|A|G|27 interacts with 6JQ5|1|B|C|77
pMakeNodes probed for insert:  a=6JQ5|1|B|C|77 B=6JQ5|1|A|G|27
  7 Basepair    77   27 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6797 - Nucleotides    30 to    64, length   3
pMakeNodes starting loop:     a=6JQ5|1|A|G|30 B=6JQ5|1|A|C|64
    Insertion on left  6JQ5|1|A|G|30
pMakeNodesProbeForInsertions:  a 6JQ5|1|A|G|31 interacts with 6JQ5|1|A|C|64
pMakeNodesProbeForInsertions:  B 6JQ5|1|A|C|64 interacts with 6JQ5|1|A|G|31
pMakeNodesProbeForInsertions:  B 6JQ5|1|A|C|64 interacts with 6JQ5|1|A|G|31
  9 Initial     30 (1 insertion) and   64 (0 insertion)
 10 Basepair    31   64 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  11   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ5|1|A|G|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ5|1|A|G|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ5|1|A|G|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ5|1|B|U|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U70 - 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: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            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: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U71 - A65 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 12
             Insertion: []
                    id: 'J6797'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JQ5|1|A|G|29'
              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: 12
             Insertion: []
                    id: 'J6797'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 12
             Insertion: []
                    id: 'J6797'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A74 - C64 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 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: '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 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'UG'
               Comment: ' // Basepair A74 - G29 tWS '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 8
             Insertion: []
                    id: 'J6797'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JQ5|1|A|G|31'
              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: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JQ5|1|A|G|66'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 C77 - G27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
            RightIndex: 12
             Insertion: []
                    id: 'J6797'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6JQ5|1|A|G|30 - 6JQ5|1|A|C|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 16

ans = 

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

                  type: 'Fixed'
              nextnode: 17
             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 6JQ5|1|B|U|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 17

ans = 

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

                  type: 'Initial'
              nextnode: 18
             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 18

ans = 

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

                  type: 'Basepair'
              nextnode: 19
             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 G31 - C64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 19

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  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   6  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  15   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  17   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  18  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  19   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
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: 4
            RightIndex: 9
             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: 16
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: 'J6797'
        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 6JQ5|1|A|G|30 - 6JQ5|1|A|C|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 J3_58453.1. Nodes 7 and 15 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 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_58453.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.7268

Timestamp 18-Jul-2025 00:13:01
pMakeSCFGModels: Making JAR3D model for motif group J3_59914.1, number 53 of 88
pMakeNodes starting loop:     a=4KR9|1|M|U|8 B=4KR9|1|M|G|28
  2 Basepair     8   28 UG cWW 
pMakeNodes probe for inserts:  a=4KR9|1|M|A|9 B=4KR9|1|M|A|27
    Insertion on left  4KR9|1|M|A|9
pMakeNodes probed for insert:  a=4KR9|1|M|G|10 B=4KR9|1|M|A|27
pMakeNodesJunction: a=4KR9|1|M|G|10 r=4KR9|1|M|G|10 s=4KR9|1|M|C|15 t=4KR9|1|M|U|16 u=B=4KR9|1|M|A|27
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 4KR9|1|M|G|10 and 4KR9|1|M|C|15 and between 4KR9|1|M|U|16 and 4KR9|1|M|A|27
pMakeNodesJunction: about to make a junction: a=4KR9|1|M|G|10 s=4KR9|1|M|C|15 t=4KR9|1|M|U|16 B=4KR9|1|M|A|27
pMakeNodesJunction: first branch starts at   4KR9|1|M|G|10
pMakeNodesJunction: first branch ends around 4KR9|1|M|C|15
pMakeNodesJunction: second branch starts at  4KR9|1|M|U|16
pMakeNodesJunction: junction ends at         4KR9|1|M|A|27
pMakeNodesJunction: first branch strand start goes up to  4KR9|1|M|G|10
pMakeNodesJunction: first branch strand end goes down to  4KR9|1|M|C|15
pMakeNodesJunction: second branch strand start goes up to 4KR9|1|M|U|17
pMakeNodesJunction: last strand of junction goes down to  4KR9|1|M|A|26

Junction with 2 loops, call it J6550
Actual Branch 1 of junction J6550 - Nucleotides 4KR9|1|M|G|10 to 4KR9|1|M|C|15, length   2
Actual Branch 2 of junction J6550 - Nucleotides 4KR9|1|M|U|16 to 4KR9|1|M|A|27, length   4
  3 Junction

2B Branch 1 of 2 of junction J6550 - Nucleotides    10 to    15, length   2
pMakeNodes starting loop:     a=4KR9|1|M|G|10 B=4KR9|1|M|C|15
  5 Basepair    10   15 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J6550 - Nucleotides    16 to    27, length   4
pMakeNodes starting loop:     a=4KR9|1|M|U|16 B=4KR9|1|M|A|27
  8 Basepair    16   27 UA cWW 
No need to probe because of interaction between a=4KR9|1|M|U|17 B=4KR9|1|M|A|26
  9 Basepair    17   26 UA cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  8
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  8
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR9|1|M|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'G'
               Comment: ' // Basepair U8 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 8
             Insertion: []
                    id: 'J6550'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR9|1|M|A|9'
              NumLoops: 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: 8
             Insertion: []
                    id: 'J6550'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 8
             Insertion: []
                    id: 'J6550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G10 - A27 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: []

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: '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: []

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 - C15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 8
             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: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U16 - A27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U17 - A26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: [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     Fixed Left  2 Right  8
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  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, 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: 'J6550'
        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: 8
             Insertion: []
                    id: 'J6550'
        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 J3_59914.1. 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
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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_59914.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4388

Timestamp 18-Jul-2025 00:13:01
pMakeSCFGModels: Making JAR3D model for motif group J3_64069.1, number 54 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|G|2812 B=5J7L|1|DA|C|2888||A
  2 Basepair  2812 2888 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2813 B=5J7L|1|DA|A|2887||A
  3 Basepair  2813 2887 AA cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2814 B=5J7L|1|DA|A|2886||A
  4 Basepair  2814 2886 AA tSH 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2815 B=5J7L|1|DA|A|2883
pMakeNodes probed for insert:  a=5J7L|1|DA|C|2815 B=5J7L|1|DA|A|2883
pMakeNodesJunction: a=5J7L|1|DA|C|2815 r=5J7L|1|DA|C|2815 s=5J7L|1|DA|G|2831 t=5J7L|1|DA|U|2832 u=B=5J7L|1|DA|A|2883
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|C|2815 and 5J7L|1|DA|G|2831 and between 5J7L|1|DA|U|2832 and 5J7L|1|DA|A|2883
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|C|2815 s=5J7L|1|DA|G|2831 t=5J7L|1|DA|U|2832 B=5J7L|1|DA|A|2883
pMakeNodesJunction: first branch starts at   5J7L|1|DA|C|2815
pMakeNodesJunction: first branch ends around 5J7L|1|DA|G|2831
pMakeNodesJunction: second branch starts at  5J7L|1|DA|U|2832
pMakeNodesJunction: junction ends at         5J7L|1|DA|A|2883
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|2815
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|2831
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|U|2836
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|A|2882

Junction with 2 loops, call it J1626
Actual Branch 1 of junction J1626 - Nucleotides 5J7L|1|DA|C|2815 to 5J7L|1|DA|G|2831, length   2
Actual Branch 2 of junction J1626 - Nucleotides 5J7L|1|DA|U|2832 to 5J7L|1|DA|A|2883, length   5
  5 Junction

2B Branch 1 of 2 of junction J1626 - Nucleotides  2815 to  2831, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|C|2815 B=5J7L|1|DA|G|2831
  7 Basepair  2815 2831 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J1626 - Nucleotides  2832 to  2883, length   5
pMakeNodes starting loop:     a=5J7L|1|DA|U|2832 B=5J7L|1|DA|A|2883
    Insertion on left  5J7L|1|DA|U|2832
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|2834 interacts with 5J7L|1|DA|A|2883
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2883 interacts with 5J7L|1|DA|G|2834
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2883 interacts with 5J7L|1|DA|G|2834
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  9 Initial   2832 (1 insertion) and 2883 (0 insertion)
 10 Basepair  2834 2883 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|U|2836 B=5J7L|1|DA|A|2882
 11 Basepair  2836 2882 UA cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  12   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2832
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: []
           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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G2812 - C2888 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 A2813 - A2887 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2814 - A2886 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 5

ans = 

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

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: 'J1626'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C2815 - A2883 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: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: '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: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2815 - G2831 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J1626'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|2832 - 5J7L|1|DA|A|2883 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: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|U|2832'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2834 - A2883 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 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2836 - A2882 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   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 hairpin at node 14
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: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J1626'
        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: 6
            RightIndex: 10
             Insertion: []
                    id: 'J1626'
        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 5J7L|1|DA|U|2832 - 5J7L|1|DA|A|2883 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_64069.1. Nodes 6 and 9 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 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 hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_64069.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.6293

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J3_65070.2, number 55 of 88
pMakeNodes starting loop:     a=7A0S|1|X|G|485 B=7A0S|1|X|C|31
  2 Basepair   485   31 GC cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|U|486 B=7A0S|1|X|G|30
pMakeNodes probed for insert:  a=7A0S|1|X|U|486 B=7A0S|1|X|G|30
pMakeNodesJunction: a=7A0S|1|X|U|486 r=7A0S|1|X|U|486 s=7A0S|1|X|C|519 t=7A0S|1|X|C|520 u=B=7A0S|1|X|G|30
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|U|486 and 7A0S|1|X|C|519 and between 7A0S|1|X|C|520 and 7A0S|1|X|G|30
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|U|486 s=7A0S|1|X|C|519 t=7A0S|1|X|C|520 B=7A0S|1|X|G|30
pMakeNodesJunction: first branch starts at   7A0S|1|X|U|486
pMakeNodesJunction: first branch ends around 7A0S|1|X|C|519
pMakeNodesJunction: second branch starts at  7A0S|1|X|C|520
pMakeNodesJunction: junction ends at         7A0S|1|X|G|30
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|A|491
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|C|519
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|C|520
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|G|30

Junction with 2 loops, call it J1189
Actual Branch 1 of junction J1189 - Nucleotides 7A0S|1|X|U|486 to 7A0S|1|X|C|519, length   8
Actual Branch 2 of junction J1189 - Nucleotides 7A0S|1|X|C|520 to 7A0S|1|X|G|30, length   2
  3 Junction

2B Branch 1 of 2 of junction J1189 - Nucleotides   486 to   519, length   8
pMakeNodes starting loop:     a=7A0S|1|X|U|486 B=7A0S|1|X|C|519
pMakeNodesProbeForInsertions:  a 7A0S|1|X|U|486 interacts with 7A0S|1|X|A|490
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|519 interacts with 7A0S|1|X|G|492
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|519 interacts with 7A0S|1|X|G|492
  4 Initial    486 (0 insertion) and  519 (0 insertion)
pMakeNodes making a cluster near strand break a=7A0S|1|X|U|486 B=7A0S|1|X|C|519
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 8 and then 9 to 9
aa is 8 bb is 9
  5 Cluster   7A0S|1|X|U|486:7A0S|1|X|G|492 7A0S|1|X|C|519:7A0S|1|X|C|519
    LR Inter  7A0S|1|X|G|492 7A0S|1|X|C|519 cWW 
    LL Inter  7A0S|1|X|U|486 7A0S|1|X|A|490 tWH 
    LL Inter  7A0S|1|X|G|487 7A0S|1|X|A|491 tSH 
    Left  strand conserved insertion 7A0S|1|X|A|488 at position 3
    Left  strand conserved insertion 7A0S|1|X|A|489 at position 4
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  6 Hairpin type *

2B Branch 2 of 2 of junction J1189 - Nucleotides   520 to    30, length   2
pMakeNodes starting loop:     a=7A0S|1|X|C|520 B=7A0S|1|X|G|30
  8 Basepair   520   30 CG cWW 
  9 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  9
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   7   Initial Left 10 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   9   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G485 - C31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 11
             Insertion: []
                    id: 'J1189'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U486 - G30 ID J1189'
              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: 9
             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 7A0S|1|X|U|486 - 7A0S|1|X|C|519 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]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAAAAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 7A0S|1|X|U|486:7A0S|1|X|G|492 and 7A0S|1|X|C|519:7A0S|1|X|C|519'
              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]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [3 4]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: '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: []
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C520 - G30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  9 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   8   Initial Left 10 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   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 7
pNextNodeJunction: Found a junction child at node 8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Finished at node 10 out of 10, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: 'J1189'
        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: []
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|486 - 7A0S|1|X|C|519 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: 9
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: 'J1189'
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Motif J3_65070.2. Nodes 4 and 8 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 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 hairpin at node 10
pNextNodeJunction: Finished at node 10 out of 10, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_65070.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0614
   -7.7355
   -7.1716

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J3_65990.1, number 56 of 88
pMakeNodes starting loop:     a=3PDR|1|X|C|54 B=3PDR|1|X|G|120
  2 Basepair    54  120 CG cWW 
No need to probe because of interaction between a=3PDR|1|X|U|55 B=3PDR|1|X|A|118
  3 Basepair    55  118 UA cWW 
pMakeNodes probe for inserts:  a=3PDR|1|X|G|56 B=3PDR|1|X|A|117
    Insertion on right 3PDR|1|X|A|117
pMakeNodes probed for insert:  a=3PDR|1|X|G|56 B=3PDR|1|X|U|116
pMakeNodesJunction: a=3PDR|1|X|G|56 r=3PDR|1|X|G|56 s=3PDR|1|X|U|85 t=3PDR|1|X|A|87 u=B=3PDR|1|X|U|116
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3PDR|1|X|G|56 and 3PDR|1|X|U|85 and between 3PDR|1|X|A|87 and 3PDR|1|X|U|116
pMakeNodesJunction: about to make a junction: a=3PDR|1|X|G|56 s=3PDR|1|X|U|85 t=3PDR|1|X|A|87 B=3PDR|1|X|U|116
pMakeNodesJunction: first branch starts at   3PDR|1|X|G|56
pMakeNodesJunction: first branch ends around 3PDR|1|X|U|85
pMakeNodesJunction: second branch starts at  3PDR|1|X|A|87
pMakeNodesJunction: junction ends at         3PDR|1|X|U|116
pMakeNodesJunction: first branch strand start goes up to  3PDR|1|X|G|56
pMakeNodesJunction: first branch strand end goes down to  3PDR|1|X|U|85
pMakeNodesJunction: second branch strand start goes up to 3PDR|1|X|G|91
pMakeNodesJunction: last strand of junction goes down to  3PDR|1|X|U|115

Junction with 2 loops, call it J4983
Actual Branch 1 of junction J4983 - Nucleotides 3PDR|1|X|G|56 to 3PDR|1|X|U|85, length   2
Actual Branch 2 of junction J4983 - Nucleotides 3PDR|1|X|A|87 to 3PDR|1|X|U|116, length   7
  4 Junction

2B Branch 1 of 2 of junction J4983 - Nucleotides    56 to    85, length   2
pMakeNodes starting loop:     a=3PDR|1|X|G|56 B=3PDR|1|X|U|85
  6 Basepair    56   85 GU cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J4983 - Nucleotides    87 to   116, length   7
pMakeNodes starting loop:     a=3PDR|1|X|A|87 B=3PDR|1|X|U|116
  9 Basepair    87  116 AU tHW 
pMakeNodes probe for inserts:  a=3PDR|1|X|A|88 B=3PDR|1|X|U|115
    Insertion on left  3PDR|1|X|A|88
    Insertion on left  3PDR|1|X|C|89
    Insertion on left  3PDR|1|X|A|90
pMakeNodesProbeForInsertions:  a 3PDR|1|X|G|91 interacts with 3PDR|1|X|U|115
pMakeNodesProbeForInsertions:  B 3PDR|1|X|U|115 interacts with 3PDR|1|X|G|91
pMakeNodesProbeForInsertions:  B 3PDR|1|X|U|115 interacts with 3PDR|1|X|G|91
pMakeNodes probed for insert:  a=3PDR|1|X|G|91 B=3PDR|1|X|U|115
 10 Basepair    91  115 GU cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 11
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 11
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3PDR|1|X|U|116
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|A|87
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|A|88
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|C|89
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 - G120 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: 'U'
           RightLetter: 'AA'
               Comment: ' // Basepair U55 - A118 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 12
             Insertion: []
                    id: 'J4983'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3PDR|1|X|U|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 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: 'J4983'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 11
             Insertion: []
                    id: 'J4983'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G56 - U116 ID J4983'
              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: '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: []
           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: 'U'
               Comment: ' // Basepair G56 - 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 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: 11
             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: []
           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: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AACA'
           RightLetter: 'U'
               Comment: ' // Basepair A87 - U116 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 12

ans = 

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

                  type: 'Fixed'
              nextnode: 13
             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 3PDR|1|X|A|87'
              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: 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 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 3PDR|1|X|A|88'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 3PDR|1|X|C|89'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

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: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G91 - U115 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   6  Junction Left  3 Right 11
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 11
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right 11
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 10
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 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 hairpin at node 19
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: 'J4983'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.0454 0.9070 0.0454 0.0023]
       rightLetterDist: [0.1667 0.5000 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: 11
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: 'J4983'
        leftLengthDist: [0.0454 0.9070 0.0454 0.0023]
        leftLetterDist: [0.1667 0.5000 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 J3_65990.1. 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
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 hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_65990.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3887

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J3_68440.1, number 57 of 88
pMakeNodes starting loop:     a=6DB9|1|R|C|9 B=6DB9|1|R|G|52
  2 Basepair     9   52 CG cWW 
No need to probe because of interaction between a=6DB9|1|R|U|10 B=6DB9|1|R|U|51
  3 Basepair    10   51 UU cWW 
pMakeNodes probe for inserts:  a=6DB9|1|R|U|11 B=6DB9|1|R|A|50
    Insertion on right 6DB9|1|R|A|50
pMakeNodes probed for insert:  a=6DB9|1|R|U|11 B=6DB9|1|R|U|49
pMakeNodesJunction: a=6DB9|1|R|U|11 r=6DB9|1|R|U|11 s=6DB9|1|R|C|31 t=6DB9|1|R|A|32 u=B=6DB9|1|R|U|49
pMakeNodesJunction: a:s count 4
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6DB9|1|R|U|11 and 6DB9|1|R|C|31 and between 6DB9|1|R|A|32 and 6DB9|1|R|U|49
pMakeNodesJunction: about to make a junction: a=6DB9|1|R|U|11 s=6DB9|1|R|C|31 t=6DB9|1|R|A|32 B=6DB9|1|R|U|49
pMakeNodesJunction: first branch starts at   6DB9|1|R|U|11
pMakeNodesJunction: first branch ends around 6DB9|1|R|C|31
pMakeNodesJunction: second branch starts at  6DB9|1|R|A|32
pMakeNodesJunction: junction ends at         6DB9|1|R|U|49
pMakeNodesJunction: first branch strand start goes up to  6DB9|1|R|A|16
pMakeNodesJunction: first branch strand end goes down to  6DB9|1|R|C|31
pMakeNodesJunction: second branch strand start goes up to 6DB9|1|R|A|32
pMakeNodesJunction: last strand of junction goes down to  6DB9|1|R|U|49

Junction with 2 loops, call it J9597
Actual Branch 1 of junction J9597 - Nucleotides 6DB9|1|R|U|11 to 6DB9|1|R|C|31, length  12
Actual Branch 2 of junction J9597 - Nucleotides 6DB9|1|R|A|32 to 6DB9|1|R|U|49, length   2
  4 Junction

2B Branch 1 of 2 of junction J9597 - Nucleotides    11 to    31, length  12
pMakeNodes starting loop:     a=6DB9|1|R|U|11 B=6DB9|1|R|C|31
pMakeNodesProbeForInsertions:  a 6DB9|1|R|U|11 interacts with 6DB9|1|R|U|20
pMakeNodesProbeForInsertions:  B 6DB9|1|R|C|31 interacts with 6DB9|1|R|G|21
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6DB9|1|R|C|31 interacts with 6DB9|1|R|G|21
  5 Initial     11 (0 insertion) and   31 (0 insertion)
pMakeNodes making a cluster near strand break a=6DB9|1|R|U|11 B=6DB9|1|R|C|31
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 13 and then 14 to 14
aa is 13 bb is 14
  6 Cluster   6DB9|1|R|U|11:6DB9|1|R|G|21 6DB9|1|R|C|31:6DB9|1|R|C|31
    LR Inter  6DB9|1|R|G|21 6DB9|1|R|C|31 cWW 
    LL Inter  6DB9|1|R|G|12 6DB9|1|R|C|19 cWW 
    LL Inter  6DB9|1|R|U|11 6DB9|1|R|U|20 cWW 
    Left  strand conserved insertion 6DB9|1|R|A|13 at position 3
    Left  strand conserved insertion 6DB9|1|R|A|14 at position 4
    Left  strand conserved insertion 6DB9|1|R|A|15 at position 5
    Left  strand conserved insertion 6DB9|1|R|A|16 at position 6
    Left  strand conserved insertion 6DB9|1|R|G|17 at position 7
    Left  strand conserved insertion 6DB9|1|R|C|18 at position 8
pMakeNodesCluster a=14 B=13 at the end
pMakeNodesCluster a=14 B=13 at the end
  7 Hairpin type *

2B Branch 2 of 2 of junction J9597 - Nucleotides    32 to    49, length   2
pMakeNodes starting loop:     a=6DB9|1|R|A|32 B=6DB9|1|R|U|49
  9 Basepair    32   49 AU cWW 
 10 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  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   6   Cluster Left  3  4  5  6  7  8  9 10 11 12 13 Right 14
pMakeMotifModelFromSSF:   7   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:   8   Initial Left 15 Right 16
pMakeMotifModelFromSSF:   9  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  10   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DB9|1|R|A|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C9 - G52 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'AU'
               Comment: ' // Basepair U10 - U51 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 17
             Insertion: []
                    id: 'J9597'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6DB9|1|R|A|50'
              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: 3
            RightIndex: 16
             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: []
           RightLetter: []
               Comment: ' // New 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: 'Junction'
              nextnode: [5 8]
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: 'J9597'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U11 - U49 ID J9597'
              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 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: 'J9597'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 6DB9|1|R|U|11 - 6DB9|1|R|C|31 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 8

ans = 

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

                  type: 'Cluster'
              nextnode: 9
             LeftIndex: [3 4 5 6 7 8 9 10 11 12 13]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAAAAGCCUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 6DB9|1|R|U|11:6DB9|1|R|G|21 and 6DB9|1|R|C|31:6DB9|1|R|C|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11]
                 Right: 1
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [3 4 5 6 7 8]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             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 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: 'J9597'
        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: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A32 - U49 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 15
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

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     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   6  Junction Left  3 Right 16
pMakeMotifModelFromSSF:   7   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   8   Cluster Left  3  4  5  6  7  8  9 10 11 12 13 Right 14
pMakeMotifModelFromSSF:   9   Initial Left 14 Right 13
pMakeMotifModelFromSSF:  10   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  11   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  12  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  13   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 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 14
             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: []
           RightLetter: []
               Comment: ' // Initial node 6DB9|1|R|U|11 - 6DB9|1|R|C|31 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: 12
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: 'J9597'
        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 J3_68440.1. Nodes 7 and 11 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 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_68440.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.6658

Timestamp 18-Jul-2025 00:13:02
pMakeSCFGModels: Making JAR3D model for motif group J3_69441.1, number 58 of 88
pMakeNodes starting loop:     a=4V9F|1|0|C|2552 B=4V9F|1|0|G|2602
  2 Basepair  2552 2602 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|C|2555 B=4V9F|1|0|A|2601
pMakeNodes probed for insert:  a=4V9F|1|0|C|2555 B=4V9F|1|0|A|2601
pMakeNodesJunction: a=4V9F|1|0|C|2555 r=4V9F|1|0|C|2555 s=4V9F|1|0|G|2580 t=4V9F|1|0|U|2581 u=B=4V9F|1|0|A|2601
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|C|2555 and 4V9F|1|0|G|2580 and between 4V9F|1|0|U|2581 and 4V9F|1|0|A|2601
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|C|2555 s=4V9F|1|0|G|2580 t=4V9F|1|0|U|2581 B=4V9F|1|0|A|2601
pMakeNodesJunction: first branch starts at   4V9F|1|0|C|2555
pMakeNodesJunction: first branch ends around 4V9F|1|0|G|2580
pMakeNodesJunction: second branch starts at  4V9F|1|0|U|2581
pMakeNodesJunction: junction ends at         4V9F|1|0|A|2601
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|C|2555
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|G|2580
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|A|2583
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|A|2596
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     1


Junction with 2 loops, call it J3403
Actual Branch 1 of junction J3403 - Nucleotides 4V9F|1|0|C|2555 to 4V9F|1|0|G|2580, length   2
Actual Branch 2 of junction J3403 - Nucleotides 4V9F|1|0|U|2581 to 4V9F|1|0|A|2601, length  10
  3 Junction

2B Branch 1 of 2 of junction J3403 - Nucleotides  2555 to  2580, length   2
pMakeNodes starting loop:     a=4V9F|1|0|C|2555 B=4V9F|1|0|G|2580
  5 Basepair  2555 2580 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J3403 - Nucleotides  2581 to  2601, length  10
pMakeNodes starting loop:     a=4V9F|1|0|U|2581 B=4V9F|1|0|A|2601
    Insertion on left  4V9F|1|0|U|2581
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|2582 interacts with 4V9F|1|0|A|2596
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2601 interacts with 4V9F|1|0|U|2597
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|2601 interacts with 4V9F|1|0|U|2597
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  7 Initial   2581 (1 insertion) and 2601 (0 insertion)
pMakeNodes making a cluster near strand break a=4V9F|1|0|G|2582 B=4V9F|1|0|A|2601
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 5 and then 8 to 13
aa is 5 bb is 8
  8 Cluster   4V9F|1|0|G|2582:4V9F|1|0|G|2582 4V9F|1|0|A|2596:4V9F|1|0|A|2601
    LR Inter  4V9F|1|0|G|2582 4V9F|1|0|A|2596 cWW 
    RR Inter  4V9F|1|0|U|2598 4V9F|1|0|A|2600 tSH 
    RR Inter  4V9F|1|0|U|2597 4V9F|1|0|A|2601 tWH 
    Right strand conserved insertion 4V9F|1|0|A|2599 at position 4
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=4V9F|1|0|A|2583 B=4V9F|1|0|U|2595
  9 Basepair  2583 2595 AU cWW 
 10 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   Cluster Left  5 Right  8  9 10 11 12 13
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|2555
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2552 - G2602 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 13
             Insertion: []
                    id: 'J3403'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C2555 - A2601 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: []
          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: '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: []
          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 C2555 - G2580 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 13
             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 4V9F|1|0|U|2581 - 4V9F|1|0|A|2601 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: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|2555'
              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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: 4

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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 10

ans = 

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

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: 5
            RightIndex: [8 9 10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'AUUAAA'
               Comment: ' // Cluster node 4V9F|1|0|G|2582:4V9F|1|0|G|2582 and 4V9F|1|0|A|2596:4V9F|1|0|A|2601'
              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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: 4

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after 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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2583 - U2595 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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
          LeftNotInter: []
         RightNotInter: []

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   Cluster Left  5 Right  8  9 10 11 12 13
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, 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: '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: []
          LeftNotInter: []
         RightNotInter: []


ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 13
             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 4V9F|1|0|U|2581 - 4V9F|1|0|A|2601 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 J3_69441.1. 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
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 2 and 12
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 12
pConservedInteractionList: did not find a substitution probability matrix for cWH  between 4 and 14
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 2 and 12
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 3 and 12
pConservedInteractionList: did not find a substitution probability matrix for cWH  between 4 and 14
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_69441.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.8991

Timestamp 18-Jul-2025 00:13:03
pMakeSCFGModels: Making JAR3D model for motif group J3_72575.1, number 59 of 88
pMakeNodes starting loop:     a=3NDB|1|M|G|145 B=3NDB|1|M|C|233
  2 Basepair   145  233 GC cWW 
No need to probe because of interaction between a=3NDB|1|M|G|146 B=3NDB|1|M|A|232
  3 Basepair   146  232 GA cWW 
pMakeNodes probe for inserts:  a=3NDB|1|M|U|147 B=3NDB|1|M|G|231
pMakeNodes probed for insert:  a=3NDB|1|M|U|147 B=3NDB|1|M|G|231
pMakeNodesJunction: a=3NDB|1|M|U|147 r=3NDB|1|M|U|147 s=3NDB|1|M|U|183 t=3NDB|1|M|U|184 u=B=3NDB|1|M|G|231
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3NDB|1|M|U|147 and 3NDB|1|M|U|183 and between 3NDB|1|M|U|184 and 3NDB|1|M|G|231
pMakeNodesJunction: about to make a junction: a=3NDB|1|M|U|147 s=3NDB|1|M|U|183 t=3NDB|1|M|U|184 B=3NDB|1|M|G|231
pMakeNodesJunction: first branch starts at   3NDB|1|M|U|147
pMakeNodesJunction: first branch ends around 3NDB|1|M|U|183
pMakeNodesJunction: second branch starts at  3NDB|1|M|U|184
pMakeNodesJunction: junction ends at         3NDB|1|M|G|231
pMakeNodesJunction: first branch strand start goes up to  3NDB|1|M|G|148
pMakeNodesJunction: first branch strand end goes down to  3NDB|1|M|C|182
pMakeNodesJunction: second branch strand start goes up to 3NDB|1|M|C|187
pMakeNodesJunction: last strand of junction goes down to  3NDB|1|M|G|231

Junction with 2 loops, call it J5852
Actual Branch 1 of junction J5852 - Nucleotides 3NDB|1|M|U|147 to 3NDB|1|M|U|183, length   4
Actual Branch 2 of junction J5852 - Nucleotides 3NDB|1|M|U|184 to 3NDB|1|M|G|231, length   5
  4 Junction

2B Branch 1 of 2 of junction J5852 - Nucleotides   147 to   183, length   4
pMakeNodes starting loop:     a=3NDB|1|M|U|147 B=3NDB|1|M|U|183
  6 Basepair   147  183 UU cWW 
No need to probe because of interaction between a=3NDB|1|M|G|148 B=3NDB|1|M|C|182
  7 Basepair   148  182 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J5852 - Nucleotides   184 to   231, length   5
pMakeNodes starting loop:     a=3NDB|1|M|U|184 B=3NDB|1|M|G|231
pMakeNodesProbeForInsertions:  a 3NDB|1|M|U|184 interacts with 3NDB|1|M|A|186
pMakeNodesProbeForInsertions:  B 3NDB|1|M|G|231 interacts with 3NDB|1|M|C|187
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3NDB|1|M|G|231 interacts with 3NDB|1|M|C|187
  9 Initial    184 (0 insertion) and  231 (0 insertion)
pMakeNodes making a cluster near strand break a=3NDB|1|M|U|184 B=3NDB|1|M|G|231
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 10 and then 11 to 11
aa is 10 bb is 11
 10 Cluster   3NDB|1|M|U|184:3NDB|1|M|C|187 3NDB|1|M|G|231:3NDB|1|M|G|231
    LR Inter  3NDB|1|M|C|187 3NDB|1|M|G|231 cWW 
    LL Inter  3NDB|1|M|U|184 3NDB|1|M|A|186 tSS 
    Left  strand conserved insertion 3NDB|1|M|U|185 at position 2
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 11
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 11
pMakeMotifModelFromSSF:  10   Cluster Left  7  8  9 10 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: []
          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: 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 G145 - C233 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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: 'A'
               Comment: ' // Basepair G146 - A232 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 9]
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U147 - G231 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: []
          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: 6
             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: []
          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: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U147 - U183 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G148 - C182 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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
          LeftNotInter: []
         RightNotInter: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 11
             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 3NDB|1|M|U|184 - 3NDB|1|M|G|231 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: 'Cluster'
              nextnode: 11
             LeftIndex: [7 8 9 10]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 3NDB|1|M|U|184:3NDB|1|M|C|187 and 3NDB|1|M|G|231:3NDB|1|M|G|231'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: 2
         RightNotInter: [1×0 double]

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             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 12

ans = 

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

                  type: 'Hairpin'
              nextnode: 13
             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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  3 Right 11
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 11
pMakeMotifModelFromSSF:  10   Cluster Left  7  8  9 10 Right 11
pMakeMotifModelFromSSF:  11   Initial Left 11 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pNextNodeJunction: Found a junction at node 4
pNextNodeJunction: Found a junction child at node 5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin
pUpdateModelWithSSF: J3_72575.1 allow insertions from initial node 11?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             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: []
          LeftNotInter: []
         RightNotInter: []


ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 11
             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 3NDB|1|M|U|184 - 3NDB|1|M|G|231 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 J3_72575.1. Nodes 5 and 9 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 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSW  between 1 and 8
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 8 and 13
pConservedInteractionList: did not find a substitution probability matrix for tSW  between 1 and 8
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 8 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_72575.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2681

Timestamp 18-Jul-2025 00:13:03
pMakeSCFGModels: Making JAR3D model for motif group J3_72804.1, number 60 of 88
pMakeNodes starting loop:     a=3IWN|1|A|G|4 B=3IWN|1|A|C|88
pMakeNodes making a cluster near strand break a=3IWN|1|A|G|4 B=3IWN|1|A|C|88
pMakeNodesCluster: amax is 5 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 16 to 16
aa is 2 bb is 16
  2 Cluster   3IWN|1|A|G|4:3IWN|1|A|A|6 3IWN|1|A|C|88:3IWN|1|A|C|88
    LR Inter  3IWN|1|A|G|4 3IWN|1|A|C|88 cWW 
    LL Inter  3IWN|1|A|G|4 3IWN|1|A|A|6 cSH 
pMakeNodesCluster a=3 B=15 at the end
pMakeNodesCluster a=3 B=15 at the end
pMakeNodes probe for inserts:  a=3IWN|1|A|A|8 B=3IWN|1|A|C|87
    Insertion on left  3IWN|1|A|A|8
    Insertion on left  3IWN|1|A|G|9
    Insertion on left  3IWN|1|A|G|10
    Insertion on right 3IWN|1|A|C|87
    Insertion on right 3IWN|1|A|A|86
  3 Initial      8 (3 insertion) and   87 (2 insertion)
pMakeNodes probed for insert:  a=3IWN|1|A|G|11 B=3IWN|1|A|U|85
pMakeNodesJunction: a=3IWN|1|A|G|11 r=3IWN|1|A|G|11 s=3IWN|1|A|C|36 t=3IWN|1|A|A|38 u=B=3IWN|1|A|U|85
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 3IWN|1|A|G|11 and 3IWN|1|A|C|36 and between 3IWN|1|A|A|38 and 3IWN|1|A|U|85
pMakeNodesJunction: about to make a junction: a=3IWN|1|A|G|11 s=3IWN|1|A|C|36 t=3IWN|1|A|A|38 B=3IWN|1|A|U|85
pMakeNodesJunction: first branch starts at   3IWN|1|A|G|11
pMakeNodesJunction: first branch ends around 3IWN|1|A|C|36
pMakeNodesJunction: second branch starts at  3IWN|1|A|A|38
pMakeNodesJunction: junction ends at         3IWN|1|A|U|85
pMakeNodesJunction: first branch strand start goes up to  3IWN|1|A|G|11
pMakeNodesJunction: first branch strand end goes down to  3IWN|1|A|C|36
pMakeNodesJunction: second branch strand start goes up to 3IWN|1|A|C|41
pMakeNodesJunction: last strand of junction goes down to  3IWN|1|A|G|83

Junction with 2 loops, call it J2238
Actual Branch 1 of junction J2238 - Nucleotides 3IWN|1|A|G|11 to 3IWN|1|A|C|36, length   2
Actual Branch 2 of junction J2238 - Nucleotides 3IWN|1|A|A|38 to 3IWN|1|A|U|85, length   6
  4 Junction

2B Branch 1 of 2 of junction J2238 - Nucleotides    11 to    36, length   2
pMakeNodes starting loop:     a=3IWN|1|A|G|11 B=3IWN|1|A|C|36
  6 Basepair    11   36 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2238 - Nucleotides    38 to    85, length   6
pMakeNodes starting loop:     a=3IWN|1|A|A|38 B=3IWN|1|A|U|85
  9 Basepair    38   85 AU tHW 
No need to probe because of interaction between a=3IWN|1|A|G|40 B=3IWN|1|A|U|84
 10 Basepair    40   84 GU cWW 
No need to probe because of interaction between a=3IWN|1|A|C|41 B=3IWN|1|A|G|83
 11 Basepair    41   83 CG cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   4  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  8 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IWN|1|A|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IWN|1|A|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IWN|1|A|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IWN|1|A|G|83
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IWN|1|A|C|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 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: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Cluster node 3IWN|1|A|G|4:3IWN|1|A|A|6 and 3IWN|1|A|C|88:3IWN|1|A|C|88'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2502
           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: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGG'
           RightLetter: 'AC'
               Comment: ' // Initial node 3IWN|1|A|A|8 - 3IWN|1|A|C|87 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: 15
             Insertion: []
                    id: 'J2238'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IWN|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: []
          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: 15
             Insertion: []
                    id: 'J2238'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: 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 3IWN|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: []
          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: 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: 7
                     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: 5
            RightIndex: 15
             Insertion: []
                    id: 'J2238'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IWN|1|A|A|8'
              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: 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: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IWN|1|A|G|83'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 12

ans = 

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

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IWN|1|A|C|41'
              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: []
          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: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 14

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J2238'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G11 - U85 ID J2238'
              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: 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: []
          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: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G11 - C36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          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: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 18

ans = 

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

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 13
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 19

ans = 

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

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A38 - U85 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 20

ans = 

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

                  type: 'Basepair'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G40 - U84 cWW '
              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: '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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C41 - G83 cWW '
              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 22

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

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  14  Junction Left  6 Right 13
pMakeMotifModelFromSSF:  15   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  16  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  17   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  18   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  19  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  20  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  21  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  22   Hairpin Left 11 Right 10
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 22
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: 16
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J2238'
        leftLengthDist: 1
        leftLetterDist: []
       rightLengthDist: [0.0454 0.9070 0.0454 0.0023]
       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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

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

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: 'J2238'
        leftLengthDist: [0.0454 0.9070 0.0454 0.0023]
        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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Motif J3_72804.1. Nodes 15 and 18 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 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 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_72804.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.1214

Timestamp 18-Jul-2025 00:13:04
pMakeSCFGModels: Making JAR3D model for motif group J3_75187.1, number 61 of 88
pMakeNodes starting loop:     a=3PDR|1|X|G|43 B=3PDR|1|X|C|142
  2 Basepair    43  142 GC cWW 
No need to probe because of interaction between a=3PDR|1|X|A|44 B=3PDR|1|X|G|141
  3 Basepair    44  141 AG cWW 
No need to probe because of interaction between a=3PDR|1|X|G|45 B=3PDR|1|X|U|140
  4 Basepair    45  140 GU tSH 
pMakeNodes probe for inserts:  a=3PDR|1|X|A|46 B=3PDR|1|X|A|139
    Insertion on left  3PDR|1|X|A|46
    Insertion on left  3PDR|1|X|U|47
    Insertion on right 3PDR|1|X|A|139
    Insertion on right 3PDR|1|X|U|138
pMakeNodes probed for insert:  a=3PDR|1|X|C|49 B=3PDR|1|X|C|137
pMakeNodesJunction: a=3PDR|1|X|C|49 r=3PDR|1|X|C|49 s=3PDR|1|X|U|125 t=3PDR|1|X|G|126 u=B=3PDR|1|X|C|137
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3PDR|1|X|C|49 and 3PDR|1|X|U|125 and between 3PDR|1|X|G|126 and 3PDR|1|X|C|137
pMakeNodesJunction: about to make a junction: a=3PDR|1|X|C|49 s=3PDR|1|X|U|125 t=3PDR|1|X|G|126 B=3PDR|1|X|C|137
pMakeNodesJunction: first branch starts at   3PDR|1|X|C|49
pMakeNodesJunction: first branch ends around 3PDR|1|X|U|125
pMakeNodesJunction: second branch starts at  3PDR|1|X|G|126
pMakeNodesJunction: junction ends at         3PDR|1|X|C|137
pMakeNodesJunction: first branch strand start goes up to  3PDR|1|X|G|50
pMakeNodesJunction: first branch strand end goes down to  3PDR|1|X|C|124
pMakeNodesJunction: second branch strand start goes up to 3PDR|1|X|G|126
pMakeNodesJunction: last strand of junction goes down to  3PDR|1|X|C|137

Junction with 2 loops, call it J7512
Actual Branch 1 of junction J7512 - Nucleotides 3PDR|1|X|C|49 to 3PDR|1|X|U|125, length   4
Actual Branch 2 of junction J7512 - Nucleotides 3PDR|1|X|G|126 to 3PDR|1|X|C|137, length   2
  5 Junction

2B Branch 1 of 2 of junction J7512 - Nucleotides    49 to   125, length   4
pMakeNodes starting loop:     a=3PDR|1|X|C|49 B=3PDR|1|X|U|125
  7 Basepair    49  125 CU tHS 
No need to probe because of interaction between a=3PDR|1|X|G|50 B=3PDR|1|X|C|124
  8 Basepair    50  124 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J7512 - Nucleotides   126 to   137, length   2
pMakeNodes starting loop:     a=3PDR|1|X|G|126 B=3PDR|1|X|C|137
 11 Basepair   126  137 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  10   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|A|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|U|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3PDR|1|X|U|138
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3PDR|1|X|C|137
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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 G43 - C142 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A44 - G141 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'UAU'
               Comment: ' // Basepair G45 - U140 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 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J7512'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3PDR|1|X|A|46'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: 'J7512'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3PDR|1|X|U|47'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3PDR|1|X|U|138'
              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 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: 'J7512'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3PDR|1|X|C|137'
              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: 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 13

ans = 

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

                  type: 'Junction'
              nextnode: [6 10]
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J7512'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C49 - C137 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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: '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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C49 - U125 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: 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 G50 - C124 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
            RightIndex: 11
             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 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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G126 - C137 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  13  Junction Left  6 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  19  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  20   Hairpin Left 11 Right 10
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 20
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: 15
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J7512'
        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: 10
            RightIndex: 11
             Insertion: []
                    id: 'J7512'
        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 J3_75187.1. Nodes 14 and 18 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 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 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_75187.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.0148

Timestamp 18-Jul-2025 00:13:04
pMakeSCFGModels: Making JAR3D model for motif group J3_79305.1, number 62 of 88
pMakeNodes starting loop:     a=6CZR|1|1a|G|1157 B=6CZR|1|1a|C|1144
pMakeNodes making a cluster near strand break a=6CZR|1|1a|G|1157 B=6CZR|1|1a|C|1144
pMakeNodesCluster: amax is 8 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 8 and then 14 to 19
aa is 8 bb is 14
  2 Cluster   6CZR|1|1a|G|1157:6CZR|1|1a|G|1164 6CZR|1|1a|G|1139:6CZR|1|1a|C|1144
    LR Inter  6CZR|1|1a|A|1161 6CZR|1|1a|G|1139 tWS 
    LR Inter  6CZR|1|1a|G|1160 6CZR|1|1a|A|1140 tSW 
    LR Inter  6CZR|1|1a|A|1158 6CZR|1|1a|G|1143 cWW 
    LR Inter  6CZR|1|1a|G|1164 6CZR|1|1a|G|1143 cWH 
    LR Inter  6CZR|1|1a|G|1157 6CZR|1|1a|C|1144 cWW 
    LL Inter  6CZR|1|1a|G|1159 6CZR|1|1a|G|1163 tWH 
    RR Inter  6CZR|1|1a|U|1142 6CZR|1|1a|C|1144 cSH 
    Left  strand conserved insertion 6CZR|1|1a|A|1162 at position 6
    Right strand conserved insertion 6CZR|1|1a|C|1141 at position 3
pMakeNodesCluster a=9 B=13 at the end
pMakeNodesCluster a=9 B=13 at the end
pMakeNodes probe for inserts:  a=6CZR|1|1a|G|1166 B=6CZR|1|1a|G|1138
  3 Initial   1166 (0 insertion) and 1138 (0 insertion)
pMakeNodes probed for insert:  a=6CZR|1|1a|G|1166 B=6CZR|1|1a|G|1138
pMakeNodesJunction: a=6CZR|1|1a|G|1166 r=6CZR|1|1a|G|1166 s=6CZR|1|1a|C|1099 t=6CZR|1|1a|G|1100 u=B=6CZR|1|1a|G|1138
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6CZR|1|1a|G|1166 and 6CZR|1|1a|C|1099 and between 6CZR|1|1a|G|1100 and 6CZR|1|1a|G|1138
pMakeNodesJunction: about to make a junction: a=6CZR|1|1a|G|1166 s=6CZR|1|1a|C|1099 t=6CZR|1|1a|G|1100 B=6CZR|1|1a|G|1138
pMakeNodesJunction: first branch starts at   6CZR|1|1a|G|1166
pMakeNodesJunction: first branch ends around 6CZR|1|1a|C|1099
pMakeNodesJunction: second branch starts at  6CZR|1|1a|G|1100
pMakeNodesJunction: junction ends at         6CZR|1|1a|G|1138
pMakeNodesJunction: first branch strand start goes up to  6CZR|1|1a|G|1166
pMakeNodesJunction: first branch strand end goes down to  6CZR|1|1a|C|1099
pMakeNodesJunction: second branch strand start goes up to 6CZR|1|1a|C|1101
pMakeNodesJunction: last strand of junction goes down to  6CZR|1|1a|G|1138

Junction with 2 loops, call it J2550
Actual Branch 1 of junction J2550 - Nucleotides 6CZR|1|1a|G|1166 to 6CZR|1|1a|C|1099, length   2
Actual Branch 2 of junction J2550 - Nucleotides 6CZR|1|1a|G|1100 to 6CZR|1|1a|G|1138, length   3
  4 Junction

2B Branch 1 of 2 of junction J2550 - Nucleotides  1166 to  1099, length   2
pMakeNodes starting loop:     a=6CZR|1|1a|G|1166 B=6CZR|1|1a|C|1099
  6 Basepair  1166 1099 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2550 - Nucleotides  1100 to  1138, length   3
pMakeNodes starting loop:     a=6CZR|1|1a|G|1100 B=6CZR|1|1a|G|1138
    Insertion on left  6CZR|1|1a|G|1100
pMakeNodesProbeForInsertions:  a 6CZR|1|1a|C|1101 interacts with 6CZR|1|1a|G|1138
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|G|1138 interacts with 6CZR|1|1a|C|1101
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|G|1138 interacts with 6CZR|1|1a|C|1101
  8 Initial   1100 (1 insertion) and 1138 (0 insertion)
  9 Basepair  1101 1138 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8 Right 14 15 16 17 18 19
pMakeMotifModelFromSSF:   3   Initial Left  9 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  9 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  9 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  10   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|G|1157
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 0 0 0 0 0 0 0 1 1 1 1 1 0 0 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 3 4 5 6 7 8]
            RightIndex: [14 15 16 17 18 19]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAGGAAGG'
           RightLetter: 'GACUGC'
               Comment: ' // Cluster node 6CZR|1|1a|G|1157:6CZR|1|1a|G|1164 and 6CZR|1|1a|G|1139:6CZR|1|1a|C|1144'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: [1 2 3 4 5 6]
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
          LeftNotInter: 6
         RightNotInter: 3
              NormCons: 0.0873
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             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: []
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|G|1166 - 6CZR|1|1a|G|1138 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: 9
            RightIndex: 13
             Insertion: []
                    id: 'J2550'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1166 - G1138 ID J2550'
              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: 9
            RightIndex: 10
             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: []
          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: 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 G1166 - C1099 cWW '
              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: 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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J2550'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|G|1100 - 6CZR|1|1a|G|1138 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: 'Fixed'
              nextnode: 10
             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 6CZR|1|1a|G|1157'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             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: [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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             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 C1101 - G1138 cWW '
              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: 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8 Right 14 15 16 17 18 19
pMakeMotifModelFromSSF:   3   Initial Left  9 Right 13
pMakeMotifModelFromSSF:   4  Junction Left  9 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  9 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 13
pMakeMotifModelFromSSF:   9     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  12   Hairpin Left 13 Right 12
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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J2550'
        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: 11
            RightIndex: 13
             Insertion: []
                    id: 'J2550'
        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 6CZR|1|1a|G|1100 - 6CZR|1|1a|G|1138 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 J3_79305.1. Nodes 5 and 8 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 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 hairpin at node 12
pNextNodeJunction: Finished at node 12 out of 12, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_79305.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1205

Timestamp 18-Jul-2025 00:13:05
pMakeSCFGModels: Making JAR3D model for motif group J3_82061.2, number 63 of 88
pMakeNodes starting loop:     a=5T5A|1|A|C|13 B=5T5A|1|A|G|48
  2 Basepair    13   48 CG cWW 
pMakeNodes probe for inserts:  a=5T5A|1|A|C|14 B=5T5A|1|A|G|46
    Insertion on left  5T5A|1|A|C|14
    Insertion on left  5T5A|1|A|A|15
pMakeNodes probed for insert:  a=5T5A|1|A|G|16 B=5T5A|1|A|G|46
pMakeNodesJunction: a=5T5A|1|A|G|16 r=5T5A|1|A|G|16 s=5T5A|1|A|C|34 t=5T5A|1|A|C|35 u=B=5T5A|1|A|G|46
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5T5A|1|A|G|16 and 5T5A|1|A|C|34 and between 5T5A|1|A|C|35 and 5T5A|1|A|G|46
pMakeNodesJunction: about to make a junction: a=5T5A|1|A|G|16 s=5T5A|1|A|C|34 t=5T5A|1|A|C|35 B=5T5A|1|A|G|46
pMakeNodesJunction: first branch starts at   5T5A|1|A|G|16
pMakeNodesJunction: first branch ends around 5T5A|1|A|C|34
pMakeNodesJunction: second branch starts at  5T5A|1|A|C|35
pMakeNodesJunction: junction ends at         5T5A|1|A|G|46
pMakeNodesJunction: first branch strand start goes up to  5T5A|1|A|G|16
pMakeNodesJunction: first branch strand end goes down to  5T5A|1|A|C|34
pMakeNodesJunction: second branch strand start goes up to 5T5A|1|A|C|35
pMakeNodesJunction: last strand of junction goes down to  5T5A|1|A|G|46

Junction with 2 loops, call it J5059
Actual Branch 1 of junction J5059 - Nucleotides 5T5A|1|A|G|16 to 5T5A|1|A|C|34, length   2
Actual Branch 2 of junction J5059 - Nucleotides 5T5A|1|A|C|35 to 5T5A|1|A|G|46, length   2
  3 Junction

2B Branch 1 of 2 of junction J5059 - Nucleotides    16 to    34, length   2
pMakeNodes starting loop:     a=5T5A|1|A|G|16 B=5T5A|1|A|C|34
  5 Basepair    16   34 GC cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J5059 - Nucleotides    35 to    46, length   2
pMakeNodes starting loop:     a=5T5A|1|A|C|35 B=5T5A|1|A|G|46
  8 Basepair    35   46 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Junction Left  4 Right  7
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  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T5A|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T5A|1|A|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: [0.0082 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: 'CCA'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G48 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
             Insertion: []
                    id: 'J5059'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5T5A|1|A|C|14'
              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: 7
             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: []
                  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: 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 5T5A|1|A|A|15'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 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: 7
             Insertion: []
                    id: 'J5059'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G16 - G46 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 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: '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 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G16 - C34 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 7
             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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C35 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 13

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     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Junction Left  4 Right  7
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  7
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, 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: 'J5059'
        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: 7
             Insertion: []
                    id: 'J5059'
        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 J3_82061.2. 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
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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_82061.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9256
   -9.1070
   -6.9789

Timestamp 18-Jul-2025 00:13:05
pMakeSCFGModels: Making JAR3D model for motif group J3_82365.1, number 64 of 88
pMakeNodes starting loop:     a=4V88|1|A6|G|1386 B=4V88|1|A6|C|1338
  2 Basepair  1386 1338 GC cWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|G|1387 B=4V88|1|A6|A|1337
    Insertion on left  4V88|1|A6|G|1387
    Insertion on left  4V88|1|A6|A|1388
    Insertion on right 4V88|1|A6|A|1337
pMakeNodes probed for insert:  a=4V88|1|A6|C|1389 B=4V88|1|A6|A|1336
pMakeNodesJunction: a=4V88|1|A6|C|1389 r=4V88|1|A6|C|1389 s=4V88|1|A6|G|1412 t=4V88|1|A6|U|1413 u=B=4V88|1|A6|A|1336
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|C|1389 and 4V88|1|A6|G|1412 and between 4V88|1|A6|U|1413 and 4V88|1|A6|A|1336
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|C|1389 s=4V88|1|A6|G|1412 t=4V88|1|A6|U|1413 B=4V88|1|A6|A|1336
pMakeNodesJunction: first branch starts at   4V88|1|A6|C|1389
pMakeNodesJunction: first branch ends around 4V88|1|A6|G|1412
pMakeNodesJunction: second branch starts at  4V88|1|A6|U|1413
pMakeNodesJunction: junction ends at         4V88|1|A6|A|1336
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|C|1389
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|G|1412
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|U|1415
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|A|1336

Junction with 2 loops, call it J6990
Actual Branch 1 of junction J6990 - Nucleotides 4V88|1|A6|C|1389 to 4V88|1|A6|G|1412, length   2
Actual Branch 2 of junction J6990 - Nucleotides 4V88|1|A6|U|1413 to 4V88|1|A6|A|1336, length   3
  3 Junction

2B Branch 1 of 2 of junction J6990 - Nucleotides  1389 to  1412, length   2
pMakeNodes starting loop:     a=4V88|1|A6|C|1389 B=4V88|1|A6|G|1412
  5 Basepair  1389 1412 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J6990 - Nucleotides  1413 to  1336, length   3
pMakeNodes starting loop:     a=4V88|1|A6|U|1413 B=4V88|1|A6|A|1336
    Insertion on left  4V88|1|A6|U|1413
pMakeNodesProbeForInsertions:  a 4V88|1|A6|U|1415 interacts with 4V88|1|A6|A|1336
pMakeNodesProbeForInsertions:  B 4V88|1|A6|A|1336 interacts with 4V88|1|A6|U|1415
pMakeNodesProbeForInsertions:  B 4V88|1|A6|A|1336 interacts with 4V88|1|A6|U|1415
  7 Initial   1413 (1 insertion) and 1336 (0 insertion)
  8 Basepair  1415 1336 UA cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Junction Left  4 Right  8
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  8
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1337
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|C|1338
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V88|1|A6|U|1413
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1388
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0082 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 G1386 - C1338 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
             Insertion: []
                    id: 'J6990'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1337'
              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: 9
             Insertion: []
                    id: 'J6990'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 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 4V88|1|A6|C|1338'
              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: 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 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: '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 4V88|1|A6|U|1413'
              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: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              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: 8
             Insertion: []
                    id: 'J6990'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1389 - A1336 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 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: '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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1389 - G1412 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 8
             Insertion: []
                    id: 'J6990'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|U|1413 - 4V88|1|A6|A|1336 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: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V88|1|A6|A|1388'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1415 - A1336 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   9  Junction Left  4 Right  8
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  8
pMakeMotifModelFromSSF:  14     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  15   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J6990'
        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: 14
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: 'J6990'
        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: 'U'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|U|1413 - 4V88|1|A6|A|1336 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_82365.1. 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
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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_82365.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9822
   -7.6785
   -8.4819

Timestamp 18-Jul-2025 00:13:06
pMakeSCFGModels: Making JAR3D model for motif group J3_82572.1, number 65 of 88
pMakeNodes starting loop:     a=4LFB|1|A|C|990 B=4LFB|1|A|G|1215
  2 Basepair   990 1215 CG cWW 
No need to probe because of interaction between a=4LFB|1|A|U|991 B=4LFB|1|A|A|1213
  3 Basepair   991 1213 UA tWH 
pMakeNodes probe for inserts:  a=4LFB|1|A|U|992 B=4LFB|1|A|U|1211
    Insertion on left  4LFB|1|A|U|992
pMakeNodes probed for insert:  a=4LFB|1|A|G|993 B=4LFB|1|A|U|1211
pMakeNodesJunction: a=4LFB|1|A|G|993 r=4LFB|1|A|G|993 s=4LFB|1|A|C|1045 t=4LFB|1|A|A|1046 u=B=4LFB|1|A|U|1211
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|G|993 and 4LFB|1|A|C|1045 and between 4LFB|1|A|A|1046 and 4LFB|1|A|U|1211
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|G|993 s=4LFB|1|A|C|1045 t=4LFB|1|A|A|1046 B=4LFB|1|A|U|1211
pMakeNodesJunction: first branch starts at   4LFB|1|A|G|993
pMakeNodesJunction: first branch ends around 4LFB|1|A|C|1045
pMakeNodesJunction: second branch starts at  4LFB|1|A|A|1046
pMakeNodesJunction: junction ends at         4LFB|1|A|U|1211
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|G|993
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|C|1045
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|G|1047
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|C|1210

Junction with 2 loops, call it J8909
Actual Branch 1 of junction J8909 - Nucleotides 4LFB|1|A|G|993 to 4LFB|1|A|C|1045, length   2
Actual Branch 2 of junction J8909 - Nucleotides 4LFB|1|A|A|1046 to 4LFB|1|A|U|1211, length   4
  4 Junction

2B Branch 1 of 2 of junction J8909 - Nucleotides   993 to  1045, length   2
pMakeNodes starting loop:     a=4LFB|1|A|G|993 B=4LFB|1|A|C|1045
  6 Basepair   993 1045 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J8909 - Nucleotides  1046 to  1211, length   4
pMakeNodes starting loop:     a=4LFB|1|A|A|1046 B=4LFB|1|A|U|1211
  9 Basepair  1046 1211 AU tHS 
No need to probe because of interaction between a=4LFB|1|A|G|1047 B=4LFB|1|A|C|1210
 10 Basepair  1047 1210 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  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  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|992
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C990 - G1215 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: 'A'
               Comment: ' // Basepair U991 - A1213 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: '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 4LFB|1|A|U|992'
              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: 9
             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 6

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: 'J8909'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G993 - U1211 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 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: '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 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 G993 - C1045 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 6
            RightIndex: 9
             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 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1046 - U1211 tHS '
              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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1047 - C1210 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6  Junction Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a 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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J8909'
        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: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: 'J8909'
        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 J3_82572.1. Nodes 7 and 10 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 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 hairpin at node 13
pNextNodeJunction: Finished at node 13 out of 13, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWW  between 6 and 10
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 6 and 10
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_82572.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8829
   -7.8829

Timestamp 18-Jul-2025 00:13:06
pMakeSCFGModels: Making JAR3D model for motif group J3_83516.1, number 66 of 88
pMakeNodes starting loop:     a=4LFB|1|A|G|973 B=4LFB|1|A|C|962
  2 Basepair   973  962 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|974 B=4LFB|1|A|U|961
    Insertion on left  4LFB|1|A|A|974
    Insertion on left  4LFB|1|A|A|977
    Insertion on left  4LFB|1|A|C|979
    Insertion on left  4LFB|1|A|C|980
    Insertion on left  4LFB|1|A|U|981
    Insertion on left  4LFB|1|A|U|982
    Insertion on left  4LFB|1|A|A|983
    Insertion on right 4LFB|1|A|U|961
pMakeNodes probed for insert:  a=4LFB|1|A|C|984 B=4LFB|1|A|U|960
pMakeNodesJunction: a=4LFB|1|A|C|984 r=4LFB|1|A|C|984 s=4LFB|1|A|G|1221 t=4LFB|1|A|G|1222 u=B=4LFB|1|A|U|960
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4LFB|1|A|C|984 and 4LFB|1|A|G|1221 and between 4LFB|1|A|G|1222 and 4LFB|1|A|U|960
pMakeNodesJunction: about to make a junction: a=4LFB|1|A|C|984 s=4LFB|1|A|G|1221 t=4LFB|1|A|G|1222 B=4LFB|1|A|U|960
pMakeNodesJunction: first branch starts at   4LFB|1|A|C|984
pMakeNodesJunction: first branch ends around 4LFB|1|A|G|1221
pMakeNodesJunction: second branch starts at  4LFB|1|A|G|1222
pMakeNodesJunction: junction ends at         4LFB|1|A|U|960
pMakeNodesJunction: first branch strand start goes up to  4LFB|1|A|C|984
pMakeNodesJunction: first branch strand end goes down to  4LFB|1|A|G|1221
pMakeNodesJunction: second branch strand start goes up to 4LFB|1|A|A|1225
pMakeNodesJunction: last strand of junction goes down to  4LFB|1|A|U|955
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J9592
Actual Branch 1 of junction J9592 - Nucleotides 4LFB|1|A|C|984 to 4LFB|1|A|G|1221, length   2
Actual Branch 2 of junction J9592 - Nucleotides 4LFB|1|A|G|1222 to 4LFB|1|A|U|960, length  10
  3 Junction

2B Branch 1 of 2 of junction J9592 - Nucleotides   984 to  1221, length   2
pMakeNodes starting loop:     a=4LFB|1|A|C|984 B=4LFB|1|A|G|1221
  5 Basepair   984 1221 CG cWW 
  6 Hairpin type *

2B Branch 2 of 2 of junction J9592 - Nucleotides  1222 to   960, length  10
pMakeNodes starting loop:     a=4LFB|1|A|G|1222 B=4LFB|1|A|U|960
    Insertion on left  4LFB|1|A|G|1222
    Insertion on left  4LFB|1|A|C|1223
    Insertion on left  4LFB|1|A|G|1224
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|1225 interacts with 4LFB|1|A|U|955
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|960 interacts with 4LFB|1|A|U|956
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|960 interacts with 4LFB|1|A|U|956
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  7 Initial   1222 (3 insertion) and  960 (0 insertion)
pMakeNodes making a cluster near strand break a=4LFB|1|A|A|1225 B=4LFB|1|A|U|960
pMakeNodesCluster: amax is 14 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 14 to 14 and then 15 to 20
aa is 14 bb is 15
  8 Cluster   4LFB|1|A|A|1225:4LFB|1|A|A|1225 4LFB|1|A|U|955:4LFB|1|A|U|960
    LR Inter  4LFB|1|A|A|1225 4LFB|1|A|U|955 cWW 
    RR Inter  4LFB|1|A|U|957 4LFB|1|A|A|959 tSH 
    RR Inter  4LFB|1|A|U|956 4LFB|1|A|U|960 tWW 
    Right strand conserved insertion 4LFB|1|A|A|958 at position 4
pMakeNodesCluster a=15 B=14 at the end
pMakeNodesCluster a=15 B=14 at the end
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Junction Left  9 Right 20
pMakeMotifModelFromSSF:   4   Initial Left  9 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:   7   Initial Left 11 Right 20
pMakeMotifModelFromSSF:   8   Cluster Left 14 Right 15 16 17 18 19 20
pMakeMotifModelFromSSF:   9   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|956
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|957
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|958
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|959
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|960
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|961
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|962
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|1221
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|975
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|976
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|977
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: []
          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: 22
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAACCUUA'
           RightLetter: 'UC'
               Comment: ' // Basepair G973 - C962 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 21
             Insertion: []
                    id: 'J9592'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|956'
              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: 21
             Insertion: []
                    id: 'J9592'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            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|U|957'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            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: 10
                     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: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 21
             Insertion: []
                    id: 'J9592'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|958'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             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: 'A'
           RightLetter: 'UUUAAU'
               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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: 4

Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|959'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|960'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  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: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|961'
              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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               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: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|962'
              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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      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: 21
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|1221'
              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: 9
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      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: 'Junction'
              nextnode: [4 7]
             LeftIndex: 9
            RightIndex: 20
             Insertion: []
                    id: 'J9592'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C984 - U960 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: []
          LeftNotInter: []
         RightNotInter: []

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: '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: []
          LeftNotInter: []
         RightNotInter: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C984 - G1221 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 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
          LeftNotInter: []
         RightNotInter: []

Node 23

ans = 

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

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 20
             Insertion: []
                    id: 'J9592'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCG'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1222 - 4LFB|1|A|U|960 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 24

ans = 

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

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|975'
              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 25

ans = 

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

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 12
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 26

ans = 

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

                  type: 'Fixed'
              nextnode: 27
             LeftIndex: 12
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|976'
              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 27

ans = 

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

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 13
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 28

ans = 

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

                  type: 'Fixed'
              nextnode: 29
             LeftIndex: 13
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|977'
              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 29

ans = 

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

                  type: 'Initial'
              nextnode: 30
             LeftIndex: 14
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 30

ans = 

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

                  type: 'Cluster'
              nextnode: 31
             LeftIndex: 14
            RightIndex: [15 16 17 18 19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UUUAAU'
               Comment: ' // Cluster node 4LFB|1|A|A|1225:4LFB|1|A|A|1225 and 4LFB|1|A|U|955:4LFB|1|A|U|960'
              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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: 4

Node 31

ans = 

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

                  type: 'Initial'
              nextnode: 32
             LeftIndex: 15
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 32

ans = 

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

                  type: 'Hairpin'
              nextnode: 34
             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 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 21
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 21
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 21
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 21
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 21
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 21
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 21
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 21
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 21
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 21
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 21
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 21
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 21
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 21
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 21
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 20
pMakeMotifModelFromSSF:  19  Junction Left  9 Right 20
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 20
pMakeMotifModelFromSSF:  24     Fixed Left 11 Right 20
pMakeMotifModelFromSSF:  25   Initial Left 12 Right 20
pMakeMotifModelFromSSF:  26     Fixed Left 12 Right 20
pMakeMotifModelFromSSF:  27   Initial Left 13 Right 20
pMakeMotifModelFromSSF:  28     Fixed Left 13 Right 20
pMakeMotifModelFromSSF:  29   Initial Left 14 Right 20
pMakeMotifModelFromSSF:  30   Cluster Left 14 Right 15 16 17 18 19 20
pMakeMotifModelFromSSF:  31   Initial Left 15 Right 14
pMakeMotifModelFromSSF:  32   Hairpin Left 15 Right 14
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 32
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin
pUpdateModelWithSSF: J3_83516.1 allow insertions from initial node 31?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J9592'
        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: []
          LeftNotInter: []
         RightNotInter: []


ans = 

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

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 20
             Insertion: []
                    id: 'J9592'
        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: 'GCG'
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1222 - 4LFB|1|A|U|960 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 J3_83516.1. 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 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 32
pNextNodeJunction: Finished at node 32 out of 32, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 10 and 19
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 10 and 19
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_83516.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.1163
  -14.1163
  -15.6094

Timestamp 18-Jul-2025 00:13:07
pMakeSCFGModels: Making JAR3D model for motif group J3_84189.2, number 67 of 88
pMakeNodes starting loop:     a=7A0S|1|X|C|1621 B=7A0S|1|X|G|1322
  2 Basepair  1621 1322 CG cWW 
No need to probe because of interaction between a=7A0S|1|X|G|1622 B=7A0S|1|X|A|1321
pMakeNodes making a cluster near strand break a=7A0S|1|X|G|1622 B=7A0S|1|X|A|1321
pMakeNodesCluster: amax is 5 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 12 to 12
aa is 4 bb is 12
  3 Cluster   7A0S|1|X|G|1622:7A0S|1|X|A|1624 7A0S|1|X|A|1321:7A0S|1|X|A|1321
    LR Inter  7A0S|1|X|G|1622 7A0S|1|X|A|1321 tSH 
    LR Inter  7A0S|1|X|A|1624 7A0S|1|X|A|1321 tWW 
    Left  strand conserved insertion 7A0S|1|X|C|1623 at position 2
pMakeNodesCluster a=5 B=11 at the end
pMakeNodesCluster a=5 B=11 at the end
pMakeNodes probe for inserts:  a=7A0S|1|X|A|1626 B=7A0S|1|X|A|1320
    Insertion on left  7A0S|1|X|A|1626
    Insertion on right 7A0S|1|X|A|1320
  4 Initial   1626 (1 insertion) and 1320 (1 insertion)
pMakeNodes probed for insert:  a=7A0S|1|X|C|1627 B=7A0S|1|X|C|1319
pMakeNodesJunction: a=7A0S|1|X|C|1627 r=7A0S|1|X|C|1627 s=7A0S|1|X|G|1636 t=7A0S|1|X|U|1637 u=B=7A0S|1|X|C|1319
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 7A0S|1|X|C|1627 and 7A0S|1|X|G|1636 and between 7A0S|1|X|U|1637 and 7A0S|1|X|C|1319
pMakeNodesJunction: about to make a junction: a=7A0S|1|X|C|1627 s=7A0S|1|X|G|1636 t=7A0S|1|X|U|1637 B=7A0S|1|X|C|1319
pMakeNodesJunction: first branch starts at   7A0S|1|X|C|1627
pMakeNodesJunction: first branch ends around 7A0S|1|X|G|1636
pMakeNodesJunction: second branch starts at  7A0S|1|X|U|1637
pMakeNodesJunction: junction ends at         7A0S|1|X|C|1319
pMakeNodesJunction: first branch strand start goes up to  7A0S|1|X|C|1627
pMakeNodesJunction: first branch strand end goes down to  7A0S|1|X|G|1636
pMakeNodesJunction: second branch strand start goes up to 7A0S|1|X|G|1638
pMakeNodesJunction: last strand of junction goes down to  7A0S|1|X|C|1319

Junction with 2 loops, call it J5472
Actual Branch 1 of junction J5472 - Nucleotides 7A0S|1|X|C|1627 to 7A0S|1|X|G|1636, length   2
Actual Branch 2 of junction J5472 - Nucleotides 7A0S|1|X|U|1637 to 7A0S|1|X|C|1319, length   3
  5 Junction

2B Branch 1 of 2 of junction J5472 - Nucleotides  1627 to  1636, length   2
pMakeNodes starting loop:     a=7A0S|1|X|C|1627 B=7A0S|1|X|G|1636
  7 Basepair  1627 1636 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J5472 - Nucleotides  1637 to  1319, length   3
pMakeNodes starting loop:     a=7A0S|1|X|U|1637 B=7A0S|1|X|C|1319
    Insertion on left  7A0S|1|X|U|1637
pMakeNodesProbeForInsertions:  a 7A0S|1|X|G|1638 interacts with 7A0S|1|X|C|1319
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|1319 interacts with 7A0S|1|X|G|1638
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|1319 interacts with 7A0S|1|X|G|1638
  9 Initial   1637 (1 insertion) and 1319 (0 insertion)
 10 Basepair  1638 1319 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|C|1621
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|1627
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|1624
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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1621 - G1322 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|X|G|1622:7A0S|1|X|A|1624 and 7A0S|1|X|A|1321:7A0S|1|X|A|1321'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2635
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Initial node 7A0S|1|X|A|1626 - 7A0S|1|X|A|1320 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: 5
            RightIndex: 11
             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 7A0S|1|X|C|1621'
              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: 6
            RightIndex: 11
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7A0S|1|X|C|1627'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     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: 'Junction'
              nextnode: [6 9]
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J5472'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C1627 - C1319 ID J5472'
              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: '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: []
          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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1627 - G1636 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 10
             Insertion: []
                    id: 'J5472'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|1637 - 7A0S|1|X|C|1319 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: 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 7A0S|1|X|A|1624'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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 G1638 - C1319 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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: [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  3  4 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   9  Junction Left  6 Right 10
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 10
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   Hairpin Left 10 Right  9
pNextNodeJunction: Found a 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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: 'J5472'
        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: []
          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: 10
             Insertion: []
                    id: 'J5472'
        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: 'U'
           RightLetter: []
               Comment: ' // Initial node 7A0S|1|X|U|1637 - 7A0S|1|X|C|1319 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 J3_84189.2. 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
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

pConservedInteractionList: did not find a substitution probability matrix for tHH  between 3 and 9
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 4 and 8
pConservedInteractionList: did not find a substitution probability matrix for tHH  between 3 and 9
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 4 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_84189.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9732
  -12.3085
   -7.9732

Timestamp 18-Jul-2025 00:13:08
pMakeSCFGModels: Making JAR3D model for motif group J3_84625.1, number 68 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|G|70 B=5J7L|1|DA|C|57
  2 Basepair    70   57 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|71 B=5J7L|1|DA|A|56
    Insertion on left  5J7L|1|DA|A|71
    Insertion on left  5J7L|1|DA|U|72
    Insertion on left  5J7L|1|DA|A|73
pMakeNodes probed for insert:  a=5J7L|1|DA|G|75 B=5J7L|1|DA|A|56
pMakeNodesJunction: a=5J7L|1|DA|G|75 r=5J7L|1|DA|G|75 s=5J7L|1|DA|A|111 t=5J7L|1|DA|U|112 u=B=5J7L|1|DA|A|56
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|G|75 and 5J7L|1|DA|A|111 and between 5J7L|1|DA|U|112 and 5J7L|1|DA|A|56
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|G|75 s=5J7L|1|DA|A|111 t=5J7L|1|DA|U|112 B=5J7L|1|DA|A|56
pMakeNodesJunction: first branch starts at   5J7L|1|DA|G|75
pMakeNodesJunction: first branch ends around 5J7L|1|DA|A|111
pMakeNodesJunction: second branch starts at  5J7L|1|DA|U|112
pMakeNodesJunction: junction ends at         5J7L|1|DA|A|56
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|C|76
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|G|110
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|U|114
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|A|56

Junction with 2 loops, call it J1386
Actual Branch 1 of junction J1386 - Nucleotides 5J7L|1|DA|G|75 to 5J7L|1|DA|A|111, length   4
Actual Branch 2 of junction J1386 - Nucleotides 5J7L|1|DA|U|112 to 5J7L|1|DA|A|56, length   4
  3 Junction

2B Branch 1 of 2 of junction J1386 - Nucleotides    75 to   111, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|G|75 B=5J7L|1|DA|A|111
  5 Basepair    75  111 GA cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|76 B=5J7L|1|DA|G|110
  6 Basepair    76  110 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1386 - Nucleotides   112 to    56, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|U|112 B=5J7L|1|DA|A|56
    Insertion on left  5J7L|1|DA|U|112
    Insertion on left  5J7L|1|DA|U|113
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|U|114 interacts with 5J7L|1|DA|A|56
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|56 interacts with 5J7L|1|DA|U|114
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|56 interacts with 5J7L|1|DA|U|114
  8 Initial    112 (2 insertion) and   56 (0 insertion)
  9 Basepair   114   56 UA cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  5 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|71
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|76
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|110
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 1 1 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: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUA'
           RightLetter: 'C'
               Comment: ' // Basepair G70 - 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: []
              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: '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 5J7L|1|DA|C|57'
              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: '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: []
                  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 5J7L|1|DA|G|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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|71'
              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: 5
            RightIndex: 12
             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: 'UU'
           RightLetter: []
               Comment: ' // New 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: 5
            RightIndex: 12
             Insertion: []
                    id: 'J1386'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G75 - A56 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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             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 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             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 G75 - A111 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 C76 - 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 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 12
             Insertion: []
                    id: 'J1386'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|112 - 5J7L|1|DA|A|56 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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|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: []

Node 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             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 17

ans = 

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

                  type: 'Fixed'
              nextnode: 18
             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 5J7L|1|DA|G|110'
              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: 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: []
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Node 19

ans = 

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

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 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: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U114 - A56 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  16   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  20   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 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

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J1386'
        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: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: 'J1386'
        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 5J7L|1|DA|U|112 - 5J7L|1|DA|A|56 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_84625.1. Nodes 10 and 14 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_84625.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2692
   -8.2692

Timestamp 18-Jul-2025 00:13:08
pMakeSCFGModels: Making JAR3D model for motif group J3_85054.2, number 69 of 88
pMakeNodes starting loop:     a=4WF9|1|X|C|1342 B=4WF9|1|X|G|1667
  2 Basepair  1342 1667 CG cWW 
No need to probe because of interaction between a=4WF9|1|X|U|1343 B=4WF9|1|X|A|1666
  3 Basepair  1343 1666 UA tSH 
No need to probe because of interaction between a=4WF9|1|X|A|1344 B=4WF9|1|X|U|1665
  4 Basepair  1344 1665 AU cWS 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|1345 B=4WF9|1|X|G|1664
pMakeNodes probed for insert:  a=4WF9|1|X|A|1345 B=4WF9|1|X|G|1664
pMakeNodesJunction: a=4WF9|1|X|A|1345 r=4WF9|1|X|A|1345 s=4WF9|1|X|G|1650 t=4WF9|1|X|C|1651 u=B=4WF9|1|X|G|1664
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|A|1345 and 4WF9|1|X|G|1650 and between 4WF9|1|X|C|1651 and 4WF9|1|X|G|1664
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|A|1345 s=4WF9|1|X|G|1650 t=4WF9|1|X|C|1651 B=4WF9|1|X|G|1664
pMakeNodesJunction: first branch starts at   4WF9|1|X|A|1345
pMakeNodesJunction: first branch ends around 4WF9|1|X|G|1650
pMakeNodesJunction: second branch starts at  4WF9|1|X|C|1651
pMakeNodesJunction: junction ends at         4WF9|1|X|G|1664
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|1346
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|C|1649
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|C|1655
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|G|1664

Junction with 2 loops, call it J1492
Actual Branch 1 of junction J1492 - Nucleotides 4WF9|1|X|A|1345 to 4WF9|1|X|G|1650, length   4
Actual Branch 2 of junction J1492 - Nucleotides 4WF9|1|X|C|1651 to 4WF9|1|X|G|1664, length   4
  5 Junction

2B Branch 1 of 2 of junction J1492 - Nucleotides  1345 to  1650, length   4
pMakeNodes starting loop:     a=4WF9|1|X|A|1345 B=4WF9|1|X|G|1650
  7 Basepair  1345 1650 AG tHS 
No need to probe because of interaction between a=4WF9|1|X|G|1346 B=4WF9|1|X|C|1649
  8 Basepair  1346 1649 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J1492 - Nucleotides  1651 to  1664, length   4
pMakeNodes starting loop:     a=4WF9|1|X|C|1651 B=4WF9|1|X|G|1664
    Insertion on left  4WF9|1|X|C|1651
    Insertion on left  4WF9|1|X|A|1652
pMakeNodesProbeForInsertions:  a 4WF9|1|X|C|1655 interacts with 4WF9|1|X|G|1664
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1664 interacts with 4WF9|1|X|C|1655
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1664 interacts with 4WF9|1|X|C|1655
 10 Initial   1651 (2 insertion) and 1664 (0 insertion)
 11 Basepair  1655 1664 CG cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|1651
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|1652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C1342 - G1667 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 U1343 - A1666 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 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1344 - U1665 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Junction'
              nextnode: [6 10]
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J1492'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1345 - G1664 ID J1492'
              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: 4
            RightIndex: 7
             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: []
                  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: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1345 - G1650 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: 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 G1346 - C1649 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1492'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|C|1651 - 4WF9|1|X|G|1664 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: 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 4WF9|1|X|C|1651'
              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: 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 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             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 4WF9|1|X|A|1652'
              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: 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 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1655 - G1664 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  14   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   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 hairpin at node 16
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: 4
            RightIndex: 7
             Insertion: []
                    id: 'J1492'
        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: 11
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: 'J1492'
        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: 'CA'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|C|1651 - 4WF9|1|X|G|1664 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_85054.2. Nodes 6 and 10 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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWW  between 9 and 12
pConservedInteractionList: did not find a substitution probability matrix for tWW  between 9 and 12
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_85054.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.3697
   -9.0748
   -9.0748
  -10.5197

Timestamp 18-Jul-2025 00:13:09
pMakeSCFGModels: Making JAR3D model for motif group J3_86907.1, number 70 of 88
pMakeNodes starting loop:     a=6CZR|1|1a|G|951 B=6CZR|1|1a|C|940
  2 Basepair   951  940 GC cWW 
pMakeNodes probe for inserts:  a=6CZR|1|1a|A|952 B=6CZR|1|1a|U|939
    Insertion on left  6CZR|1|1a|A|952
    Insertion on left  6CZR|1|1a|A|955
    Insertion on left  6CZR|1|1a|C|957
    Insertion on left  6CZR|1|1a|C|958
    Insertion on left  6CZR|1|1a|U|959
    Insertion on left  6CZR|1|1a|U|960
    Insertion on left  6CZR|1|1a|A|961
    Insertion on right 6CZR|1|1a|U|939
pMakeNodes probed for insert:  a=6CZR|1|1a|C|962 B=6CZR|1|1a|U|938
pMakeNodesJunction: a=6CZR|1|1a|C|962 r=6CZR|1|1a|C|962 s=6CZR|1|1a|G|1203 t=6CZR|1|1a|G|1204 u=B=6CZR|1|1a|U|938
pMakeNodesJunction: a:s count 4
pMakeNodesJunction: t:B count 4
pMakeNodesJunction: Found nested interactions between 6CZR|1|1a|C|962 and 6CZR|1|1a|G|1203 and between 6CZR|1|1a|G|1204 and 6CZR|1|1a|U|938
pMakeNodesJunction: about to make a junction: a=6CZR|1|1a|C|962 s=6CZR|1|1a|G|1203 t=6CZR|1|1a|G|1204 B=6CZR|1|1a|U|938
pMakeNodesJunction: first branch starts at   6CZR|1|1a|C|962
pMakeNodesJunction: first branch ends around 6CZR|1|1a|G|1203
pMakeNodesJunction: second branch starts at  6CZR|1|1a|G|1204
pMakeNodesJunction: junction ends at         6CZR|1|1a|U|938
pMakeNodesJunction: first branch strand start goes up to  6CZR|1|1a|C|963
pMakeNodesJunction: first branch strand end goes down to  6CZR|1|1a|G|1202
pMakeNodesJunction: second branch strand start goes up to 6CZR|1|1a|C|1208
pMakeNodesJunction: last strand of junction goes down to  6CZR|1|1a|U|933
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     0     0     1


Junction with 2 loops, call it J2575
Actual Branch 1 of junction J2575 - Nucleotides 6CZR|1|1a|C|962 to 6CZR|1|1a|G|1203, length   4
Actual Branch 2 of junction J2575 - Nucleotides 6CZR|1|1a|G|1204 to 6CZR|1|1a|U|938, length  12
  3 Junction

2B Branch 1 of 2 of junction J2575 - Nucleotides   962 to  1203, length   4
pMakeNodes starting loop:     a=6CZR|1|1a|C|962 B=6CZR|1|1a|G|1203
  5 Basepair   962 1203 CG cWW 
No need to probe because of interaction between a=6CZR|1|1a|C|963 B=6CZR|1|1a|G|1202
  6 Basepair   963 1202 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2575 - Nucleotides  1204 to   938, length  12
pMakeNodes starting loop:     a=6CZR|1|1a|G|1204 B=6CZR|1|1a|U|938
    Insertion on left  6CZR|1|1a|G|1204
    Insertion on left  6CZR|1|1a|C|1205
    Insertion on left  6CZR|1|1a|G|1206
pMakeNodesProbeForInsertions:  a 6CZR|1|1a|A|1207 interacts with 6CZR|1|1a|U|933
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|U|938 interacts with 6CZR|1|1a|U|934
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|U|938 interacts with 6CZR|1|1a|U|934
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  8 Initial   1204 (3 insertion) and  938 (0 insertion)
pMakeNodes making a cluster near strand break a=6CZR|1|1a|A|1207 B=6CZR|1|1a|U|938
pMakeNodesCluster: amax is 17 bmin is 18, use_amax is 1
pMakeNodesCluster: Cluster goes from 16 to 16 and then 19 to 24
aa is 16 bb is 19
  9 Cluster   6CZR|1|1a|A|1207:6CZR|1|1a|A|1207 6CZR|1|1a|U|933:6CZR|1|1a|U|938
    LR Inter  6CZR|1|1a|A|1207 6CZR|1|1a|U|933 cWW 
    RR Inter  6CZR|1|1a|U|935 6CZR|1|1a|A|937 tSH 
    RR Inter  6CZR|1|1a|U|934 6CZR|1|1a|U|938 tSW 
    Right strand conserved insertion 6CZR|1|1a|A|936 at position 4
pMakeNodesCluster a=17 B=18 at the end
pMakeNodesCluster a=17 B=18 at the end
No need to probe because of interaction between a=6CZR|1|1a|C|1208 B=6CZR|1|1a|G|932
 10 Basepair  1208  932 CG cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 26
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 26
pMakeMotifModelFromSSF:   3  Junction Left  9 Right 24
pMakeMotifModelFromSSF:   4   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   7   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:   8   Initial Left 13 Right 24
pMakeMotifModelFromSSF:   9   Cluster Left 16 Right 19 20 21 22 23 24
pMakeMotifModelFromSSF:  10  Basepair Left 17 Right 18
pMakeMotifModelFromSSF:  11   Hairpin Left 18 Right 17
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|U|933
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|U|934
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|U|935
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|A|936
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|A|937
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|U|938
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|U|939
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6CZR|1|1a|G|1204
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|G|954
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|A|955
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6CZR|1|1a|A|956
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 26
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [26×26 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 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: 26
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAACCUUA'
           RightLetter: 'UC'
               Comment: ' // Basepair G951 - C940 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 25
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|U|933'
              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: 25
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            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 6CZR|1|1a|U|934'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            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: '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: []
          LeftNotInter: []
         RightNotInter: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            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 6CZR|1|1a|U|935'
              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
          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: 25
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GCG'
           RightLetter: []
               Comment: ' // New 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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            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 6CZR|1|1a|A|936'
              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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: [1×0 double]
         RightNotInter: 4

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            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: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            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 6CZR|1|1a|A|937'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            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: [5×5 double]
                     Z: []
           MiddleIndex: 18
                     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 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            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 6CZR|1|1a|U|938'
              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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            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: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            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 6CZR|1|1a|U|939'
              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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            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: []
              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: 25
             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 6CZR|1|1a|G|1204'
              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: 9
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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: 'Junction'
              nextnode: [4 8]
             LeftIndex: 9
            RightIndex: 24
             Insertion: []
                    id: 'J2575'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C962 - U938 ID J2575'
              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 20

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 12
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 21

ans = 

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

                  type: 'Basepair'
              nextnode: 22
             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: 'G'
               Comment: ' // Basepair C962 - G1203 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C963 - G1202 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 23

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: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: []
         RightNotInter: []

Node 24

ans = 

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

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 13
            RightIndex: 24
             Insertion: []
                    id: 'J2575'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCG'
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|G|1204 - 6CZR|1|1a|U|938 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 25

ans = 

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

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 13
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|G|954'
              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 26

ans = 

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

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 14
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 27

ans = 

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

                  type: 'Fixed'
              nextnode: 28
             LeftIndex: 14
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|955'
              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 28

ans = 

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

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 15
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 29

ans = 

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

                  type: 'Fixed'
              nextnode: 30
             LeftIndex: 15
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|956'
              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 30

ans = 

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

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 16
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 31

ans = 

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

                  type: 'Cluster'
              nextnode: 32
             LeftIndex: 16
            RightIndex: [19 20 21 22 23 24]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UUUAAU'
               Comment: ' // Cluster node 6CZR|1|1a|A|1207:6CZR|1|1a|A|1207 and 6CZR|1|1a|U|933:6CZR|1|1a|U|938'
              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 5 6]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1
          LeftNotInter: [1×0 double]
         RightNotInter: 4

Node 32

ans = 

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

                  type: 'Initial'
              nextnode: 33
             LeftIndex: 17
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after 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 33

ans = 

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

                  type: 'Basepair'
              nextnode: 34
             LeftIndex: 17
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1208 - G932 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 34

ans = 

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

                  type: 'Hairpin'
              nextnode: 36
             LeftIndex: 18
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 18
                     P: [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 26
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 26
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 25
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 25
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 25
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 25
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 25
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 25
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 25
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 25
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 25
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 25
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 25
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 25
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 25
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 25
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 25
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 24
pMakeMotifModelFromSSF:  19  Junction Left  9 Right 24
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  22  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  23   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  24   Initial Left 13 Right 24
pMakeMotifModelFromSSF:  25     Fixed Left 13 Right 24
pMakeMotifModelFromSSF:  26   Initial Left 14 Right 24
pMakeMotifModelFromSSF:  27     Fixed Left 14 Right 24
pMakeMotifModelFromSSF:  28   Initial Left 15 Right 24
pMakeMotifModelFromSSF:  29     Fixed Left 15 Right 24
pMakeMotifModelFromSSF:  30   Initial Left 16 Right 24
pMakeMotifModelFromSSF:  31   Cluster Left 16 Right 19 20 21 22 23 24
pMakeMotifModelFromSSF:  32   Initial Left 17 Right 18
pMakeMotifModelFromSSF:  33  Basepair Left 17 Right 18
pMakeMotifModelFromSSF:  34   Hairpin Left 18 Right 17
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 34
pNextNodeJunction: Finished at node 34 out of 34, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 12
             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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []


ans = 

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

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 13
            RightIndex: 24
             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: 'GCG'
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|G|1204 - 6CZR|1|1a|U|938 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 J3_86907.1. Nodes 20 and 24 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 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a junction child at node 24
pNextNodeJunction: Found a hairpin at node 34
pNextNodeJunction: Finished at node 34 out of 34, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tSS  between 12 and 23
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 12 and 23
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_86907.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -17.9597

Timestamp 18-Jul-2025 00:13:10
pMakeSCFGModels: Making JAR3D model for motif group J3_89044.1, number 71 of 88
pMakeNodes starting loop:     a=4R4V|1|A|C|610 B=4R4V|1|A|G|775
  2 Basepair   610  775 CG cWW 
No need to probe because of interaction between a=4R4V|1|A|G|611 B=4R4V|1|A|A|774
  3 Basepair   611  774 GA cSW 
pMakeNodes probe for inserts:  a=4R4V|1|A|C|612 B=4R4V|1|A|G|773
    Insertion on left  4R4V|1|A|C|612
pMakeNodes probed for insert:  a=4R4V|1|A|A|613 B=4R4V|1|A|G|773
pMakeNodesJunction: a=4R4V|1|A|A|613 r=4R4V|1|A|A|613 s=4R4V|1|A|A|645 t=4R4V|1|A|G|646 u=B=4R4V|1|A|G|773
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4R4V|1|A|A|613 and 4R4V|1|A|A|645 and between 4R4V|1|A|G|646 and 4R4V|1|A|G|773
pMakeNodesJunction: about to make a junction: a=4R4V|1|A|A|613 s=4R4V|1|A|A|645 t=4R4V|1|A|G|646 B=4R4V|1|A|G|773
pMakeNodesJunction: first branch starts at   4R4V|1|A|A|613
pMakeNodesJunction: first branch ends around 4R4V|1|A|A|645
pMakeNodesJunction: second branch starts at  4R4V|1|A|G|646
pMakeNodesJunction: junction ends at         4R4V|1|A|G|773
pMakeNodesJunction: first branch strand start goes up to  4R4V|1|A|C|616
pMakeNodesJunction: first branch strand end goes down to  4R4V|1|A|G|643
pMakeNodesJunction: second branch strand start goes up to 4R4V|1|A|G|646
pMakeNodesJunction: last strand of junction goes down to  4R4V|1|A|C|772
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     0


Junction with 2 loops, call it J8407
Actual Branch 1 of junction J8407 - Nucleotides 4R4V|1|A|A|613 to 4R4V|1|A|A|645, length   7
Actual Branch 2 of junction J8407 - Nucleotides 4R4V|1|A|G|646 to 4R4V|1|A|G|773, length   3
  4 Junction

2B Branch 1 of 2 of junction J8407 - Nucleotides   613 to   645, length   7
pMakeNodes starting loop:     a=4R4V|1|A|A|613 B=4R4V|1|A|A|645
  6 Basepair   613  645 AA cSW 
No need to probe because of interaction between a=4R4V|1|A|A|614 B=4R4V|1|A|U|644
  7 Basepair   614  644 AU cHW 
pMakeNodes probe for inserts:  a=4R4V|1|A|U|615 B=4R4V|1|A|G|643
    Insertion on left  4R4V|1|A|U|615
pMakeNodesProbeForInsertions:  a 4R4V|1|A|C|616 interacts with 4R4V|1|A|G|643
pMakeNodesProbeForInsertions:  B 4R4V|1|A|G|643 interacts with 4R4V|1|A|C|616
pMakeNodesProbeForInsertions:  B 4R4V|1|A|G|643 interacts with 4R4V|1|A|C|616
pMakeNodes probed for insert:  a=4R4V|1|A|C|616 B=4R4V|1|A|G|643
  8 Basepair   616  643 CG cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J8407 - Nucleotides   646 to   773, length   3
pMakeNodes starting loop:     a=4R4V|1|A|G|646 B=4R4V|1|A|G|773
    Insertion on right 4R4V|1|A|G|773
pMakeNodesProbeForInsertions:  a 4R4V|1|A|G|646 interacts with 4R4V|1|A|C|772
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|772 interacts with 4R4V|1|A|G|646
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|772 interacts with 4R4V|1|A|G|646
 10 Initial    646 (0 insertion) and  773 (1 insertion)
 11 Basepair   646  772 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  10   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|C|612
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|U|615
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4R4V|1|A|G|773
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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C610 - G775 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: 'GC'
           RightLetter: 'A'
               Comment: ' // Basepair G611 - A774 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: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|C|612'
              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: 13
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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 10]
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: 'J8407'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A613 - G773 ID J8407'
              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: 10
             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: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 A613 - A645 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 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'U'
               Comment: ' // Basepair A614 - U644 cHW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 6
            RightIndex: 8
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|U|615'
              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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C616 - G643 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J8407'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'G'
               Comment: ' // Initial node 4R4V|1|A|G|646 - 4R4V|1|A|G|773 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: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4R4V|1|A|G|773'
              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: 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 17

ans = 

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

                  type: 'Basepair'
              nextnode: 18
             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 G646 - C772 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 21
             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  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   6  Junction Left  4 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  14   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  15     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  16   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  17  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  18   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 6
pNextNodeJunction: Found a junction child at node 7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             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: []
              NormCons: []


ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 11
            RightIndex: 13
             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: []
           RightLetter: 'G'
               Comment: ' // Initial node 4R4V|1|A|G|646 - 4R4V|1|A|G|773 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_89044.1. Nodes 7 and 14 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 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cWW  between 5 and 13
pConservedInteractionList: did not find a substitution probability matrix for cWW  between 5 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_89044.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8314

Timestamp 18-Jul-2025 00:13:10
pMakeSCFGModels: Making JAR3D model for motif group J3_89368.2, number 72 of 88
pMakeNodes starting loop:     a=5J7L|1|DA|G|2223 B=5J7L|1|DA|C|2200
  2 Basepair  2223 2200 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|2224 B=5J7L|1|DA|A|2199
  3 Basepair  2224 2199 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|2225 B=5J7L|1|DA|U|2197
  4 Basepair  2225 2197 AU tHW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2226 B=5J7L|1|DA|C|2196
    Insertion on left  5J7L|1|DA|C|2226
pMakeNodes probed for insert:  a=5J7L|1|DA|A|2227 B=5J7L|1|DA|C|2196
pMakeNodesJunction: a=5J7L|1|DA|A|2227 r=5J7L|1|DA|A|2227 s=5J7L|1|DA|U|2092 t=5J7L|1|DA|G|2093 u=B=5J7L|1|DA|C|2196
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5J7L|1|DA|A|2227 and 5J7L|1|DA|U|2092 and between 5J7L|1|DA|G|2093 and 5J7L|1|DA|C|2196
pMakeNodesJunction: about to make a junction: a=5J7L|1|DA|A|2227 s=5J7L|1|DA|U|2092 t=5J7L|1|DA|G|2093 B=5J7L|1|DA|C|2196
pMakeNodesJunction: first branch starts at   5J7L|1|DA|A|2227
pMakeNodesJunction: first branch ends around 5J7L|1|DA|U|2092
pMakeNodesJunction: second branch starts at  5J7L|1|DA|G|2093
pMakeNodesJunction: junction ends at         5J7L|1|DA|C|2196
pMakeNodesJunction: first branch strand start goes up to  5J7L|1|DA|G|2228
pMakeNodesJunction: first branch strand end goes down to  5J7L|1|DA|C|2091
pMakeNodesJunction: second branch strand start goes up to 5J7L|1|DA|G|2093
pMakeNodesJunction: last strand of junction goes down to  5J7L|1|DA|C|2196

Junction with 2 loops, call it J2542
Actual Branch 1 of junction J2542 - Nucleotides 5J7L|1|DA|A|2227 to 5J7L|1|DA|U|2092, length   4
Actual Branch 2 of junction J2542 - Nucleotides 5J7L|1|DA|G|2093 to 5J7L|1|DA|C|2196, length   2
  5 Junction

2B Branch 1 of 2 of junction J2542 - Nucleotides  2227 to  2092, length   4
pMakeNodes starting loop:     a=5J7L|1|DA|A|2227 B=5J7L|1|DA|U|2092
  7 Basepair  2227 2092 AU tHH 
No need to probe because of interaction between a=5J7L|1|DA|G|2228 B=5J7L|1|DA|C|2091
  8 Basepair  2228 2091 GC cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J2542 - Nucleotides  2093 to  2196, length   2
pMakeNodes starting loop:     a=5J7L|1|DA|G|2093 B=5J7L|1|DA|C|2196
 11 Basepair  2093 2196 GC cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  10   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   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|C|2196
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G2223 - C2200 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2224 - A2199 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 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: 'U'
               Comment: ' // Basepair A2225 - U2197 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 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: '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 5J7L|1|DA|C|2196'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 10
             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: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Junction'
              nextnode: [6 10]
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: 'J2542'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A2227 - C2196 ID J2542'
              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: 5
            RightIndex: 8
             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: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2227 - U2092 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: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2228 - C2091 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: '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: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2093 - C2196 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: [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  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   7  Junction Left  5 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
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 hairpin at node 14
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: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J2542'
        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: 13
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: 'J2542'
        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 J3_89368.2. Nodes 8 and 12 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 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

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_89368.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1631
   -6.4218
   -6.3368

Timestamp 18-Jul-2025 00:13:11
pMakeSCFGModels: Making JAR3D model for motif group J3_89737.1, number 73 of 88
pMakeNodes starting loop:     a=4V9F|1|9|C|9 B=4V9F|1|9|G|114
  2 Basepair     9  114 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|9|C|10 B=4V9F|1|9|U|112
    Insertion on left  4V9F|1|9|C|10
pMakeNodes probed for insert:  a=4V9F|1|9|A|11 B=4V9F|1|9|U|112
pMakeNodesJunction: a=4V9F|1|9|A|11 r=4V9F|1|9|A|11 s=4V9F|1|9|G|68 t=4V9F|1|9|U|69 u=B=4V9F|1|9|U|112
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|9|A|11 and 4V9F|1|9|G|68 and between 4V9F|1|9|U|69 and 4V9F|1|9|U|112
pMakeNodesJunction: about to make a junction: a=4V9F|1|9|A|11 s=4V9F|1|9|G|68 t=4V9F|1|9|U|69 B=4V9F|1|9|U|112
pMakeNodesJunction: first branch starts at   4V9F|1|9|A|11
pMakeNodesJunction: first branch ends around 4V9F|1|9|G|68
pMakeNodesJunction: second branch starts at  4V9F|1|9|U|69
pMakeNodesJunction: junction ends at         4V9F|1|9|U|112
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|9|G|14
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|9|C|67
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|9|C|71
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|9|G|110

Junction with 2 loops, call it J8142
Actual Branch 1 of junction J8142 - Nucleotides 4V9F|1|9|A|11 to 4V9F|1|9|G|68, length   5
Actual Branch 2 of junction J8142 - Nucleotides 4V9F|1|9|U|69 to 4V9F|1|9|U|112, length   6
  3 Junction

2B Branch 1 of 2 of junction J8142 - Nucleotides    11 to    68, length   5
pMakeNodes starting loop:     a=4V9F|1|9|A|11 B=4V9F|1|9|G|68
  5 Basepair    11   68 AG tSS 
pMakeNodes probe for inserts:  a=4V9F|1|9|A|13 B=4V9F|1|9|C|67
    Insertion on left  4V9F|1|9|A|13
pMakeNodesProbeForInsertions:  a 4V9F|1|9|G|14 interacts with 4V9F|1|9|C|67
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|67 interacts with 4V9F|1|9|G|14
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|67 interacts with 4V9F|1|9|G|14
pMakeNodes probed for insert:  a=4V9F|1|9|G|14 B=4V9F|1|9|C|67
  6 Basepair    14   67 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J8142 - Nucleotides    69 to   112, length   6
pMakeNodes starting loop:     a=4V9F|1|9|U|69 B=4V9F|1|9|U|112
  9 Basepair    69  112 UU cWW 
No need to probe because of interaction between a=4V9F|1|9|U|70 B=4V9F|1|9|U|111
 10 Basepair    70  111 UU cWW 
No need to probe because of interaction between a=4V9F|1|9|C|71 B=4V9F|1|9|G|110
 11 Basepair    71  110 CG cWW 
 12 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  7
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  8 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
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 4V9F|1|9|C|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|9|C|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 1 1 1 0 0 1 1 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: 'CC'
           RightLetter: 'G'
               Comment: ' // Basepair C9 - G114 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: '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 4V9F|1|9|C|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
              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: '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: []

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: 'J8142'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A11 - U112 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: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: '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: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'G'
               Comment: ' // Basepair A11 - G68 tSS '
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 6
             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 4V9F|1|9|C|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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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 G14 - C67 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 13
             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: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U69 - U112 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U70 - U111 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 15

ans = 

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

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C71 - 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 16

ans = 

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

                  type: 'Hairpin'
              nextnode: 19
             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  3 Right 13
pMakeMotifModelFromSSF:   5  Junction Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  6
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  8 Right 13
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   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 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 16
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: 7
             Insertion: []
                    id: 'J8142'
        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: 8
            RightIndex: 13
             Insertion: []
                    id: 'J8142'
        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 J3_89737.1. Nodes 6 and 12 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 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_89737.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8695

Timestamp 18-Jul-2025 00:13:11
pMakeSCFGModels: Making JAR3D model for motif group J3_90256.1, number 74 of 88
pMakeNodes starting loop:     a=6JQ6|1|U|G|69 B=6JQ6|1|U|C|68||||11_555
pMakeNodes making a cluster near strand break a=6JQ6|1|U|G|69 B=6JQ6|1|U|C|68||||11_555
pMakeNodesCluster: amax is 6 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 16 to 17
aa is 5 bb is 16
  2 Cluster   6JQ6|1|U|G|69:6JQ6|1|U|A|74||A 6JQ6|1|U|A|67||||11_555:6JQ6|1|U|C|68||||11_555
    LR Inter  6JQ6|1|U|U|70 6JQ6|1|U|A|67||||11_555 cWW 
    LR Inter  6JQ6|1|U|A|74||A 6JQ6|1|U|A|67||||11_555 cWS 
    LR Inter  6JQ6|1|U|G|69 6JQ6|1|U|C|68||||11_555 cWW 
    LR Inter  6JQ6|1|U|A|73 6JQ6|1|U|C|68||||11_555 cWS 
    Left  strand conserved insertion 6JQ6|1|U|A|72 at position 3
pMakeNodesCluster a=6 B=15 at the end
pMakeNodesCluster a=6 B=15 at the end
pMakeNodes probe for inserts:  a=6JQ6|1|U|A|75 B=6JQ6|1|U|G|66||||11_555
    Insertion on right 6JQ6|1|U|G|66||||11_555
    Insertion on right 6JQ6|1|U|A|65||||11_555
  3 Initial     75 (0 insertion) and   66 (2 insertion)
pMakeNodes probed for insert:  a=6JQ6|1|U|A|75 B=6JQ6|1|U|C|64||||11_555
pMakeNodesJunction: a=6JQ6|1|U|A|75 r=6JQ6|1|U|A|75 s=6JQ6|1|U|G|29||||11_555 t=6JQ6|1|U|G|30||||11_555 u=B=6JQ6|1|U|C|64||||11_555
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6JQ6|1|U|A|75 and 6JQ6|1|U|G|29||||11_555 and between 6JQ6|1|U|G|30||||11_555 and 6JQ6|1|U|C|64||||11_555
pMakeNodesJunction: about to make a junction: a=6JQ6|1|U|A|75 s=6JQ6|1|U|G|29||||11_555 t=6JQ6|1|U|G|30||||11_555 B=6JQ6|1|U|C|64||||11_555
pMakeNodesJunction: first branch starts at   6JQ6|1|U|A|75
pMakeNodesJunction: first branch ends around 6JQ6|1|U|G|29||||11_555
pMakeNodesJunction: second branch starts at  6JQ6|1|U|G|30||||11_555
pMakeNodesJunction: junction ends at         6JQ6|1|U|C|64||||11_555
pMakeNodesJunction: first branch strand start goes up to  6JQ6|1|U|C|77
pMakeNodesJunction: first branch strand end goes down to  6JQ6|1|U|G|27||||11_555
pMakeNodesJunction: second branch strand start goes up to 6JQ6|1|U|G|31||||11_555
pMakeNodesJunction: last strand of junction goes down to  6JQ6|1|U|C|64||||11_555

Junction with 2 loops, call it J2435
Actual Branch 1 of junction J2435 - Nucleotides 6JQ6|1|U|A|75 to 6JQ6|1|U|G|29||||11_555, length   5
Actual Branch 2 of junction J2435 - Nucleotides 6JQ6|1|U|G|30||||11_555 to 6JQ6|1|U|C|64||||11_555, length   3
  4 Junction

2B Branch 1 of 2 of junction J2435 - Nucleotides    75 to    29, length   5
pMakeNodes starting loop:     a=6JQ6|1|U|A|75 B=6JQ6|1|U|G|29||||11_555
  6 Basepair    75   29 AG tHS 
pMakeNodes probe for inserts:  a=6JQ6|1|U|C|77 B=6JQ6|1|U|U|28||||11_555
    Insertion on right 6JQ6|1|U|U|28||||11_555
pMakeNodesProbeForInsertions:  a 6JQ6|1|U|C|77 interacts with 6JQ6|1|U|G|27||||11_555
pMakeNodesProbeForInsertions:  B 6JQ6|1|U|G|27||||11_555 interacts with 6JQ6|1|U|C|77
pMakeNodesProbeForInsertions:  B 6JQ6|1|U|G|27||||11_555 interacts with 6JQ6|1|U|C|77
pMakeNodes probed for insert:  a=6JQ6|1|U|C|77 B=6JQ6|1|U|G|27||||11_555
  7 Basepair    77   27 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J2435 - Nucleotides    30 to    64, length   3
pMakeNodes starting loop:     a=6JQ6|1|U|G|30||||11_555 B=6JQ6|1|U|C|64||||11_555
    Insertion on left  6JQ6|1|U|G|30||||11_555
pMakeNodesProbeForInsertions:  a 6JQ6|1|U|G|31||||11_555 interacts with 6JQ6|1|U|C|64||||11_555
pMakeNodesProbeForInsertions:  B 6JQ6|1|U|C|64||||11_555 interacts with 6JQ6|1|U|G|31||||11_555
pMakeNodesProbeForInsertions:  B 6JQ6|1|U|C|64||||11_555 interacts with 6JQ6|1|U|G|31||||11_555
  9 Initial     30 (1 insertion) and   64 (0 insertion)
 10 Basepair    31   64 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 16 17
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 15
pMakeMotifModelFromSSF:   4  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  11   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ6|1|U|A|73
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ6|1|U|A|72
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ6|1|U|A|67||||11_555
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ6|1|U|G|69
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           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 3 4 5]
            RightIndex: [16 17]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUAAA'
           RightLetter: 'AC'
               Comment: ' // Cluster node 6JQ6|1|U|G|69:6JQ6|1|U|A|74||A and 6JQ6|1|U|A|67||||11_555:6JQ6|1|U|C|68||||11_555'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0625
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'AG'
               Comment: ' // Initial node 6JQ6|1|U|A|75 - 6JQ6|1|U|G|66||||11_555 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: 6
            RightIndex: 15
             Insertion: []
                    id: 'J2435'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JQ6|1|U|A|73'
              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: 6
            RightIndex: 14
             Insertion: []
                    id: 'J2435'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: 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 6JQ6|1|U|A|72'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           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: 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: '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: 'Junction'
              nextnode: [5 9]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J2435'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A75 - C64 ID J2435'
              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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'UG'
               Comment: ' // Basepair A75 - G29 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JQ6|1|U|A|67||||11_555'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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 C77 - G27 cWW '
              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 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

Node 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J2435'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6JQ6|1|U|G|30||||11_555 - 6JQ6|1|U|C|64||||11_555 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 16

ans = 

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

                  type: 'Fixed'
              nextnode: 17
             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 6JQ6|1|U|G|69'
              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: 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: []
          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: 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 G31 - C64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          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: 21
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 16 17
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   6     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   8  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right  9
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 11 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  17   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  18  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  19   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 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
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: 6
            RightIndex: 10
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []


ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J2435'
        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 6JQ6|1|U|G|30||||11_555 - 6JQ6|1|U|C|64||||11_555 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 J3_90256.1. Nodes 9 and 15 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 14
pNextNodeJunction: Found a junction child at node 15
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Finished at node 19 out of 19, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_90256.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.0711
  -11.0711

Timestamp 18-Jul-2025 00:13:12
pMakeSCFGModels: Making JAR3D model for motif group J3_90744.1, number 75 of 88
pMakeNodes starting loop:     a=4OJI|1|A|G|35 B=4OJI|1|A|C|20
  2 Basepair    35   20 GC cWW 
pMakeNodes probe for inserts:  a=4OJI|1|A|A|36 B=4OJI|1|A|G|19
    Insertion on left  4OJI|1|A|A|36
    Insertion on left  4OJI|1|A|U|37
    Insertion on left  4OJI|1|A|A|38
    Insertion on left  4OJI|1|A|A|39
pMakeNodes probed for insert:  a=4OJI|1|A|A|40 B=4OJI|1|A|G|19
pMakeNodesJunction: a=4OJI|1|A|A|40 r=4OJI|1|A|A|40 s=4OJI|1|A|C|14 t=4OJI|1|A|C|15 u=B=4OJI|1|A|G|19
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4OJI|1|A|A|40 and 4OJI|1|A|C|14 and between 4OJI|1|A|C|15 and 4OJI|1|A|G|19
pMakeNodesJunction: about to make a junction: a=4OJI|1|A|A|40 s=4OJI|1|A|C|14 t=4OJI|1|A|C|15 B=4OJI|1|A|G|19
pMakeNodesJunction: first branch starts at   4OJI|1|A|A|40
pMakeNodesJunction: first branch ends around 4OJI|1|A|C|14
pMakeNodesJunction: second branch starts at  4OJI|1|A|C|15
pMakeNodesJunction: junction ends at         4OJI|1|A|G|19
pMakeNodesJunction: first branch strand start goes up to  4OJI|1|A|A|41
pMakeNodesJunction: first branch strand end goes down to  4OJI|1|A|U|12
pMakeNodesJunction: second branch strand start goes up to 4OJI|1|A|C|15
pMakeNodesJunction: last strand of junction goes down to  4OJI|1|A|G|19

Junction with 2 loops, call it J9292
Actual Branch 1 of junction J9292 - Nucleotides 4OJI|1|A|A|40 to 4OJI|1|A|C|14, length   5
Actual Branch 2 of junction J9292 - Nucleotides 4OJI|1|A|C|15 to 4OJI|1|A|G|19, length   2
  3 Junction

2B Branch 1 of 2 of junction J9292 - Nucleotides    40 to    14, length   5
pMakeNodes starting loop:     a=4OJI|1|A|A|40 B=4OJI|1|A|C|14
  5 Basepair    40   14 AC cSS 
pMakeNodes probe for inserts:  a=4OJI|1|A|A|41 B=4OJI|1|A|G|13
    Insertion on right 4OJI|1|A|G|13
pMakeNodesProbeForInsertions:  a 4OJI|1|A|A|41 interacts with 4OJI|1|A|U|12
pMakeNodesProbeForInsertions:  B 4OJI|1|A|U|12 interacts with 4OJI|1|A|A|41
pMakeNodesProbeForInsertions:  B 4OJI|1|A|U|12 interacts with 4OJI|1|A|A|41
pMakeNodes probed for insert:  a=4OJI|1|A|A|41 B=4OJI|1|A|U|12
  6 Basepair    41   12 AU cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J9292 - Nucleotides    15 to    19, length   2
pMakeNodes starting loop:     a=4OJI|1|A|C|15 B=4OJI|1|A|G|19
  9 Basepair    15   19 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  6 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OJI|1|A|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OJI|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OJI|1|A|C|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4OJI|1|A|G|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4OJI|1|A|U|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: [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: 'GAUAA'
           RightLetter: 'C'
               Comment: ' // Basepair G35 - C20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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 4OJI|1|A|G|13'
              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: '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: []
                  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 4OJI|1|A|C|14'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 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: 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 4OJI|1|A|C|15'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           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: 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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: '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 4OJI|1|A|G|19'
              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: 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 11

ans = 

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

                  type: 'Junction'
              nextnode: [4 8]
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: 'J9292'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A40 - G19 ID J9292'
              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: 10
             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: []
                  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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'GC'
               Comment: ' // Basepair A40 - C14 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 14

ans = 

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

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4OJI|1|A|U|37'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A41 - U12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 11
            RightIndex: 12
             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: []
                  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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C15 - G19 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11  Junction Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  15   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  20   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
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: 13
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J9292'
        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: 12
             Insertion: []
                    id: 'J9292'
        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 J3_90744.1. Nodes 12 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 11
pNextNodeJunction: Found a junction child at node 12
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a junction child at node 18
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Finished at node 20 out of 20, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_90744.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1009

Timestamp 18-Jul-2025 00:13:12
pMakeSCFGModels: Making JAR3D model for motif group J3_91491.2, number 76 of 88
pMakeNodes starting loop:     a=4WF9|1|X|C|2359 B=4WF9|1|X|G|2350
  2 Basepair  2359 2350 CG cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|2360 B=4WF9|1|X|A|2349
    Insertion on left  4WF9|1|X|A|2360
pMakeNodes probed for insert:  a=4WF9|1|X|A|2362 B=4WF9|1|X|A|2349
  3 Basepair  2362 2349 AA tWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|2363 B=4WF9|1|X|G|2348
    Insertion on left  4WF9|1|X|A|2363
pMakeNodes probed for insert:  a=4WF9|1|X|G|2364 B=4WF9|1|X|G|2348
pMakeNodesJunction: a=4WF9|1|X|G|2364 r=4WF9|1|X|G|2364 s=4WF9|1|X|C|2322 t=4WF9|1|X|U|2323 u=B=4WF9|1|X|G|2348
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4WF9|1|X|G|2364 and 4WF9|1|X|C|2322 and between 4WF9|1|X|U|2323 and 4WF9|1|X|G|2348
pMakeNodesJunction: about to make a junction: a=4WF9|1|X|G|2364 s=4WF9|1|X|C|2322 t=4WF9|1|X|U|2323 B=4WF9|1|X|G|2348
pMakeNodesJunction: first branch starts at   4WF9|1|X|G|2364
pMakeNodesJunction: first branch ends around 4WF9|1|X|C|2322
pMakeNodesJunction: second branch starts at  4WF9|1|X|U|2323
pMakeNodesJunction: junction ends at         4WF9|1|X|G|2348
pMakeNodesJunction: first branch strand start goes up to  4WF9|1|X|G|2364
pMakeNodesJunction: first branch strand end goes down to  4WF9|1|X|C|2322
pMakeNodesJunction: second branch strand start goes up to 4WF9|1|X|C|2324
pMakeNodesJunction: last strand of junction goes down to  4WF9|1|X|G|2348

Junction with 2 loops, call it J3499
Actual Branch 1 of junction J3499 - Nucleotides 4WF9|1|X|G|2364 to 4WF9|1|X|C|2322, length   2
Actual Branch 2 of junction J3499 - Nucleotides 4WF9|1|X|U|2323 to 4WF9|1|X|G|2348, length   3
  4 Junction

2B Branch 1 of 2 of junction J3499 - Nucleotides  2364 to  2322, length   2
pMakeNodes starting loop:     a=4WF9|1|X|G|2364 B=4WF9|1|X|C|2322
  6 Basepair  2364 2322 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J3499 - Nucleotides  2323 to  2348, length   3
pMakeNodes starting loop:     a=4WF9|1|X|U|2323 B=4WF9|1|X|G|2348
    Insertion on left  4WF9|1|X|U|2323
pMakeNodesProbeForInsertions:  a 4WF9|1|X|C|2324 interacts with 4WF9|1|X|G|2348
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|2348 interacts with 4WF9|1|X|C|2324
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|2348 interacts with 4WF9|1|X|C|2324
  8 Initial   2323 (1 insertion) and 2348 (0 insertion)
  9 Basepair  2324 2348 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   4  Junction Left  5 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|2323
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|G|2348
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|2359
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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 C2359 - G2350 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|2323'
              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 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: '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: []
                  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: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'A'
               Comment: ' // Basepair A2362 - A2349 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 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|G|2348'
              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: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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 8

ans = 

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

                  type: 'Junction'
              nextnode: [5 8]
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: 'J3499'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2364 - G2348 ID J3499'
              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: 5
            RightIndex: 6
             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: []
                  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: 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 G2364 - C2322 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 7
            RightIndex: 9
             Insertion: []
                    id: 'J3499'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|U|2323 - 4WF9|1|X|G|2348 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: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|C|2359'
              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: 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: []
           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: 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 C2324 - G2348 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8  Junction Left  5 Right  9
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  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pNextNodeJunction: Found a 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 16
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: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: 'J3499'
        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: 9
             Insertion: []
                    id: 'J3499'
        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: 'U'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|U|2323 - 4WF9|1|X|G|2348 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_91491.2. 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
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 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tHW  between 3 and 7
pConservedInteractionList: did not find a substitution probability matrix for tHW  between 3 and 7
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_91491.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7302
   -5.7302
   -5.9388
   -5.9388
   -6.4866
   -7.1349

Timestamp 18-Jul-2025 00:13:13
pMakeSCFGModels: Making JAR3D model for motif group J3_93059.1, number 77 of 88
pMakeNodes starting loop:     a=6MWN|1|B|C|610 B=6MWN|1|B|G|667
  2 Basepair   610  667 CG cWW 
pMakeNodes probe for inserts:  a=6MWN|1|B|U|611 B=6MWN|1|B|G|666
pMakeNodes probed for insert:  a=6MWN|1|B|U|611 B=6MWN|1|B|G|666
pMakeNodesJunction: a=6MWN|1|B|U|611 r=6MWN|1|B|U|611 s=6MWN|1|B|U|640 t=6MWN|1|B|C|641 u=B=6MWN|1|B|G|666
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6MWN|1|B|U|611 and 6MWN|1|B|U|640 and between 6MWN|1|B|C|641 and 6MWN|1|B|G|666
pMakeNodesJunction: about to make a junction: a=6MWN|1|B|U|611 s=6MWN|1|B|U|640 t=6MWN|1|B|C|641 B=6MWN|1|B|G|666
pMakeNodesJunction: first branch starts at   6MWN|1|B|U|611
pMakeNodesJunction: first branch ends around 6MWN|1|B|U|640
pMakeNodesJunction: second branch starts at  6MWN|1|B|C|641
pMakeNodesJunction: junction ends at         6MWN|1|B|G|666
pMakeNodesJunction: first branch strand start goes up to  6MWN|1|B|U|616
pMakeNodesJunction: first branch strand end goes down to  6MWN|1|B|C|639
pMakeNodesJunction: second branch strand start goes up to 6MWN|1|B|C|641
pMakeNodesJunction: last strand of junction goes down to  6MWN|1|B|G|666

Junction with 2 loops, call it J1965
Actual Branch 1 of junction J1965 - Nucleotides 6MWN|1|B|U|611 to 6MWN|1|B|U|640, length   9
Actual Branch 2 of junction J1965 - Nucleotides 6MWN|1|B|C|641 to 6MWN|1|B|G|666, length   2
  3 Junction

2B Branch 1 of 2 of junction J1965 - Nucleotides   611 to   640, length   9
pMakeNodes starting loop:     a=6MWN|1|B|U|611 B=6MWN|1|B|U|640
pMakeNodesProbeForInsertions:  a 6MWN|1|B|U|611 interacts with 6MWN|1|B|A|615
pMakeNodesProbeForInsertions:  B 6MWN|1|B|U|640 interacts with 6MWN|1|B|U|616
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6MWN|1|B|U|640 interacts with 6MWN|1|B|U|616
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial    611 (0 insertion) and  640 (0 insertion)
pMakeNodes making a cluster near strand break a=6MWN|1|B|U|611 B=6MWN|1|B|U|640
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 7 and then 10 to 10
aa is 7 bb is 10
  5 Cluster   6MWN|1|B|U|611:6MWN|1|B|U|616 6MWN|1|B|U|640:6MWN|1|B|U|640
    LR Inter  6MWN|1|B|U|616 6MWN|1|B|U|640 cWW 
    LL Inter  6MWN|1|B|U|612 6MWN|1|B|A|614 tSH 
    LL Inter  6MWN|1|B|U|611 6MWN|1|B|A|615 tWH 
    Left  strand conserved insertion 6MWN|1|B|A|613 at position 3
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=6MWN|1|B|G|617 B=6MWN|1|B|C|639
  6 Basepair   617  639 GC cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J1965 - Nucleotides   641 to   666, length   2
pMakeNodes starting loop:     a=6MWN|1|B|C|641 B=6MWN|1|B|G|666
  9 Basepair   641  666 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  10   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C610 - G667 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 12
             Insertion: []
                    id: 'J1965'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U611 - G666 ID J1965'
              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: 10
             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 6MWN|1|B|U|611 - 6MWN|1|B|U|640 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]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAAAU'
           RightLetter: 'U'
               Comment: ' // Cluster node 6MWN|1|B|U|611:6MWN|1|B|U|616 and 6MWN|1|B|U|640:6MWN|1|B|U|640'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 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 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G617 - C639 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 11
            RightIndex: 12
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             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 C641 - G666 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 11

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

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

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: 'J1965'
        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 6MWN|1|B|U|611 - 6MWN|1|B|U|640 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: 11
            RightIndex: 12
             Insertion: []
                    id: 'J1965'
        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 J3_93059.1. Nodes 4 and 9 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 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_93059.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9631

Timestamp 18-Jul-2025 00:13:14
pMakeSCFGModels: Making JAR3D model for motif group J3_93637.1, number 78 of 88
pMakeNodes starting loop:     a=3KTW|1|C|U|144 B=3KTW|1|C|A|234
  2 Basepair   144  234 UA cWW 
pMakeNodes probe for inserts:  a=3KTW|1|C|A|145 B=3KTW|1|C|U|233
    Insertion on left  3KTW|1|C|A|145
    Insertion on right 3KTW|1|C|U|233
pMakeNodes probed for insert:  a=3KTW|1|C|G|146 B=3KTW|1|C|C|232
pMakeNodes making a cluster near strand break a=3KTW|1|C|G|146 B=3KTW|1|C|C|232
pMakeNodesCluster: amax is 4 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 3 and then 13 to 13
aa is 3 bb is 13
  3 Cluster   3KTW|1|C|G|146:3KTW|1|C|G|146 3KTW|1|C|C|232:3KTW|1|C|C|232
    LR Inter  3KTW|1|C|G|146 3KTW|1|C|C|232 cWS 
pMakeNodesCluster a=4 B=12 at the end
pMakeNodesCluster a=4 B=12 at the end
pMakeNodes probe for inserts:  a=3KTW|1|C|U|147 B=3KTW|1|C|G|231
  4 Initial    147 (0 insertion) and  231 (0 insertion)
pMakeNodes probed for insert:  a=3KTW|1|C|U|147 B=3KTW|1|C|G|231
pMakeNodesJunction: a=3KTW|1|C|U|147 r=3KTW|1|C|U|147 s=3KTW|1|C|U|185 t=3KTW|1|C|U|186 u=B=3KTW|1|C|G|231
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3KTW|1|C|U|147 and 3KTW|1|C|U|185 and between 3KTW|1|C|U|186 and 3KTW|1|C|G|231
pMakeNodesJunction: about to make a junction: a=3KTW|1|C|U|147 s=3KTW|1|C|U|185 t=3KTW|1|C|U|186 B=3KTW|1|C|G|231
pMakeNodesJunction: first branch starts at   3KTW|1|C|U|147
pMakeNodesJunction: first branch ends around 3KTW|1|C|U|185
pMakeNodesJunction: second branch starts at  3KTW|1|C|U|186
pMakeNodesJunction: junction ends at         3KTW|1|C|G|231
pMakeNodesJunction: first branch strand start goes up to  3KTW|1|C|C|148
pMakeNodesJunction: first branch strand end goes down to  3KTW|1|C|G|184
pMakeNodesJunction: second branch strand start goes up to 3KTW|1|C|C|189
pMakeNodesJunction: last strand of junction goes down to  3KTW|1|C|G|231

Junction with 2 loops, call it J2510
Actual Branch 1 of junction J2510 - Nucleotides 3KTW|1|C|U|147 to 3KTW|1|C|U|185, length   4
Actual Branch 2 of junction J2510 - Nucleotides 3KTW|1|C|U|186 to 3KTW|1|C|G|231, length   5
  5 Junction

2B Branch 1 of 2 of junction J2510 - Nucleotides   147 to   185, length   4
pMakeNodes starting loop:     a=3KTW|1|C|U|147 B=3KTW|1|C|U|185
  7 Basepair   147  185 UU cWW 
No need to probe because of interaction between a=3KTW|1|C|C|148 B=3KTW|1|C|G|184
  8 Basepair   148  184 CG cWW 
  9 Hairpin type *

2B Branch 2 of 2 of junction J2510 - Nucleotides   186 to   231, length   5
pMakeNodes starting loop:     a=3KTW|1|C|U|186 B=3KTW|1|C|G|231
    Insertion on left  3KTW|1|C|U|186
    Insertion on left  3KTW|1|C|G|187
    Insertion on left  3KTW|1|C|A|188
pMakeNodesProbeForInsertions:  a 3KTW|1|C|C|189 interacts with 3KTW|1|C|G|231
pMakeNodesProbeForInsertions:  B 3KTW|1|C|G|231 interacts with 3KTW|1|C|C|189
pMakeNodesProbeForInsertions:  B 3KTW|1|C|G|231 interacts with 3KTW|1|C|C|189
 10 Initial    186 (3 insertion) and  231 (0 insertion)
 11 Basepair   189  231 CG cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3   Cluster Left  3 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|A|145
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3KTW|1|C|U|233
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|U|186
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|G|187
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|A|188
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'UA'
           RightLetter: 'UA'
               Comment: ' // Basepair U144 - A234 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|A|145'
              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 3KTW|1|C|G|146 - 3KTW|1|C|C|232 cWS '}
      JunctionDeletion: []
          InterIndices: [3 13]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

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: 'J2510'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3KTW|1|C|U|233'
              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: 13
             Insertion: []
                    id: 'J2510'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Cluster node 3KTW|1|C|G|146:3KTW|1|C|G|146 and 3KTW|1|C|C|232:3KTW|1|C|C|232'
              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 3KTW|1|C|G|146 - 3KTW|1|C|C|232 cWS '}
      JunctionDeletion: []
          InterIndices: [3 13]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000
           numbranches: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 3KTW|1|C|U|147 - 3KTW|1|C|G|231 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: [6 10]
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J2510'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U147 - G231 ID J2510'
              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: 4
            RightIndex: 7
             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: []
          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: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U147 - U185 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C148 - G184 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 8
            RightIndex: 12
             Insertion: []
                    id: 'J2510'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGA'
           RightLetter: []
               Comment: ' // Initial node 3KTW|1|C|U|186 - 3KTW|1|C|G|231 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 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|U|186'
              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: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 17

ans = 

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

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|G|187'
              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: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 19

ans = 

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

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|A|188'
              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 20

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 21

ans = 

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

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C189 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 22

ans = 

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

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: [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 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   Cluster Left  3 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   9  Junction Left  4 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  21  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  22   Hairpin Left 12 Right 11
pNextNodeJunction: Found a junction at node 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 22
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: 11
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J2510'
        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: 8
            RightIndex: 12
             Insertion: []
                    id: 'J2510'
        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: 'UGA'
           RightLetter: []
               Comment: ' // Initial node 3KTW|1|C|U|186 - 3KTW|1|C|G|231 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 J3_93637.1. Nodes 10 and 14 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 9
pNextNodeJunction: Found a junction child at node 10
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a junction child at node 14
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Finished at node 22 out of 22, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for bif  between 3 and 12
pConservedInteractionList: did not find a substitution probability matrix for bif  between 3 and 12
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_93637.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6551

Timestamp 18-Jul-2025 00:13:14
pMakeSCFGModels: Making JAR3D model for motif group J3_94515.1, number 79 of 88
pMakeNodes starting loop:     a=4V88|1|A6|U|785 B=4V88|1|A6|G|775
  2 Basepair   785  775 UG cWW 
No need to probe because of interaction between a=4V88|1|A6|C|786 B=4V88|1|A6|A|774
  3 Basepair   786  774 CA tWW 
pMakeNodes probe for inserts:  a=4V88|1|A6|G|787 B=4V88|1|A6|C|773
    Insertion on left  4V88|1|A6|G|787
    Insertion on left  4V88|1|A6|A|788
pMakeNodes probed for insert:  a=4V88|1|A6|A|789 B=4V88|1|A6|C|773
pMakeNodesJunction: a=4V88|1|A6|A|789 r=4V88|1|A6|A|789 s=4V88|1|A6|G|761 t=4V88|1|A6|A|762 u=B=4V88|1|A6|C|773
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|A|789 and 4V88|1|A6|G|761 and between 4V88|1|A6|A|762 and 4V88|1|A6|C|773
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|A|789 s=4V88|1|A6|G|761 t=4V88|1|A6|A|762 B=4V88|1|A6|C|773
pMakeNodesJunction: first branch starts at   4V88|1|A6|A|789
pMakeNodesJunction: first branch ends around 4V88|1|A6|G|761
pMakeNodesJunction: second branch starts at  4V88|1|A6|A|762
pMakeNodesJunction: junction ends at         4V88|1|A6|C|773
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|U|790
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|A|760
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|G|763
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|C|773

Junction with 2 loops, call it J6160
Actual Branch 1 of junction J6160 - Nucleotides 4V88|1|A6|A|789 to 4V88|1|A6|G|761, length   4
Actual Branch 2 of junction J6160 - Nucleotides 4V88|1|A6|A|762 to 4V88|1|A6|C|773, length   3
  4 Junction

2B Branch 1 of 2 of junction J6160 - Nucleotides   789 to   761, length   4
pMakeNodes starting loop:     a=4V88|1|A6|A|789 B=4V88|1|A6|G|761
  6 Basepair   789  761 AG tHS 
No need to probe because of interaction between a=4V88|1|A6|U|790 B=4V88|1|A6|A|760
  7 Basepair   790  760 UA cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J6160 - Nucleotides   762 to   773, length   3
pMakeNodes starting loop:     a=4V88|1|A6|A|762 B=4V88|1|A6|C|773
    Insertion on left  4V88|1|A6|A|762
pMakeNodesProbeForInsertions:  a 4V88|1|A6|G|763 interacts with 4V88|1|A6|C|773
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|773 interacts with 4V88|1|A6|G|763
pMakeNodesProbeForInsertions:  B 4V88|1|A6|C|773 interacts with 4V88|1|A6|G|763
  9 Initial    762 (1 insertion) and  773 (0 insertion)
 10 Basepair   763  773 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Junction Left  5 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|762
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|G|763
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|C|786
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U785 - G775 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: 'CGA'
           RightLetter: 'A'
               Comment: ' // Basepair C786 - A774 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: '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 4V88|1|A6|A|762'
              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: 11
             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 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V88|1|A6|G|763'
              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 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '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 8

ans = 

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

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: 'J6160'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A789 - C773 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 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: '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 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A789 - G761 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 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U790 - A760 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: 'J6160'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|A|762 - 4V88|1|A6|C|773 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: 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 4V88|1|A6|C|786'
              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 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 'C'
               Comment: ' // Basepair G763 - C773 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8  Junction Left  5 Right 11
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 11
pMakeMotifModelFromSSF:  14     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  15   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 10
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 17
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: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: 'J6160'
        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: 11
             Insertion: []
                    id: 'J6160'
        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 4V88|1|A6|A|762 - 4V88|1|A6|C|773 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_94515.1. Nodes 9 and 13 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 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 17
pNextNodeJunction: Finished at node 17 out of 17, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_94515.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7202

Timestamp 18-Jul-2025 00:13:15
pMakeSCFGModels: Making JAR3D model for motif group J3_94652.1, number 80 of 88
pMakeNodes starting loop:     a=1G1X|1|I|C|586 B=1G1X|1|J|G|755
  2 Basepair   586  755 CG cWW 
pMakeNodes probe for inserts:  a=1G1X|1|I|G|587 B=1G1X|1|J|C|754
    Insertion on left  1G1X|1|I|G|587
pMakeNodes probed for insert:  a=1G1X|1|I|G|588 B=1G1X|1|J|C|754
pMakeNodesJunction: a=1G1X|1|I|G|588 r=1G1X|1|I|G|588 s=1G1X|1|I|C|651 t=1G1X|1|I|U|652 u=B=1G1X|1|J|C|754
pMakeNodesJunction: a:s count 4
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 1G1X|1|I|G|588 and 1G1X|1|I|C|651 and between 1G1X|1|I|U|652 and 1G1X|1|J|C|754
pMakeNodesJunction: about to make a junction: a=1G1X|1|I|G|588 s=1G1X|1|I|C|651 t=1G1X|1|I|U|652 B=1G1X|1|J|C|754
pMakeNodesJunction: first branch starts at   1G1X|1|I|G|588
pMakeNodesJunction: first branch ends around 1G1X|1|I|C|651
pMakeNodesJunction: second branch starts at  1G1X|1|I|U|652
pMakeNodesJunction: junction ends at         1G1X|1|J|C|754
pMakeNodesJunction: first branch strand start goes up to  1G1X|1|I|C|589
pMakeNodesJunction: first branch strand end goes down to  1G1X|1|I|G|650
pMakeNodesJunction: second branch strand start goes up to 1G1X|1|I|G|654
pMakeNodesJunction: last strand of junction goes down to  1G1X|1|J|C|754

Junction with 2 loops, call it J4732
Actual Branch 1 of junction J4732 - Nucleotides 1G1X|1|I|G|588 to 1G1X|1|I|C|651, length   4
Actual Branch 2 of junction J4732 - Nucleotides 1G1X|1|I|U|652 to 1G1X|1|J|C|754, length   3
  3 Junction

2B Branch 1 of 2 of junction J4732 - Nucleotides   588 to   651, length   4
pMakeNodes starting loop:     a=1G1X|1|I|G|588 B=1G1X|1|I|C|651
  5 Basepair   588  651 GC cWW 
No need to probe because of interaction between a=1G1X|1|I|C|589 B=1G1X|1|I|G|650
  6 Basepair   589  650 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J4732 - Nucleotides   652 to   754, length   3
pMakeNodes starting loop:     a=1G1X|1|I|U|652 B=1G1X|1|J|C|754
    Insertion on left  1G1X|1|I|U|652
pMakeNodesProbeForInsertions:  a 1G1X|1|I|G|654 interacts with 1G1X|1|J|C|754
pMakeNodesProbeForInsertions:  B 1G1X|1|J|C|754 interacts with 1G1X|1|I|G|654
pMakeNodesProbeForInsertions:  B 1G1X|1|J|C|754 interacts with 1G1X|1|I|G|654
  8 Initial    652 (1 insertion) and  754 (0 insertion)
  9 Basepair   654  754 GC cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Junction Left  3 Right  9
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  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|I|G|587
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1G1X|1|I|U|652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.0826 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 C586 - G755 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
             Insertion: []
                    id: 'J4732'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1G1X|1|I|G|587'
              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: 9
             Insertion: []
                    id: 'J4732'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 9
             Insertion: []
                    id: 'J4732'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G588 - C754 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 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: '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 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: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G588 - C651 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C589 - G650 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 9
             Insertion: []
                    id: 'J4732'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 1G1X|1|I|U|652 - 1G1X|1|J|C|754 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: 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 1G1X|1|I|U|652'
              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 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G654 - C754 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5  Junction Left  3 Right  9
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  9
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right  8
pNextNodeJunction: Found a 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 hairpin at node 14
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: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: 'J4732'
        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: 9
             Insertion: []
                    id: 'J4732'
        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 1G1X|1|I|U|652 - 1G1X|1|J|C|754 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_94652.1. 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
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 hairpin at node 14
pNextNodeJunction: Finished at node 14 out of 14, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_94652.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9354

Timestamp 18-Jul-2025 00:13:15
pMakeSCFGModels: Making JAR3D model for motif group J3_96170.1, number 81 of 88
pMakeNodes starting loop:     a=6JQ5|1|A|U|70 B=6JQ5|1|B|A|67
pMakeNodes making a cluster near strand break a=6JQ5|1|A|U|70 B=6JQ5|1|B|A|67
pMakeNodesCluster: amax is 6 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 16 to 16
aa is 4 bb is 16
  2 Cluster   6JQ5|1|A|U|70:6JQ5|1|A|A|73 6JQ5|1|B|A|67:6JQ5|1|B|A|67
    LR Inter  6JQ5|1|A|U|70 6JQ5|1|B|A|67 cWW 
    LR Inter  6JQ5|1|A|U|71 6JQ5|1|B|A|67 tHS 
    LR Inter  6JQ5|1|A|A|73 6JQ5|1|B|A|67 cWS 
    LL Inter  6JQ5|1|A|U|70 6JQ5|1|A|A|72 cSH 
    LL Inter  6JQ5|1|A|U|71 6JQ5|1|A|A|73 cWH 
pMakeNodesCluster a=5 B=15 at the end
pMakeNodesCluster a=5 B=15 at the end
pMakeNodes probe for inserts:  a=6JQ5|1|A|A|74 B=6JQ5|1|B|G|66
    Insertion on left  6JQ5|1|A|A|74
    Insertion on right 6JQ5|1|B|G|66
    Insertion on right 6JQ5|1|B|A|65
  3 Initial     74 (1 insertion) and   66 (2 insertion)
pMakeNodes probed for insert:  a=6JQ5|1|A|A|75 B=6JQ5|1|B|C|64
pMakeNodesJunction: a=6JQ5|1|A|A|75 r=6JQ5|1|A|A|75 s=6JQ5|1|B|G|29 t=6JQ5|1|B|G|30 u=B=6JQ5|1|B|C|64
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6JQ5|1|A|A|75 and 6JQ5|1|B|G|29 and between 6JQ5|1|B|G|30 and 6JQ5|1|B|C|64
pMakeNodesJunction: about to make a junction: a=6JQ5|1|A|A|75 s=6JQ5|1|B|G|29 t=6JQ5|1|B|G|30 B=6JQ5|1|B|C|64
pMakeNodesJunction: first branch starts at   6JQ5|1|A|A|75
pMakeNodesJunction: first branch ends around 6JQ5|1|B|G|29
pMakeNodesJunction: second branch starts at  6JQ5|1|B|G|30
pMakeNodesJunction: junction ends at         6JQ5|1|B|C|64
pMakeNodesJunction: first branch strand start goes up to  6JQ5|1|A|C|77
pMakeNodesJunction: first branch strand end goes down to  6JQ5|1|B|G|27
pMakeNodesJunction: second branch strand start goes up to 6JQ5|1|B|G|31
pMakeNodesJunction: last strand of junction goes down to  6JQ5|1|B|C|64

Junction with 2 loops, call it J3516
Actual Branch 1 of junction J3516 - Nucleotides 6JQ5|1|A|A|75 to 6JQ5|1|B|G|29, length   5
Actual Branch 2 of junction J3516 - Nucleotides 6JQ5|1|B|G|30 to 6JQ5|1|B|C|64, length   3
  4 Junction

2B Branch 1 of 2 of junction J3516 - Nucleotides    75 to    29, length   5
pMakeNodes starting loop:     a=6JQ5|1|A|A|75 B=6JQ5|1|B|G|29
  6 Basepair    75   29 AG tHS 
pMakeNodes probe for inserts:  a=6JQ5|1|A|C|77 B=6JQ5|1|B|U|28
    Insertion on right 6JQ5|1|B|U|28
pMakeNodesProbeForInsertions:  a 6JQ5|1|A|C|77 interacts with 6JQ5|1|B|G|27
pMakeNodesProbeForInsertions:  B 6JQ5|1|B|G|27 interacts with 6JQ5|1|A|C|77
pMakeNodesProbeForInsertions:  B 6JQ5|1|B|G|27 interacts with 6JQ5|1|A|C|77
pMakeNodes probed for insert:  a=6JQ5|1|A|C|77 B=6JQ5|1|B|G|27
  7 Basepair    77   27 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J3516 - Nucleotides    30 to    64, length   3
pMakeNodes starting loop:     a=6JQ5|1|B|G|30 B=6JQ5|1|B|C|64
    Insertion on left  6JQ5|1|B|G|30
pMakeNodesProbeForInsertions:  a 6JQ5|1|B|G|31 interacts with 6JQ5|1|B|C|64
pMakeNodesProbeForInsertions:  B 6JQ5|1|B|C|64 interacts with 6JQ5|1|B|G|31
pMakeNodesProbeForInsertions:  B 6JQ5|1|B|C|64 interacts with 6JQ5|1|B|G|31
  9 Initial     30 (1 insertion) and   64 (0 insertion)
 10 Basepair    31   64 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   4  Junction Left  6 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  11   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ5|1|A|A|74
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ5|1|B|A|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ5|1|B|C|64
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JQ5|1|B|G|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JQ5|1|B|G|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           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 3 4]
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAA'
           RightLetter: 'A'
               Comment: ' // Cluster node 6JQ5|1|A|U|70:6JQ5|1|A|A|73 and 6JQ5|1|B|A|67:6JQ5|1|B|A|67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0027
           numbranches: []
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AG'
               Comment: ' // Initial node 6JQ5|1|A|A|74 - 6JQ5|1|B|G|66 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: 5
            RightIndex: 15
             Insertion: []
                    id: 'J3516'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JQ5|1|A|A|74'
              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: 6
            RightIndex: 15
             Insertion: []
                    id: 'J3516'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               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: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JQ5|1|B|A|65'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          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: 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: []
          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: 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 6JQ5|1|B|C|64'
              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: 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: 8
                     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: 'Junction'
              nextnode: [5 9]
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: 'J3516'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A75 - C64 ID J3516'
              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 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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

Node 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'UG'
               Comment: ' // Basepair A75 - G29 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           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: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JQ5|1|B|G|27'
              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 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []
                  lpar: []
                  rpar: []

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 C77 - G27 cWW '
              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: '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: []
          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: 11
            RightIndex: 13
             Insertion: []
                    id: 'J3516'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 6JQ5|1|B|G|30 - 6JQ5|1|B|C|64 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 18

ans = 

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

                  type: 'Fixed'
              nextnode: 19
             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 6JQ5|1|B|G|29'
              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 19

ans = 

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

                  type: 'Initial'
              nextnode: 20
             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: []
          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: 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 G31 - C64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          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: 23
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
           numbranches: []
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  10  Junction Left  6 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  17   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  18     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  19   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  20  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  21   Hairpin Left 13 Right 12
pNextNodeJunction: Found a junction at node 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 21
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: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: 'J3516'
        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: 18
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: 'J3516'
        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 6JQ5|1|B|G|30 - 6JQ5|1|B|C|64 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 J3_96170.1. Nodes 11 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 10
pNextNodeJunction: Found a junction child at node 11
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a junction child at node 17
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Finished at node 21 out of 21, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_96170.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5863

Timestamp 18-Jul-2025 00:13:15
pMakeSCFGModels: Making JAR3D model for motif group J3_96372.1, number 82 of 88
pMakeNodes starting loop:     a=3MXH|1|R|G|14 B=3MXH|1|R|C|93
pMakeNodes making a cluster near strand break a=3MXH|1|R|G|14 B=3MXH|1|R|C|93
pMakeNodesCluster: amax is 6 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 16 to 16
aa is 3 bb is 16
  2 Cluster   3MXH|1|R|G|14:3MXH|1|R|C|17 3MXH|1|R|C|93:3MXH|1|R|C|93
    LR Inter  3MXH|1|R|G|14 3MXH|1|R|C|93 cWW 
    LR Inter  3MXH|1|R|C|17 3MXH|1|R|C|93 cWS 
    LL Inter  3MXH|1|R|G|14 3MXH|1|R|A|16 cSH 
pMakeNodesCluster a=4 B=15 at the end
pMakeNodesCluster a=4 B=15 at the end
pMakeNodes probe for inserts:  a=3MXH|1|R|A|18 B=3MXH|1|R|C|92
    Insertion on left  3MXH|1|R|A|18
  3 Initial     18 (1 insertion) and   92 (0 insertion)
pMakeNodes probed for insert:  a=3MXH|1|R|G|19 B=3MXH|1|R|C|92
  4 Basepair    19   92 GC cWS 
pMakeNodes probe for inserts:  a=3MXH|1|R|G|20 B=3MXH|1|R|A|91
    Insertion on left  3MXH|1|R|G|20
    Insertion on right 3MXH|1|R|A|91
pMakeNodes probed for insert:  a=3MXH|1|R|G|21 B=3MXH|1|R|U|90
pMakeNodesJunction: a=3MXH|1|R|G|21 r=3MXH|1|R|G|21 s=3MXH|1|R|C|46 t=3MXH|1|R|A|47 u=B=3MXH|1|R|U|90
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 3MXH|1|R|G|21 and 3MXH|1|R|C|46 and between 3MXH|1|R|A|47 and 3MXH|1|R|U|90
pMakeNodesJunction: about to make a junction: a=3MXH|1|R|G|21 s=3MXH|1|R|C|46 t=3MXH|1|R|A|47 B=3MXH|1|R|U|90
pMakeNodesJunction: first branch starts at   3MXH|1|R|G|21
pMakeNodesJunction: first branch ends around 3MXH|1|R|C|46
pMakeNodesJunction: second branch starts at  3MXH|1|R|A|47
pMakeNodesJunction: junction ends at         3MXH|1|R|U|90
pMakeNodesJunction: first branch strand start goes up to  3MXH|1|R|G|21
pMakeNodesJunction: first branch strand end goes down to  3MXH|1|R|C|46
pMakeNodesJunction: second branch strand start goes up to 3MXH|1|R|G|50
pMakeNodesJunction: last strand of junction goes down to  3MXH|1|R|U|89

Junction with 2 loops, call it J8308
Actual Branch 1 of junction J8308 - Nucleotides 3MXH|1|R|G|21 to 3MXH|1|R|C|46, length   2
Actual Branch 2 of junction J8308 - Nucleotides 3MXH|1|R|A|47 to 3MXH|1|R|U|90, length   5
  5 Junction

2B Branch 1 of 2 of junction J8308 - Nucleotides    21 to    46, length   2
pMakeNodes starting loop:     a=3MXH|1|R|G|21 B=3MXH|1|R|C|46
  7 Basepair    21   46 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J8308 - Nucleotides    47 to    90, length   5
pMakeNodes starting loop:     a=3MXH|1|R|A|47 B=3MXH|1|R|U|90
    Insertion on left  3MXH|1|R|A|47
pMakeNodesProbeForInsertions:  a 3MXH|1|R|A|48 interacts with 3MXH|1|R|U|90
pMakeNodesProbeForInsertions:  B 3MXH|1|R|U|90 interacts with 3MXH|1|R|A|48
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3MXH|1|R|U|90 interacts with 3MXH|1|R|A|48
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  9 Initial     47 (1 insertion) and   90 (0 insertion)
 10 Basepair    48   90 AU tHW 
No need to probe because of interaction between a=3MXH|1|R|G|50 B=3MXH|1|R|U|89
 11 Basepair    50   89 GU cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 15
pMakeMotifModelFromSSF:   5  Junction Left  7 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  11  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3MXH|1|R|C|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3MXH|1|R|G|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3MXH|1|R|U|89
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3MXH|1|R|C|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAC'
           RightLetter: 'C'
               Comment: ' // Cluster node 3MXH|1|R|G|14:3MXH|1|R|C|17 and 3MXH|1|R|C|93:3MXH|1|R|C|93'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0605
                  lpar: []
                  rpar: []
           numbranches: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 15
             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 3MXH|1|R|A|18 - 3MXH|1|R|C|92 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3MXH|1|R|C|17'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: 'J8308'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [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: []
                  lpar: []
                  rpar: []
           numbranches: 2

Node 6

ans = 

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

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            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: 'GG'
           RightLetter: 'AC'
               Comment: ' // Basepair G19 - C92 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             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 3MXH|1|R|G|19'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []
           numbranches: []

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: 'J8308'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3MXH|1|R|U|89'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

Node 11

ans = 

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

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: 'J8308'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G21 - U90 ID J8308'
              NumLoops: 2
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: 2

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: '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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

Node 13

ans = 

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

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G21 - 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

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

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: '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 3MXH|1|R|A|47 - 3MXH|1|R|U|90 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

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 3MXH|1|R|C|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

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: 'U'
               Comment: ' // Basepair A48 - U90 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: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

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: 'U'
               Comment: ' // Basepair G50 - U89 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []

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

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right 16
pMakeMotifModelFromSSF:   3   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 15
pMakeMotifModelFromSSF:   7     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 14
pMakeMotifModelFromSSF:   9     Fixed Left  7 Right 14
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 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

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: 'J8308'
        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: []
                  lpar: []
                  rpar: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: 'J8308'
        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 3MXH|1|R|A|47 - 3MXH|1|R|U|90 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []
           numbranches: []

Motif J3_96372.1. 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 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

pConservedInteractionList: did not find a substitution probability matrix for wat  between 5 and 9
pConservedInteractionList: did not find a substitution probability matrix for wat  between 5 and 9
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_96372.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.9324
  -13.6287

Timestamp 18-Jul-2025 00:13:16
pMakeSCFGModels: Making JAR3D model for motif group J3_97609.1, number 83 of 88
pMakeNodes starting loop:     a=4V9F|1|0|G|2131 B=4V9F|1|0|C|2262
  2 Basepair  2131 2262 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|C|2132 B=4V9F|1|0|C|2261
  3 Basepair  2132 2261 CC bif 
No need to probe because of interaction between a=4V9F|1|0|U|2133 B=4V9F|1|0|A|2260
  4 Basepair  2133 2260 UA tHH 
pMakeNodes probe for inserts:  a=4V9F|1|0|G|2134 B=4V9F|1|0|C|2259
    Insertion on right 4V9F|1|0|C|2259
pMakeNodes probed for insert:  a=4V9F|1|0|G|2134 B=4V9F|1|0|A|2258
pMakeNodesJunction: a=4V9F|1|0|G|2134 r=4V9F|1|0|G|2134 s=4V9F|1|0|C|2241 t=4V9F|1|0|U|2242 u=B=4V9F|1|0|A|2258
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V9F|1|0|G|2134 and 4V9F|1|0|C|2241 and between 4V9F|1|0|U|2242 and 4V9F|1|0|A|2258
pMakeNodesJunction: about to make a junction: a=4V9F|1|0|G|2134 s=4V9F|1|0|C|2241 t=4V9F|1|0|U|2242 B=4V9F|1|0|A|2258
pMakeNodesJunction: first branch starts at   4V9F|1|0|G|2134
pMakeNodesJunction: first branch ends around 4V9F|1|0|C|2241
pMakeNodesJunction: second branch starts at  4V9F|1|0|U|2242
pMakeNodesJunction: junction ends at         4V9F|1|0|A|2258
pMakeNodesJunction: first branch strand start goes up to  4V9F|1|0|G|2134
pMakeNodesJunction: first branch strand end goes down to  4V9F|1|0|C|2241
pMakeNodesJunction: second branch strand start goes up to 4V9F|1|0|C|2245
pMakeNodesJunction: last strand of junction goes down to  4V9F|1|0|G|2256

Junction with 2 loops, call it J5852
Actual Branch 1 of junction J5852 - Nucleotides 4V9F|1|0|G|2134 to 4V9F|1|0|C|2241, length   2
Actual Branch 2 of junction J5852 - Nucleotides 4V9F|1|0|U|2242 to 4V9F|1|0|A|2258, length   6
  5 Junction

2B Branch 1 of 2 of junction J5852 - Nucleotides  2134 to  2241, length   2
pMakeNodes starting loop:     a=4V9F|1|0|G|2134 B=4V9F|1|0|C|2241
  7 Basepair  2134 2241 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J5852 - Nucleotides  2242 to  2258, length   6
pMakeNodes starting loop:     a=4V9F|1|0|U|2242 B=4V9F|1|0|A|2258
 10 Basepair  2242 2258 UA tWH 
No need to probe because of interaction between a=4V9F|1|0|A|2244 B=4V9F|1|0|G|2257
 11 Basepair  2244 2257 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|C|2245 B=4V9F|1|0|G|2256
 12 Basepair  2245 2256 CG cWW 
 13 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Junction Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  13   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|2258
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G2131 - C2262 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C2132 - C2261 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 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'CA'
               Comment: ' // Basepair U2133 - A2260 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: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J5852'
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|2258'
              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 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: '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 7

ans = 

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

                  type: 'Junction'
              nextnode: [6 9]
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: 'J5852'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G2134 - A2258 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 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: '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 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2134 - C2241 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2242 - A2258 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: '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 A2244 - G2257 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 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2245 - G2256 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: [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  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 12
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  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a 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 hairpin at node 15
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: 9
             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: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: 'J5852'
        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 J3_97609.1. 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
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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_97609.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0976

Timestamp 18-Jul-2025 00:13:17
pMakeSCFGModels: Making JAR3D model for motif group J3_98102.1, number 84 of 88
pMakeNodes starting loop:     a=4V88|1|A6|C|1215 B=4V88|1|A6|G|1448
  2 Basepair  1215 1448 CG cWW 
No need to probe because of interaction between a=4V88|1|A6|C|1216 B=4V88|1|A6|A|1446
  3 Basepair  1216 1446 CA tWH 
pMakeNodes probe for inserts:  a=4V88|1|A6|G|1218 B=4V88|1|A6|A|1444
    Insertion on left  4V88|1|A6|G|1218
    Insertion on right 4V88|1|A6|A|1444
pMakeNodes probed for insert:  a=4V88|1|A6|A|1219 B=4V88|1|A6|U|1443
pMakeNodesJunction: a=4V88|1|A6|A|1219 r=4V88|1|A6|A|1219 s=4V88|1|A6|G|1264 t=4V88|1|A6|G|1265 u=B=4V88|1|A6|U|1443
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4V88|1|A6|A|1219 and 4V88|1|A6|G|1264 and between 4V88|1|A6|G|1265 and 4V88|1|A6|U|1443
pMakeNodesJunction: about to make a junction: a=4V88|1|A6|A|1219 s=4V88|1|A6|G|1264 t=4V88|1|A6|G|1265 B=4V88|1|A6|U|1443
pMakeNodesJunction: first branch starts at   4V88|1|A6|A|1219
pMakeNodesJunction: first branch ends around 4V88|1|A6|G|1264
pMakeNodesJunction: second branch starts at  4V88|1|A6|G|1265
pMakeNodesJunction: junction ends at         4V88|1|A6|U|1443
pMakeNodesJunction: first branch strand start goes up to  4V88|1|A6|C|1220
pMakeNodesJunction: first branch strand end goes down to  4V88|1|A6|G|1263
pMakeNodesJunction: second branch strand start goes up to 4V88|1|A6|G|1267
pMakeNodesJunction: last strand of junction goes down to  4V88|1|A6|U|1442

Junction with 2 loops, call it J5497
Actual Branch 1 of junction J5497 - Nucleotides 4V88|1|A6|A|1219 to 4V88|1|A6|G|1264, length   4
Actual Branch 2 of junction J5497 - Nucleotides 4V88|1|A6|G|1265 to 4V88|1|A6|U|1443, length   5
  4 Junction

2B Branch 1 of 2 of junction J5497 - Nucleotides  1219 to  1264, length   4
pMakeNodes starting loop:     a=4V88|1|A6|A|1219 B=4V88|1|A6|G|1264
  6 Basepair  1219 1264 AG tHS 
No need to probe because of interaction between a=4V88|1|A6|C|1220 B=4V88|1|A6|G|1263
  7 Basepair  1220 1263 CG cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J5497 - Nucleotides  1265 to  1443, length   5
pMakeNodes starting loop:     a=4V88|1|A6|G|1265 B=4V88|1|A6|U|1443
    Insertion on left  4V88|1|A6|G|1265
pMakeNodesProbeForInsertions:  a 4V88|1|A6|U|1266 interacts with 4V88|1|A6|U|1443
pMakeNodesProbeForInsertions:  B 4V88|1|A6|U|1443 interacts with 4V88|1|A6|U|1266
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V88|1|A6|U|1443 interacts with 4V88|1|A6|U|1266
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  9 Initial   1265 (1 insertion) and 1443 (0 insertion)
 10 Basepair  1266 1443 UU cWW 
No need to probe because of interaction between a=4V88|1|A6|G|1267 B=4V88|1|A6|U|1442
 11 Basepair  1267 1442 GU cWW 
 12 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Junction Left  4 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  11  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  12   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|A|1217
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V88|1|A6|U|1443
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V88|1|A6|G|1264
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in 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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C1215 - G1448 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'AA'
               Comment: ' // Basepair C1216 - A1446 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 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: 'J5497'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1217'
              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: 13
             Insertion: []
                    id: 'J5497'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 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 4V88|1|A6|U|1443'
              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 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Junction'
              nextnode: [5 9]
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: 'J5497'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node A1219 - U1443 ID J5497'
              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: '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: []
                  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: 'G'
               Comment: ' // Basepair A1219 - G1264 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 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 C1220 - G1263 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 12
             Insertion: []
                    id: 'J5497'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4V88|1|A6|G|1265 - 4V88|1|A6|U|1443 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: 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 4V88|1|A6|G|1264'
              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 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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New 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 16

ans = 

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

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1266 - U1443 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 G1267 - U1442 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   8  Junction Left  4 Right 12
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 12
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  17  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  18   Hairpin Left 11 Right 10
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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: 'J5497'
        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: 12
             Insertion: []
                    id: 'J5497'
        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 4V88|1|A6|G|1265 - 4V88|1|A6|U|1443 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_98102.1. 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 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 18
pNextNodeJunction: Finished at node 18 out of 18, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_98102.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2881

Timestamp 18-Jul-2025 00:13:17
pMakeSCFGModels: Making JAR3D model for motif group J3_98298.1, number 85 of 88
pMakeNodes starting loop:     a=5TBW|1|1|U|149 B=5TBW|1|1|A|123
  2 Basepair   149  123 UA cWW 
pMakeNodes probe for inserts:  a=5TBW|1|1|A|150 B=5TBW|1|1|A|122
    Insertion on left  5TBW|1|1|A|150
    Insertion on left  5TBW|1|1|A|151
    Insertion on left  5TBW|1|1|U|152
    Insertion on right 5TBW|1|1|A|122
    Insertion on right 5TBW|1|1|U|119
    Insertion on right 5TBW|1|1|U|118
    Insertion on right 5TBW|1|1|A|116
    Insertion on right 5TBW|1|1|A|115
pMakeNodes probed for insert:  a=5TBW|1|1|U|153 B=5TBW|1|1|A|114
pMakeNodesJunction: a=5TBW|1|1|U|153 r=5TBW|1|1|U|153 s=5TBW|1|1|A|265 t=5TBW|1|1|A|266 u=B=5TBW|1|1|A|114
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|U|153 and 5TBW|1|1|A|265 and between 5TBW|1|1|A|266 and 5TBW|1|1|A|114
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|U|153 s=5TBW|1|1|A|265 t=5TBW|1|1|A|266 B=5TBW|1|1|A|114
pMakeNodesJunction: first branch starts at   5TBW|1|1|U|153
pMakeNodesJunction: first branch ends around 5TBW|1|1|A|265
pMakeNodesJunction: second branch starts at  5TBW|1|1|A|266
pMakeNodesJunction: junction ends at         5TBW|1|1|A|114
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|158
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|263
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|G|267
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|C|113
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     0


Junction with 2 loops, call it J9171
Actual Branch 1 of junction J9171 - Nucleotides 5TBW|1|1|U|153 to 5TBW|1|1|A|265, length   8
Actual Branch 2 of junction J9171 - Nucleotides 5TBW|1|1|A|266 to 5TBW|1|1|A|114, length   4
  3 Junction

2B Branch 1 of 2 of junction J9171 - Nucleotides   153 to   265, length   8
pMakeNodes starting loop:     a=5TBW|1|1|U|153 B=5TBW|1|1|A|265
  5 Basepair   153  265 UA tSW 
pMakeNodes probe for inserts:  a=5TBW|1|1|U|154 B=5TBW|1|1|G|264
    Insertion on left  5TBW|1|1|U|154
    Insertion on left  5TBW|1|1|G|155
pMakeNodesProbeForInsertions:  a 5TBW|1|1|A|157 interacts with 5TBW|1|1|G|264
pMakeNodesProbeForInsertions:  B 5TBW|1|1|G|264 interacts with 5TBW|1|1|A|157
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5TBW|1|1|G|264 interacts with 5TBW|1|1|A|157
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5TBW|1|1|A|157 B=5TBW|1|1|G|264
  6 Basepair   157  264 AG tHS 
No need to probe because of interaction between a=5TBW|1|1|G|158 B=5TBW|1|1|C|263
  7 Basepair   158  263 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J9171 - Nucleotides   266 to   114, length   4
pMakeNodes starting loop:     a=5TBW|1|1|A|266 B=5TBW|1|1|A|114
    Insertion on left  5TBW|1|1|A|266
    Insertion on right 5TBW|1|1|A|114
pMakeNodesProbeForInsertions:  a 5TBW|1|1|G|267 interacts with 5TBW|1|1|C|113
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|113 interacts with 5TBW|1|1|G|267
pMakeNodesProbeForInsertions:  B 5TBW|1|1|C|113 interacts with 5TBW|1|1|G|267
  9 Initial    266 (1 insertion) and  114 (1 insertion)
 10 Basepair   267  113 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Junction Left  5 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   8   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:   9   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  10  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  11   Hairpin Left 15 Right 14
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|A|114
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|115
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|116
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|158
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|A|157
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|156
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|G|155
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|U|154
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|118
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|U|119
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|A|150
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5TBW|1|1|U|153
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: 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: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAAU'
           RightLetter: 'AAUUAA'
               Comment: ' // Basepair U149 - A123 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: '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 5TBW|1|1|A|114'
              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: '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: ''
           RightLetter: ''
               Comment: ' // New 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: 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 5TBW|1|1|A|115'
              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 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            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: '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: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|A|116'
              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 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             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: '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 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5TBW|1|1|G|158'
              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 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 20
             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: 'A'
               Comment: ' // New 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 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 5
            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 5TBW|1|1|A|157'
              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: 5
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [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

Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             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 5TBW|1|1|G|156'
              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: 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: []

Node 15

ans = 

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

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 5
            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 5TBW|1|1|G|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 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 17

ans = 

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

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5TBW|1|1|U|154'
              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: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 19

ans = 

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

                  type: 'Junction'
              nextnode: [4 9]
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: 'J9171'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node U153 - A114 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 20

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J9171'
        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: 5
            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: 'UUG'
           RightLetter: 'A'
               Comment: ' // Basepair U153 - A265 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 22

ans = 

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

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|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 23

ans = 

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

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 24

ans = 

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

                  type: 'Fixed'
              nextnode: 25
             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 5TBW|1|1|U|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 25

ans = 

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

                  type: 'Initial'
              nextnode: 26
             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 26

ans = 

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

                  type: 'Basepair'
              nextnode: 27
             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 A157 - G264 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 27

ans = 

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

                  type: 'Basepair'
              nextnode: 28
             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 G158 - C263 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 29
             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 29

ans = 

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

                  type: 'Initial'
              nextnode: 30
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J9171'
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Initial node 5TBW|1|1|A|266 - 5TBW|1|1|A|114 from 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: 13
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5TBW|1|1|A|150'
              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: 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: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Node 32

ans = 

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

                  type: 'Fixed'
              nextnode: 33
             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 5TBW|1|1|U|153'
              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 33

ans = 

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

                  type: 'Initial'
              nextnode: 34
             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 34

ans = 

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

                  type: 'Basepair'
              nextnode: 35
             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 G267 - C113 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []

Node 35

ans = 

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

                  type: 'Hairpin'
              nextnode: 38
             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 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 21
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 21
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 21
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 21
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 21
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 21
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 21
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 20
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right 20
pMakeMotifModelFromSSF:  12   Initial Left  5 Right 19
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right 19
pMakeMotifModelFromSSF:  14   Initial Left  5 Right 18
pMakeMotifModelFromSSF:  15     Fixed Left  5 Right 18
pMakeMotifModelFromSSF:  16   Initial Left  5 Right 17
pMakeMotifModelFromSSF:  17     Fixed Left  5 Right 17
pMakeMotifModelFromSSF:  18   Initial Left  5 Right 16
pMakeMotifModelFromSSF:  19  Junction Left  5 Right 16
pMakeMotifModelFromSSF:  20   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  21  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:  22     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  23   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  24     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  25   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  26  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  27  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  28   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  29   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  30     Fixed Left 13 Right 16
pMakeMotifModelFromSSF:  31   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  32     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  33   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  34  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  35   Hairpin Left 15 Right 14
pNextNodeJunction: Found a junction at node 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Found a junction child at node 29
pNextNodeJunction: Found a hairpin at node 35
pNextNodeJunction: Finished at node 35 out of 35, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: 'J9171'
        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: 30
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: 'J9171'
        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: 'A'
               Comment: ' // Initial node 5TBW|1|1|A|266 - 5TBW|1|1|A|114 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []

Motif J3_98298.1. Nodes 20 and 29 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 19
pNextNodeJunction: Found a junction child at node 20
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Found a junction child at node 29
pNextNodeJunction: Found a hairpin at node 35
pNextNodeJunction: Finished at node 35 out of 35, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for tWH  between 6 and 16
pConservedInteractionList: did not find a substitution probability matrix for tWH  between 6 and 16
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_98298.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -17.0636

Timestamp 18-Jul-2025 00:13:18
pMakeSCFGModels: Making JAR3D model for motif group J3_98484.1, number 86 of 88
pMakeNodes starting loop:     a=4R4V|1|A|C|663 B=4R4V|1|A|G|710
  2 Basepair   663  710 CG cWW 
No need to probe because of interaction between a=4R4V|1|A|U|664 B=4R4V|1|A|U|709
  3 Basepair   664  709 UU cWW 
pMakeNodes probe for inserts:  a=4R4V|1|A|C|665 B=4R4V|1|A|U|708
    Insertion on left  4R4V|1|A|C|665
pMakeNodes probed for insert:  a=4R4V|1|A|C|666 B=4R4V|1|A|U|708
pMakeNodesJunction: a=4R4V|1|A|C|666 r=4R4V|1|A|C|666 s=4R4V|1|A|G|680 t=4R4V|1|A|U|681 u=B=4R4V|1|A|U|708
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 4R4V|1|A|C|666 and 4R4V|1|A|G|680 and between 4R4V|1|A|U|681 and 4R4V|1|A|U|708
pMakeNodesJunction: about to make a junction: a=4R4V|1|A|C|666 s=4R4V|1|A|G|680 t=4R4V|1|A|U|681 B=4R4V|1|A|U|708
pMakeNodesJunction: first branch starts at   4R4V|1|A|C|666
pMakeNodesJunction: first branch ends around 4R4V|1|A|G|680
pMakeNodesJunction: second branch starts at  4R4V|1|A|U|681
pMakeNodesJunction: junction ends at         4R4V|1|A|U|708
pMakeNodesJunction: first branch strand start goes up to  4R4V|1|A|C|666
pMakeNodesJunction: first branch strand end goes down to  4R4V|1|A|G|680
pMakeNodesJunction: second branch strand start goes up to 4R4V|1|A|G|683
pMakeNodesJunction: last strand of junction goes down to  4R4V|1|A|U|703
pMakeNodesJunction: Junction includes some crossing pairs that will be lost. C1, C2, C3, C4:
     0     1     0     1


Junction with 2 loops, call it J2858
Actual Branch 1 of junction J2858 - Nucleotides 4R4V|1|A|C|666 to 4R4V|1|A|G|680, length   2
Actual Branch 2 of junction J2858 - Nucleotides 4R4V|1|A|U|681 to 4R4V|1|A|U|708, length   9
  4 Junction

2B Branch 1 of 2 of junction J2858 - Nucleotides   666 to   680, length   2
pMakeNodes starting loop:     a=4R4V|1|A|C|666 B=4R4V|1|A|G|680
  6 Basepair   666  680 CG cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J2858 - Nucleotides   681 to   708, length   9
pMakeNodes starting loop:     a=4R4V|1|A|U|681 B=4R4V|1|A|U|708
  9 Basepair   681  708 UU cWH 
pMakeNodes probe for inserts:  a=4R4V|1|A|C|682 B=4R4V|1|A|A|707
    Insertion on left  4R4V|1|A|C|682
pMakeNodesProbeForInsertions:  a 4R4V|1|A|G|683 interacts with 4R4V|1|A|U|703
pMakeNodesProbeForInsertions:  B 4R4V|1|A|A|707 interacts with 4R4V|1|A|U|705
pMakeNodesProbeForInsertions:  B 4R4V|1|A|A|707 interacts with 4R4V|1|A|U|705
pMakeNodes probed for insert:  a=4R4V|1|A|G|683 B=4R4V|1|A|A|707
pMakeNodes making a cluster near strand break a=4R4V|1|A|G|683 B=4R4V|1|A|A|707
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 8 to 8 and then 9 to 13
aa is 8 bb is 9
 10 Cluster   4R4V|1|A|G|683:4R4V|1|A|G|683 4R4V|1|A|U|703:4R4V|1|A|A|707
    LR Inter  4R4V|1|A|G|683 4R4V|1|A|U|703 cWW 
    RR Inter  4R4V|1|A|U|705 4R4V|1|A|A|707 tSH 
    Right strand conserved insertion 4R4V|1|A|G|704 at position 2
    Right strand conserved insertion 4R4V|1|A|G|706 at position 4
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
 11 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  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:  10   Cluster Left  8 Right  9 10 11 12 13
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|C|665
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|C|682
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: []
          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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C663 - G710 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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: 'UC'
           RightLetter: 'U'
               Comment: ' // Basepair U664 - U709 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: 'J2858'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|C|665'
              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 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: '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: []
                  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: 'Junction'
              nextnode: [5 8]
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: 'J2858'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node C666 - U708 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: []
          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: 5
             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: []
          LeftNotInter: []
         RightNotInter: []

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: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C666 - G680 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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 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
          LeftNotInter: []
         RightNotInter: []

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: '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: []
          LeftNotInter: []
         RightNotInter: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            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: 'UC'
           RightLetter: 'U'
               Comment: ' // Basepair U681 - U708 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 12

ans = 

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

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|C|682'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              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
          LeftNotInter: []
         RightNotInter: []

Node 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 14

ans = 

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

                  type: 'Cluster'
              nextnode: 15
             LeftIndex: 8
            RightIndex: [9 10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'UGUGA'
               Comment: ' // Cluster node 4R4V|1|A|G|683:4R4V|1|A|G|683 and 4R4V|1|A|U|703:4R4V|1|A|A|707'
              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 5]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: 1.0000
          LeftNotInter: [1×0 double]
         RightNotInter: [2 4]

Node 15

ans = 

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

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           numbranches: []
              NormCons: []
          LeftNotInter: []
         RightNotInter: []

Node 16

ans = 

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

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: [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  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  5
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  14   Cluster Left  8 Right  9 10 11 12 13
pMakeMotifModelFromSSF:  15   Initial Left  9 Right  8
pMakeMotifModelFromSSF:  16   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 hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin
pUpdateModelWithSSF: J3_98484.1 allow insertions from initial node 15?
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: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: 'J2858'
        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: 11
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: 'J2858'
        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 J3_98484.1. Nodes 7 and 10 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 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 hairpin at node 16
pNextNodeJunction: Finished at node 16 out of 16, type Hairpin

pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 13
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 13
pConservedInteractionList: did not find a substitution probability matrix for cSH  between 7 and 15
pConservedInteractionList: did not find a substitution probability matrix for cSS  between 4 and 13
pConservedInteractionList: did not find a substitution probability matrix for tSS  between 5 and 13
pConservedInteractionList: did not find a substitution probability matrix for cSH  between 7 and 15
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_98484.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7827

Timestamp 18-Jul-2025 00:13:18
pMakeSCFGModels: Making JAR3D model for motif group J3_98985.1, number 87 of 88
pMakeNodes starting loop:     a=6CZR|1|1a|G|357 B=6CZR|1|1a|C|48
  2 Basepair   357   48 GC cWW 
pMakeNodes probe for inserts:  a=6CZR|1|1a|G|358 B=6CZR|1|1a|G|47
pMakeNodes probed for insert:  a=6CZR|1|1a|G|358 B=6CZR|1|1a|G|47
pMakeNodesJunction: a=6CZR|1|1a|G|358 r=6CZR|1|1a|G|358 s=6CZR|1|1a|G|390 t=6CZR|1|1a|C|391 u=B=6CZR|1|1a|G|47
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 6CZR|1|1a|G|358 and 6CZR|1|1a|G|390 and between 6CZR|1|1a|C|391 and 6CZR|1|1a|G|47
pMakeNodesJunction: about to make a junction: a=6CZR|1|1a|G|358 s=6CZR|1|1a|G|390 t=6CZR|1|1a|C|391 B=6CZR|1|1a|G|47
pMakeNodesJunction: first branch starts at   6CZR|1|1a|G|358
pMakeNodesJunction: first branch ends around 6CZR|1|1a|G|390
pMakeNodesJunction: second branch starts at  6CZR|1|1a|C|391
pMakeNodesJunction: junction ends at         6CZR|1|1a|G|47
pMakeNodesJunction: first branch strand start goes up to  6CZR|1|1a|U|363
pMakeNodesJunction: first branch strand end goes down to  6CZR|1|1a|A|389
pMakeNodesJunction: second branch strand start goes up to 6CZR|1|1a|C|391
pMakeNodesJunction: last strand of junction goes down to  6CZR|1|1a|G|47

Junction with 2 loops, call it J7572
Actual Branch 1 of junction J7572 - Nucleotides 6CZR|1|1a|G|358 to 6CZR|1|1a|G|390, length   8
Actual Branch 2 of junction J7572 - Nucleotides 6CZR|1|1a|C|391 to 6CZR|1|1a|G|47, length   2
  3 Junction

2B Branch 1 of 2 of junction J7572 - Nucleotides   358 to   390, length   8
pMakeNodes starting loop:     a=6CZR|1|1a|G|358 B=6CZR|1|1a|G|390
pMakeNodesProbeForInsertions:  a 6CZR|1|1a|G|358 interacts with 6CZR|1|1a|U|361
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|G|390 interacts with 6CZR|1|1a|C|362
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6CZR|1|1a|G|390 interacts with 6CZR|1|1a|C|362
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial    358 (0 insertion) and  390 (0 insertion)
pMakeNodes making a cluster near strand break a=6CZR|1|1a|G|358 B=6CZR|1|1a|G|390
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 9 to 9
aa is 6 bb is 9
  5 Cluster   6CZR|1|1a|G|358:6CZR|1|1a|C|362 6CZR|1|1a|G|390:6CZR|1|1a|G|390
    LR Inter  6CZR|1|1a|C|362 6CZR|1|1a|G|390 cSW 
    LL Inter  6CZR|1|1a|G|358 6CZR|1|1a|U|361 tSW 
    Left  strand conserved insertion 6CZR|1|1a|A|359 at position 2
    Left  strand conserved insertion 6CZR|1|1a|A|360 at position 3
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=6CZR|1|1a|U|363 B=6CZR|1|1a|A|389
  6 Basepair   363  389 UA cWW 
  7 Hairpin type *

2B Branch 2 of 2 of junction J7572 - Nucleotides   391 to    47, length   2
pMakeNodes starting loop:     a=6CZR|1|1a|C|391 B=6CZR|1|1a|G|47
  9 Basepair   391   47 CG cWW 
 10 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  9
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   8   Initial Left 10 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 1 1 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  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: 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 G357 - 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: []
          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: 11
             Insertion: []
                    id: 'J7572'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G358 - G47 ID J7572'
              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: 9
             Insertion: []
                    id: 'J7572'
        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|G|358 - 6CZR|1|1a|G|390 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]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAAUC'
           RightLetter: 'G'
               Comment: ' // Cluster node 6CZR|1|1a|G|358:6CZR|1|1a|C|362 and 6CZR|1|1a|G|390:6CZR|1|1a|G|390'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
           numbranches: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
           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: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U363 - A389 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 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: 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: []
          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: 10
            RightIndex: 11
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C391 - G47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
           numbranches: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: [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 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Junction Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   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 8
pNextNodeJunction: Found a junction child at node 9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: 'J7572'
        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: []
           RightLetter: []
               Comment: ' // Initial node 6CZR|1|1a|G|358 - 6CZR|1|1a|G|390 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: 10
            RightIndex: 11
             Insertion: []
                    id: 'J7572'
        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 J3_98985.1. Nodes 4 and 9 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 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 hairpin at node 11
pNextNodeJunction: Finished at node 11 out of 11, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_98985.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3669
   -5.7013

Timestamp 18-Jul-2025 00:13:19
pMakeSCFGModels: Making JAR3D model for motif group J3_99170.1, number 88 of 88
pMakeNodes starting loop:     a=5TBW|1|1|U|1479 B=5TBW|1|1|A|1874
  2 Basepair  1479 1874 UA cWW 
No need to probe because of interaction between a=5TBW|1|1|G|1480 B=5TBW|1|1|U|1873
pMakeNodes making a cluster near strand break a=5TBW|1|1|G|1480 B=5TBW|1|1|U|1873
pMakeNodesCluster: amax is 5 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 12
aa is 4 bb is 11
  3 Cluster   5TBW|1|1|G|1480:5TBW|1|1|G|1483 5TBW|1|1|C|1872:5TBW|1|1|U|1873
    LR Inter  5TBW|1|1|A|1481 5TBW|1|1|C|1872 tHW 
    LR Inter  5TBW|1|1|G|1480 5TBW|1|1|U|1873 tSH 
    LR Inter  5TBW|1|1|G|1483 5TBW|1|1|U|1873 tWW 
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
pMakeNodes probe for inserts:  a=5TBW|1|1|U|1484 B=5TBW|1|1|U|1871
    Insertion on left  5TBW|1|1|U|1484
  4 Initial   1484 (1 insertion) and 1871 (0 insertion)
pMakeNodes probed for insert:  a=5TBW|1|1|G|1485 B=5TBW|1|1|U|1871
pMakeNodesJunction: a=5TBW|1|1|G|1485 r=5TBW|1|1|G|1485 s=5TBW|1|1|C|1857 t=5TBW|1|1|A|1858 u=B=5TBW|1|1|U|1871
pMakeNodesJunction: a:s count 2
pMakeNodesJunction: t:B count 2
pMakeNodesJunction: Found nested interactions between 5TBW|1|1|G|1485 and 5TBW|1|1|C|1857 and between 5TBW|1|1|A|1858 and 5TBW|1|1|U|1871
pMakeNodesJunction: about to make a junction: a=5TBW|1|1|G|1485 s=5TBW|1|1|C|1857 t=5TBW|1|1|A|1858 B=5TBW|1|1|U|1871
pMakeNodesJunction: first branch starts at   5TBW|1|1|G|1485
pMakeNodesJunction: first branch ends around 5TBW|1|1|C|1857
pMakeNodesJunction: second branch starts at  5TBW|1|1|A|1858
pMakeNodesJunction: junction ends at         5TBW|1|1|U|1871
pMakeNodesJunction: first branch strand start goes up to  5TBW|1|1|G|1485
pMakeNodesJunction: first branch strand end goes down to  5TBW|1|1|C|1857
pMakeNodesJunction: second branch strand start goes up to 5TBW|1|1|A|1859
pMakeNodesJunction: last strand of junction goes down to  5TBW|1|1|U|1871

Junction with 2 loops, call it J7537
Actual Branch 1 of junction J7537 - Nucleotides 5TBW|1|1|G|1485 to 5TBW|1|1|C|1857, length   2
Actual Branch 2 of junction J7537 - Nucleotides 5TBW|1|1|A|1858 to 5TBW|1|1|U|1871, length   3
  5 Junction

2B Branch 1 of 2 of junction J7537 - Nucleotides  1485 to  1857, length   2
pMakeNodes starting loop:     a=5TBW|1|1|G|1485 B=5TBW|1|1|C|1857
  7 Basepair  1485 1857 GC cWW 
  8 Hairpin type *

2B Branch 2 of 2 of junction J7537 - Nucleotides  1858 to  1871, length   3
pMakeNodes starting loop:     a=5TBW|1|1|A|1858 B=5TBW|1|1|U|1871
    Insertion on left  5TBW|1|1|A|1858
pMakeNodesProbeForInsertions:  a 5TBW|1|1|A|1859 interacts with 5TBW|1|1|U|1871
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|1871 interacts with 5TBW|1|1|A|1859
pMakeNodesProbeForInsertions:  B 5TBW|1|1|U|1871 interacts with 5TBW|1|1|A|1859
  9 Initial   1858 (1 insertion) and 1871 (0 insertion)
 10 Basepair  1859 1871 AU cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Junction Left  6 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|G|1483
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5TBW|1|1|C|1857
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 U1479 - A1874 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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 3 4]
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAG'
           RightLetter: 'CU'
               Comment: ' // Cluster node 5TBW|1|1|G|1480:5TBW|1|1|G|1483 and 5TBW|1|1|C|1872:5TBW|1|1|U|1873'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2486
           numbranches: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5TBW|1|1|U|1484 - 5TBW|1|1|U|1871 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: 5
            RightIndex: 10
             Insertion: []
                    id: 'J7537'
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 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|1483'
              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: 6
            RightIndex: 10
             Insertion: []
                    id: 'J7537'
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // New 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: 6
            RightIndex: 10
             Insertion: []
                    id: 'J7537'
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: []
           RightLetter: []
               Comment: '// Junction node G1485 - U1871 ID J7537'
              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: 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: []
          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: 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 G1485 - C1857 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J7537'
        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|1858 - 5TBW|1|1|U|1871 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: 'Fixed'
              nextnode: 13
             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 5TBW|1|1|C|1857'
              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 13

ans = 

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

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []

Node 14

ans = 

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

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1859 - U1871 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     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: 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: []
          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  3  4 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   7  Junction Left  6 Right 10
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 10
pMakeMotifModelFromSSF:  12     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  15   Hairpin Left 10 Right  9
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 hairpin at node 15
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: 9
             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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
           numbranches: []


ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: 'J7537'
        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|1858 - 5TBW|1|1|U|1871 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 J3_99170.1. Nodes 8 and 11 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 hairpin at node 15
pNextNodeJunction: Finished at node 15 out of 15, type Hairpin

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\lib\J3_99170.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6503

There are 88 motif groups, of which 78 are structured
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     5
     2     2     6
     2     2     7
     2     2     8
     2     2     9
     2     3     3
     2     3     4
     2     3     5
     2     3     6
     2     3     7
     2     3     8
     2     4     3
     2     4     4
     2     4     5
     2     4     6
     2     4     7
     2     4     9
     2     4    10
     2     4    13
     2     4    14
     2     5     4
     2     5     5
     2     5     7
     2     5     8
     2     5     9
     2     5    13
     2     6     4
     2     6     5
     2     6     6
     2     6     7
     2     6     8
     2     7     3
     2     7     4
     2     7     5
     2     7     6
     2     8     3
     2     8     4
     2     8     5
     2     9     3
     2     9     4
     2     9     5
     2     9     6
     2    10     3
     2    10     5
     2    10     6
     2    10     7
     2    11     6
     3     2     5
     3     2     6
     3     2     8
     3     3     3
     3     3     4
     3     3     5
     3     3     6
     3     3     7
     3     3     8
     3     4     3
     3     4     4
     3     4     5
     3     4     6
     3     4     7
     3     4     8
     3     4     9
     3     4    13
     3     5     4
     3     5     5
     3     5     6
     3     5     7
     3     5     8
     3     5     9
     3     5    12
     3     5    13
     3     6     4
     3     6     5
     3     6     6
     3     6     7
     3     6     8
     3     6     9
     3     6    12
     3     7     3
     3     7     4
     3     7     5
     3     7     6
     3     7     7
     3     7     8
     3     7    10
     3     7    11
     3     8     3
     3     8     4
     3     8     5
     3     8     6
     3     8    10
     3     9     3
     3     9     5
     3    10     6
     4     3     3
     4     3     4
     4     3     5
     4     3     6
     4     3     7
     4     4     4
     4     4     5
     4     4     6
     4     4     7
     4     4     8
     4     4     9
     4     5     4
     4     5     5
     4     5     6
     4     5     7
     4     5     8
     4     5     9
     4     5    12
     4     6     4
     4     6     5
     4     6     6
     4     6     7
     4     6     8
     4     6     9
     4     7     4
     4     7     5
     4     7     6
     4     7     7
     4     7     8
     4     7     9
     4     7    10
     4     8     5
     4     8     6
     4     8     8
     4     9     5
     4     9     6
     4    10     5
     5     4     5
     5     4     6
     5     4     7
     5     4     8
     5     5     4
     5     5     6
     5     5     7
     5     5     8
     5     5     9
     5     5    10
     5     6     6
     5     6     7
     5     6     8
     5     6     9
     5     7     6
     5     7     7
     5     7     8
     5     8     5
     5     8     6
     5     8    12
     5     8    13
     5     9     5
     5     9    12
     5    11    10
     5    11    11
     5    12    10
     6     5     6
     6     5     8
     6     5     9
     6     6     6
     6     6     7
     6     6     8
     6     6     9
     6     7     6
     6     7     7
     6     7     8
     6     8     7
     6     8    12
     6    11    10
     7     6     6
     7     6     8
     7     7     7
     7     9    13
     7     9    14
     7    10    13
     8     9    13

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   178     3

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13018 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12556 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13026 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12415 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12893 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13120 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13313 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12980 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13119 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12739 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 13086 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12847 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12978 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12931 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 12772 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     5
     2     2     6
     2     2     7
     2     2     8
     2     2     9
     2     3     3
     2     3     4
     2     3     5
     2     3     6
     2     3     7
     2     3     8
     2     4     3
     2     4     4
     2     4     5
     2     4     6
     2     4     7
     2     4     9
     2     4    10
     2     4    13
     2     4    14
     2     5     4
     2     5     5
     2     5     7
     2     5     8
     2     5     9
     2     5    13
     2     6     4
     2     6     5
     2     6     6
     2     6     7
     2     6     8
     2     7     3
     2     7     4
     2     7     5
     2     7     6
     2     8     3
     2     8     4
     2     8     5
     2     9     3
     2     9     4
     2     9     5
     2     9     6
     2    10     3
     2    10     5
     2    10     6
     2    10     7
     2    11     6
     3     2     5
     3     2     6
     3     2     8
     3     3     3
     3     3     4
     3     3     5
     3     3     6
     3     3     7
     3     3     8
     3     4     3
     3     4     4
     3     4     5
     3     4     6
     3     4     7
     3     4     8
     3     4     9
     3     4    13
     3     5     4
     3     5     5
     3     5     6
     3     5     7
     3     5     8
     3     5     9
     3     5    12
     3     5    13
     3     6     4
     3     6     5
     3     6     6
     3     6     7
     3     6     8
     3     6     9
     3     6    12
     3     7     3
     3     7     4
     3     7     5
     3     7     6
     3     7     7
     3     7     8
     3     7    10
     3     7    11
     3     8     3
     3     8     4
     3     8     5
     3     8     6
     3     8    10
     3     9     3
     3     9     5
     3    10     6
     4     3     3
     4     3     4
     4     3     5
     4     3     6
     4     3     7
     4     4     4
     4     4     5
     4     4     6
     4     4     7
     4     4     8
     4     4     9
     4     5     4
     4     5     5
     4     5     6
     4     5     7
     4     5     8
     4     5     9
     4     5    12
     4     6     4
     4     6     5
     4     6     6
     4     6     7
     4     6     8
     4     6     9
     4     7     4
     4     7     5
     4     7     6
     4     7     7
     4     7     8
     4     7     9
     4     7    10
     4     8     5
     4     8     6
     4     8     8
     4     9     5
     4     9     6
     4    10     5
     5     4     5
     5     4     6
     5     4     7
     5     4     8
     5     5     4
     5     5     6
     5     5     7
     5     5     8
     5     5     9
     5     5    10
     5     6     6
     5     6     7
     5     6     8
     5     6     9
     5     7     6
     5     7     7
     5     7     8
     5     8     5
     5     8     6
     5     8    12
     5     8    13
     5     9     5
     5     9    12
     5    11    10
     5    11    11
     5    12    10
     6     5     6
     6     5     8
     6     5     9
     6     6     6
     6     6     7
     6     6     8
     6     6     9
     6     7     6
     6     7     7
     6     7     8
     6     8     7
     6     8    12
     6    11    10
     7     6     6
     7     6     8
     7     7     7
     7     9    13
     7     9    14
     7    10    13
     8     9    13

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   178     3

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8492 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8383 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8396 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8833 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8658 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8611 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8538 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8684 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8434 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8571 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8478 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8185 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8421 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8500 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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pMakeRandomSequencesWeighted: Generating 5340 sequences required 8655 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     2     5
     2     2     6
     2     2     7
     2     2     8
     2     2     9
     2     3     3
     2     3     4
     2     3     5
     2     3     6
     2     3     7
     2     3     8
     2     4     3
     2     4     4
     2     4     5
     2     4     6
     2     4     7
     2     4     9
     2     4    10
     2     4    13
     2     4    14
     2     5     4
     2     5     5
     2     5     7
     2     5     8
     2     5     9
     2     5    13
     2     6     4
     2     6     5
     2     6     6
     2     6     7
     2     6     8
     2     7     3
     2     7     4
     2     7     5
     2     7     6
     2     8     3
     2     8     4
     2     8     5
     2     9     3
     2     9     4
     2     9     5
     2     9     6
     2    10     3
     2    10     5
     2    10     6
     2    10     7
     2    11     6
     3     2     5
     3     2     6
     3     2     8
     3     3     3
     3     3     4
     3     3     5
     3     3     6
     3     3     7
     3     3     8
     3     4     3
     3     4     4
     3     4     5
     3     4     6
     3     4     7
     3     4     8
     3     4     9
     3     4    13
     3     5     4
     3     5     5
     3     5     6
     3     5     7
     3     5     8
     3     5     9
     3     5    12
     3     5    13
     3     6     4
     3     6     5
     3     6     6
     3     6     7
     3     6     8
     3     6     9
     3     6    12
     3     7     3
     3     7     4
     3     7     5
     3     7     6
     3     7     7
     3     7     8
     3     7    10
     3     7    11
     3     8     3
     3     8     4
     3     8     5
     3     8     6
     3     8    10
     3     9     3
     3     9     5
     3    10     6
     4     3     3
     4     3     4
     4     3     5
     4     3     6
     4     3     7
     4     4     4
     4     4     5
     4     4     6
     4     4     7
     4     4     8
     4     4     9
     4     5     4
     4     5     5
     4     5     6
     4     5     7
     4     5     8
     4     5     9
     4     5    12
     4     6     4
     4     6     5
     4     6     6
     4     6     7
     4     6     8
     4     6     9
     4     7     4
     4     7     5
     4     7     6
     4     7     7
     4     7     8
     4     7     9
     4     7    10
     4     8     5
     4     8     6
     4     8     8
     4     9     5
     4     9     6
     4    10     5
     5     4     5
     5     4     6
     5     4     7
     5     4     8
     5     5     4
     5     5     6
     5     5     7
     5     5     8
     5     5     9
     5     5    10
     5     6     6
     5     6     7
     5     6     8
     5     6     9
     5     7     6
     5     7     7
     5     7     8
     5     8     5
     5     8     6
     5     8    12
     5     8    13
     5     9     5
     5     9    12
     5    11    10
     5    11    11
     5    12    10
     6     5     6
     6     5     8
     6     5     9
     6     6     6
     6     6     7
     6     6     8
     6     6     9
     6     7     6
     6     7     7
     6     7     8
     6     8     7
     6     8    12
     6    11    10
     7     6     6
     7     6     8
     7     7     7
     7     9    13
     7     9    14
     7    10    13
     8     9    13

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   178     3

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

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
     5     5     5     5     5     5     5     5     5     5

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.3781
    0.3342
    0.0849
    0.1068
    0.0438
    0.0521

    0.2906
    0.1437
    0.3000
    0.2656

    0.3893    0.2143    0.1607    0.2357
    0.2621    0.1172    0.4207    0.2000
    0.4093    0.2798    0.1347    0.1762
    0.3386    0.1587    0.1852    0.3175

pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Read random sequence variant file J3_RandomMotifSequences_1.fasta
max_rotation=2 r=0 n=1 a=GC*GC*GAUAC FASTA(n).Sequence=GC*GC*GAUAC
max_rotation=2 r=1 n=1 a=GC*GAUAC*GC FASTA(n).Sequence=GC*GC*GAUAC
max_rotation=2 r=2 n=1 a=GAUAC*GC*GC FASTA(n).Sequence=GC*GC*GAUAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:14:25
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   4.4429 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   4.0603 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:18:15
Parsing 5340 sequences from file J3_RandomMotifSequences_1.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   7.9911 minutes
Read random sequence variant file J3_RandomMotifSequences_2.fasta
max_rotation=2 r=0 n=1 a=CG*CG*CCGAG FASTA(n).Sequence=CG*CG*CCGAG
max_rotation=2 r=1 n=1 a=CG*CCGAG*CG FASTA(n).Sequence=CG*CG*CCGAG
max_rotation=2 r=2 n=1 a=CCGAG*CG*CG FASTA(n).Sequence=CG*CG*CCGAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:26:42
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.6240 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.4717 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:30:05
Parsing 5340 sequences from file J3_RandomMotifSequences_2.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.5039 minutes
Read random sequence variant file J3_RandomMotifSequences_3.fasta
max_rotation=2 r=0 n=1 a=GU*AC*GGACC FASTA(n).Sequence=GU*AC*GGACC
max_rotation=2 r=1 n=1 a=AC*GGACC*GU FASTA(n).Sequence=GU*AC*GGACC
max_rotation=2 r=2 n=1 a=GGACC*GU*AC FASTA(n).Sequence=GU*AC*GGACC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:38:43
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.7643 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.4462 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:42:06
Parsing 5340 sequences from file J3_RandomMotifSequences_3.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4395 minutes
Read random sequence variant file J3_RandomMotifSequences_4.fasta
max_rotation=2 r=0 n=1 a=GU*AC*GAUUC FASTA(n).Sequence=GU*AC*GAUUC
max_rotation=2 r=1 n=1 a=AC*GAUUC*GU FASTA(n).Sequence=GU*AC*GAUUC
max_rotation=2 r=2 n=1 a=GAUUC*GU*AC FASTA(n).Sequence=GU*AC*GAUUC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:50:40
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.7574 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.4735 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 00:54:03
Parsing 5340 sequences from file J3_RandomMotifSequences_4.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.5004 minutes
Read random sequence variant file J3_RandomMotifSequences_5.fasta
max_rotation=2 r=0 n=1 a=AA*UU*AAGCU FASTA(n).Sequence=AA*UU*AAGCU
max_rotation=2 r=1 n=1 a=UU*AAGCU*AA FASTA(n).Sequence=AA*UU*AAGCU
max_rotation=2 r=2 n=1 a=AAGCU*AA*UU FASTA(n).Sequence=AA*UU*AAGCU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:02:39
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.6395 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.3262 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:05:54
Parsing 5340 sequences from file J3_RandomMotifSequences_5.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.3288 minutes
Read random sequence variant file J3_RandomMotifSequences_6.fasta
max_rotation=2 r=0 n=1 a=UG*CA*UGACA FASTA(n).Sequence=UG*CA*UGACA
max_rotation=2 r=1 n=1 a=CA*UGACA*UG FASTA(n).Sequence=UG*CA*UGACA
max_rotation=2 r=2 n=1 a=UGACA*UG*CA FASTA(n).Sequence=UG*CA*UGACA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:14:20
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.8352 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.4409 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:17:39
Parsing 5340 sequences from file J3_RandomMotifSequences_6.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.3625 minutes
Read random sequence variant file J3_RandomMotifSequences_7.fasta
max_rotation=2 r=0 n=1 a=UG*CG*UGAGG FASTA(n).Sequence=UG*CG*UGAGG
max_rotation=2 r=1 n=1 a=CG*UGAGG*UG FASTA(n).Sequence=UG*CG*UGAGG
max_rotation=2 r=2 n=1 a=UGAGG*UG*CG FASTA(n).Sequence=UG*CG*UGAGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:26:14
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.9752 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.6724 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:29:48
Parsing 5340 sequences from file J3_RandomMotifSequences_7.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4779 minutes
Read random sequence variant file J3_RandomMotifSequences_8.fasta
max_rotation=2 r=0 n=1 a=GU*AC*GAUCC FASTA(n).Sequence=GU*AC*GAUCC
max_rotation=2 r=1 n=1 a=AC*GAUCC*GU FASTA(n).Sequence=GU*AC*GAUCC
max_rotation=2 r=2 n=1 a=GAUCC*GU*AC FASTA(n).Sequence=GU*AC*GAUCC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:38:26
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.9369 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.6414 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:42:00
Parsing 5340 sequences from file J3_RandomMotifSequences_8.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4340 minutes
Read random sequence variant file J3_RandomMotifSequences_9.fasta
max_rotation=2 r=0 n=1 a=AC*GU*ACAAU FASTA(n).Sequence=AC*GU*ACAAU
max_rotation=2 r=1 n=1 a=GU*ACAAU*AC FASTA(n).Sequence=AC*GU*ACAAU
max_rotation=2 r=2 n=1 a=ACAAU*AC*GU FASTA(n).Sequence=AC*GU*ACAAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:50:39
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.9405 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.6567 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 01:54:13
Parsing 5340 sequences from file J3_RandomMotifSequences_9.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.6255 minutes
Read random sequence variant file J3_RandomMotifSequences_10.fasta
max_rotation=2 r=0 n=1 a=CG*CG*CUUUG FASTA(n).Sequence=CG*CG*CUUUG
max_rotation=2 r=1 n=1 a=CG*CUUUG*CG FASTA(n).Sequence=CG*CG*CUUUG
max_rotation=2 r=2 n=1 a=CUUUG*CG*CG FASTA(n).Sequence=CG*CG*CUUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:02:58
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   4.0364 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.7158 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:06:33
Parsing 5340 sequences from file J3_RandomMotifSequences_10.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.5874 minutes
Read random sequence variant file J3_RandomMotifSequences_11.fasta
max_rotation=2 r=0 n=1 a=GC*GC*GUAGC FASTA(n).Sequence=GC*GC*GUAGC
max_rotation=2 r=1 n=1 a=GC*GUAGC*GC FASTA(n).Sequence=GC*GC*GUAGC
max_rotation=2 r=2 n=1 a=GUAGC*GC*GC FASTA(n).Sequence=GC*GC*GUAGC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:15:16
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.9805 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.6863 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:18:50
Parsing 5340 sequences from file J3_RandomMotifSequences_11.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.6448 minutes
Read random sequence variant file J3_RandomMotifSequences_12.fasta
max_rotation=2 r=0 n=1 a=CA*UG*CAUUG FASTA(n).Sequence=CA*UG*CAUUG
max_rotation=2 r=1 n=1 a=UG*CAUUG*CA FASTA(n).Sequence=CA*UG*CAUUG
max_rotation=2 r=2 n=1 a=CAUUG*CA*UG FASTA(n).Sequence=CA*UG*CAUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:27:26
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.8363 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.5750 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:30:55
Parsing 5340 sequences from file J3_RandomMotifSequences_12.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4254 minutes
Read random sequence variant file J3_RandomMotifSequences_13.fasta
max_rotation=2 r=0 n=1 a=AU*AU*AUAAU FASTA(n).Sequence=AU*AU*AUAAU
max_rotation=2 r=1 n=1 a=AU*AUAAU*AU FASTA(n).Sequence=AU*AU*AUAAU
max_rotation=2 r=2 n=1 a=AUAAU*AU*AU FASTA(n).Sequence=AU*AU*AUAAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:39:32
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.6317 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.4223 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:42:52
Parsing 5340 sequences from file J3_RandomMotifSequences_13.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4196 minutes
Read random sequence variant file J3_RandomMotifSequences_14.fasta
max_rotation=2 r=0 n=1 a=GA*UC*GAUUC FASTA(n).Sequence=GA*UC*GAUUC
max_rotation=2 r=1 n=1 a=UC*GAUUC*GA FASTA(n).Sequence=GA*UC*GAUUC
max_rotation=2 r=2 n=1 a=GAUUC*GA*UC FASTA(n).Sequence=GA*UC*GAUUC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:51:28
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.9328 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.6321 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 02:54:58
Parsing 5340 sequences from file J3_RandomMotifSequences_14.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.4538 minutes
Read random sequence variant file J3_RandomMotifSequences_15.fasta
max_rotation=2 r=0 n=1 a=AC*GU*AGCAU FASTA(n).Sequence=AC*GU*AGCAU
max_rotation=2 r=1 n=1 a=GU*AGCAU*AC FASTA(n).Sequence=AC*GU*AGCAU
max_rotation=2 r=2 n=1 a=AGCAU*AC*GU FASTA(n).Sequence=AC*GU*AGCAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:03:33
Finding core edit distance of 5340 sequences against   88 models over    3 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   3.7680 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.5458 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:06:59
Parsing 5340 sequences from file J3_RandomMotifSequences_15.fasta against 88 models over 3 rotations
Parsed against   50 models so far, total time estimate   8.6181 minutes
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_1.mat
max_rotation=2 r=0 n=1 a=GC*GC*GAUAC FASTA(n).Sequence=GC*GC*GAUAC
max_rotation=2 r=1 n=1 a=GC*GAUAC*GC FASTA(n).Sequence=GC*GC*GAUAC
max_rotation=2 r=2 n=1 a=GAUAC*GC*GC FASTA(n).Sequence=GC*GC*GAUAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:36
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_2.mat
max_rotation=2 r=0 n=1 a=CG*CG*CCGAG FASTA(n).Sequence=CG*CG*CCGAG
max_rotation=2 r=1 n=1 a=CG*CCGAG*CG FASTA(n).Sequence=CG*CG*CCGAG
max_rotation=2 r=2 n=1 a=CCGAG*CG*CG FASTA(n).Sequence=CG*CG*CCGAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:37
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_3.mat
max_rotation=2 r=0 n=1 a=GU*AC*GGACC FASTA(n).Sequence=GU*AC*GGACC
max_rotation=2 r=1 n=1 a=AC*GGACC*GU FASTA(n).Sequence=GU*AC*GGACC
max_rotation=2 r=2 n=1 a=GGACC*GU*AC FASTA(n).Sequence=GU*AC*GGACC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:37
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_4.mat
max_rotation=2 r=0 n=1 a=GU*AC*GAUUC FASTA(n).Sequence=GU*AC*GAUUC
max_rotation=2 r=1 n=1 a=AC*GAUUC*GU FASTA(n).Sequence=GU*AC*GAUUC
max_rotation=2 r=2 n=1 a=GAUUC*GU*AC FASTA(n).Sequence=GU*AC*GAUUC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:38
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_5.mat
max_rotation=2 r=0 n=1 a=AA*UU*AAGCU FASTA(n).Sequence=AA*UU*AAGCU
max_rotation=2 r=1 n=1 a=UU*AAGCU*AA FASTA(n).Sequence=AA*UU*AAGCU
max_rotation=2 r=2 n=1 a=AAGCU*AA*UU FASTA(n).Sequence=AA*UU*AAGCU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:39
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_6.mat
max_rotation=2 r=0 n=1 a=UG*CA*UGACA FASTA(n).Sequence=UG*CA*UGACA
max_rotation=2 r=1 n=1 a=CA*UGACA*UG FASTA(n).Sequence=UG*CA*UGACA
max_rotation=2 r=2 n=1 a=UGACA*UG*CA FASTA(n).Sequence=UG*CA*UGACA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:40
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_7.mat
max_rotation=2 r=0 n=1 a=UG*CG*UGAGG FASTA(n).Sequence=UG*CG*UGAGG
max_rotation=2 r=1 n=1 a=CG*UGAGG*UG FASTA(n).Sequence=UG*CG*UGAGG
max_rotation=2 r=2 n=1 a=UGAGG*UG*CG FASTA(n).Sequence=UG*CG*UGAGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:41
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_8.mat
max_rotation=2 r=0 n=1 a=GU*AC*GAUCC FASTA(n).Sequence=GU*AC*GAUCC
max_rotation=2 r=1 n=1 a=AC*GAUCC*GU FASTA(n).Sequence=GU*AC*GAUCC
max_rotation=2 r=2 n=1 a=GAUCC*GU*AC FASTA(n).Sequence=GU*AC*GAUCC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:42
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_9.mat
max_rotation=2 r=0 n=1 a=AC*GU*ACAAU FASTA(n).Sequence=AC*GU*ACAAU
max_rotation=2 r=1 n=1 a=GU*ACAAU*AC FASTA(n).Sequence=AC*GU*ACAAU
max_rotation=2 r=2 n=1 a=ACAAU*AC*GU FASTA(n).Sequence=AC*GU*ACAAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:42
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_10.mat
max_rotation=2 r=0 n=1 a=CG*CG*CUUUG FASTA(n).Sequence=CG*CG*CUUUG
max_rotation=2 r=1 n=1 a=CG*CUUUG*CG FASTA(n).Sequence=CG*CG*CUUUG
max_rotation=2 r=2 n=1 a=CUUUG*CG*CG FASTA(n).Sequence=CG*CG*CUUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:43
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_11.mat
max_rotation=2 r=0 n=1 a=GC*GC*GUAGC FASTA(n).Sequence=GC*GC*GUAGC
max_rotation=2 r=1 n=1 a=GC*GUAGC*GC FASTA(n).Sequence=GC*GC*GUAGC
max_rotation=2 r=2 n=1 a=GUAGC*GC*GC FASTA(n).Sequence=GC*GC*GUAGC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:44
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_12.mat
max_rotation=2 r=0 n=1 a=CA*UG*CAUUG FASTA(n).Sequence=CA*UG*CAUUG
max_rotation=2 r=1 n=1 a=UG*CAUUG*CA FASTA(n).Sequence=CA*UG*CAUUG
max_rotation=2 r=2 n=1 a=CAUUG*CA*UG FASTA(n).Sequence=CA*UG*CAUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:45
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_13.mat
max_rotation=2 r=0 n=1 a=AU*AU*AUAAU FASTA(n).Sequence=AU*AU*AUAAU
max_rotation=2 r=1 n=1 a=AU*AUAAU*AU FASTA(n).Sequence=AU*AU*AUAAU
max_rotation=2 r=2 n=1 a=AUAAU*AU*AU FASTA(n).Sequence=AU*AU*AUAAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:46
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_14.mat
max_rotation=2 r=0 n=1 a=GA*UC*GAUUC FASTA(n).Sequence=GA*UC*GAUUC
max_rotation=2 r=1 n=1 a=UC*GAUUC*GA FASTA(n).Sequence=GA*UC*GAUUC
max_rotation=2 r=2 n=1 a=GAUUC*GA*UC FASTA(n).Sequence=GA*UC*GAUUC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:47
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\J3\3.48\diagnostic\J3_RandomMotifSequences_15.mat
max_rotation=2 r=0 n=1 a=AC*GU*AGCAU FASTA(n).Sequence=AC*GU*AGCAU
max_rotation=2 r=1 n=1 a=GU*AGCAU*AC FASTA(n).Sequence=AC*GU*AGCAU
max_rotation=2 r=2 n=1 a=AGCAU*AC*GU FASTA(n).Sequence=AC*GU*AGCAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 03:15:47
Evaluating how sequences fit models
Saved group data

GroupData = 

  1×88 <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\J3\3.48\J3_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\J3\3.48\J3_GroupData.mat
