Timestamp 18-Jul-2025 22:26:18
pMakeSCFGModels: Looking for motifs in C:\Users\zirbel\Documents\JAR3D\Motifs\HL_3.98\mat
pMakeSCFGModels: Found 253 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 HL_00317.1
    {'> HL_00317.1  6SVS U   50 A   69'}    {'UGGCCUUUCUUAAAAAAAAA'}

pCalculateTransitions:  processing HL_00914.1
    {'> HL_00914.1  8CRE G 2514 C 2521'}    {'GGUCAAAC'}

pCalculateTransitions:  processing HL_01255.1
    {'> HL_01255.1  8Y03 C   25 G   36'}    {'CAUCCAGUAAAG'}

pCalculateTransitions:  processing HL_01609.3
  Columns 1 through 6

    {'> HL_01609.3  5…'}    {'CUGGAAAG'}    {'> HL_01609.3  7…'}    {'CUGGAAAG'}    {'> HL_01609.3  5…'}    {'CUGGGAUG'}

  Columns 7 through 12

    {'> HL_01609.3  3…'}    {'GUGAAAUUC'}    {'> HL_01609.3  6…'}    {'GUGAAAUUC'}    {'> HL_01609.3  4…'}    {'UUGGAAUA'}

  Columns 13 through 18

    {'> HL_01609.3  9…'}    {'UUGGGAAG'}    {'> HL_01609.3  4…'}    {'GUGUAAUUC'}    {'> HL_01609.3  6…'}    {'GUGAAAUUC'}

  Columns 19 through 24

    {'> HL_01609.3  4…'}    {'CUGGAAAG'}    {'> HL_01609.3  3…'}    {'GUGAAAUUC'}    {'> HL_01609.3  4…'}    {'GUGAAAUUC'}

  Columns 25 through 30

    {'> HL_01609.3  8…'}    {'UUGGAACA'}    {'> HL_01609.3  8…'}    {'UUGGAACA'}    {'> HL_01609.3  2…'}    {'CUGAGAUG'}

  Columns 31 through 36

    {'> HL_01609.3  3…'}    {'GUUCGAUCC'}    {'> HL_01609.3  8…'}    {'GUCAUCAGC'}    {'> HL_01609.3  5…'}    {'GUUACAAUC'}

pCalculateTransitions:  processing HL_01962.2
  Columns 1 through 6

    {'> HL_01962.2  5…'}    {'UUUAUUAAAAA'}    {'> HL_01962.2  9…'}    {'UUUACCAAAAA'}    {'> HL_01962.2  4…'}    {'UCUAGUAACAA'}

  Columns 7 through 12

    {'> HL_01962.2  4…'}    {'UUUAUCAAAAA'}    {'> HL_01962.2  8…'}    {'UCUAAUUAAAA'}    {'> HL_01962.2  8…'}    {'UCUAAUUAAAA'}

pCalculateTransitions:  processing HL_02483.1
    {'> HL_02483.1  4PKD U   92 G  103'}    {'UGAUCACGAAGG'}

pCalculateTransitions:  processing HL_02581.1
    {'> HL_02581.1  1WZ2 C  912…'}    {'CGAGCCUGGUCAAAG'}    {'> HL_02581.1  2ZZM C   12…'}    {'CAAGCCUGGCCAAAG'}

pCalculateTransitions:  processing HL_02817.2
    {'> HL_02817.2  8…'}    {'CCAAAUAG'}    {'> HL_02817.2  2…'}    {'CCAAAUAG'}    {'> HL_02817.2  5…'}    {'GAAUUAAC'}

pCalculateTransitions:  processing HL_02887.3
    {'> HL_02887.3  4LFB C 1314…'}    {'CUGCAACCCG'}    {'> HL_02887.3  5J7L C 1314…'}    {'CUGCAACUCG'}

pCalculateTransitions:  processing HL_04171.7
  Columns 1 through 6

    {'> HL_04171.7  4…'}    {'AUGAUAUGGUU'}    {'> HL_04171.7  4…'}    {'AUGAUAUGGUU'}    {'> HL_04171.7  1…'}    {'AUGAUAUGGUU'}

  Columns 7 through 12

    {'> HL_04171.7  8…'}    {'AUGAUAUGGUU'}    {'> HL_04171.7  3…'}    {'AUGAUAUGGUU'}    {'> HL_04171.7  5…'}    {'AUGAUAUGGUU'}

  Columns 13 through 18

    {'> HL_04171.7  3…'}    {'AUGAUAUGGUU'}    {'> HL_04171.7  7…'}    {'AUAAUAUGGUU'}    {'> HL_04171.7  4…'}    {'UUACCGUAGUA'}

pCalculateTransitions:  processing HL_04259.3
  Columns 1 through 6

    {'> HL_04259.3  4…'}    {'CCUACAAG'}    {'> HL_04259.3  9…'}    {'CCUGCAAG'}    {'> HL_04259.3  7…'}    {'CUGACACG'}

  Columns 7 through 12

    {'> HL_04259.3  8…'}    {'UAGAAAUA'}    {'> HL_04259.3  7…'}    {'UUGAAAAA'}    {'> HL_04259.3  3…'}    {'GCUUCAAAC'}

  Columns 13 through 14

    {'> HL_04259.3  3…'}    {'GGGGAACC'}

pCalculateTransitions:  processing HL_04641.1
    {'> HL_04641.1  7OS0 C   16 G   25'}    {'CAAGACGACG'}

pCalculateTransitions:  processing HL_04642.1
    {'> HL_04642.1  6…'}    {'CAGGCGGUUAG'}    {'> HL_04642.1  8…'}    {'CAGGUGGUUAG'}    {'> HL_04642.1  7…'}    {'CAGUCGGUAG'}

pCalculateTransitions:  processing HL_04725.1
    {'> HL_04725.1  4M4O G   28…'}    {'GUUACUUAGUUC'}    {'> HL_04725.1  4M6D G   28…'}    {'GUUACUUAGUUC'}

pCalculateTransitions:  processing HL_04783.2
  Columns 1 through 6

    {'> HL_04783.2  5…'}    {'CGAAAG'}    {'> HL_04783.2  3…'}    {'GGAAAC'}    {'> HL_04783.2  8…'}    {'CUAGCG'}

  Columns 7 through 12

    {'> HL_04783.2  3…'}    {'GGAACAC'}    {'> HL_04783.2  3…'}    {'AUUGAAAAU'}    {'> HL_04783.2  3…'}    {'AUUGCAAAU'}

  Columns 13 through 18

    {'> HL_04783.2  1…'}    {'UGUAAG'}    {'> HL_04783.2  4…'}    {'CGCAACG'}    {'> HL_04783.2  4…'}    {'CGUAG'}

pCalculateTransitions:  processing HL_05304.3
  Columns 1 through 6

    {'> HL_05304.3  8…'}    {'AAUGUAAAUACCU'}    {'> HL_05304.3  8…'}    {'AAUGUAAAUACCU'}    {'> HL_05304.3  4…'}    {'GAGGUAGCGGUGC'}

  Columns 7 through 10

    {'> HL_05304.3  7…'}    {'GGUCAGAAAAUCUAC'}    {'> HL_05304.3  5…'}    {'AGGUUCGAAUCCU'}

pCalculateTransitions:  processing HL_06059.6
  Columns 1 through 6

    {'> HL_06059.6  7…'}    {'CUUCCCAAG'}    {'> HL_06059.6  9…'}    {'AUUGCAAAU'}    {'> HL_06059.6  6…'}    {'GCUCAUAAC'}

  Columns 7 through 12

    {'> HL_06059.6  6…'}    {'AUUGAAAAU'}    {'> HL_06059.6  6…'}    {'GCUGAUAAC'}    {'> HL_06059.6  5…'}    {'CCUUACAAG'}

  Columns 13 through 18

    {'> HL_06059.6  7…'}    {'CCUUACAAG'}    {'> HL_06059.6  9…'}    {'GCUCAUAAC'}    {'> HL_06059.6  6…'}    {'GCUGCGAAC'}

  Columns 19 through 24

    {'> HL_06059.6  4…'}    {'GCUCAUAAC'}    {'> HL_06059.6  6…'}    {'GUUCGGGAC'}    {'> HL_06059.6  6…'}    {'GCUGAUAAC'}

  Columns 25 through 30

    {'> HL_06059.6  5…'}    {'GCUCAUAAC'}    {'> HL_06059.6  4…'}    {'AUUGAAAAU'}    {'> HL_06059.6  4…'}    {'GUUCGGGAC'}

  Columns 31 through 36

    {'> HL_06059.6  4…'}    {'UCUCGAAAA'}    {'> HL_06059.6  2…'}    {'ACUCCAGAU'}    {'> HL_06059.6  6…'}    {'CUUGGUAAG'}

  Columns 37 through 42

    {'> HL_06059.6  4…'}    {'GCUCAUAAC'}    {'> HL_06059.6  4…'}    {'AUUGAAAAU'}    {'> HL_06059.6  4…'}    {'GCUCAUAAC'}

  Columns 43 through 48

    {'> HL_06059.6  4…'}    {'GCUCAUAAC'}    {'> HL_06059.6  7…'}    {'GUUCACGUC'}    {'> HL_06059.6  1…'}    {'CCUGGAAAG'}

  Columns 49 through 54

    {'> HL_06059.6  6…'}    {'GUUCGGGAC'}    {'> HL_06059.6  4…'}    {'CGUCGUCGG'}    {'> HL_06059.6  7…'}    {'GUUCACGUC'}

  Columns 55 through 60

    {'> HL_06059.6  3…'}    {'ACUGAAAAU'}    {'> HL_06059.6  1…'}    {'AUUGCAAAU'}    {'> HL_06059.6  6…'}    {'GCUGAUAAC'}

  Columns 61 through 66

    {'> HL_06059.6  7…'}    {'AUUGAAGAU'}    {'> HL_06059.6  5…'}    {'UUUCACAAA'}    {'> HL_06059.6  7…'}    {'CCUGAAAAG'}

  Columns 67 through 72

    {'> HL_06059.6  6…'}    {'GUUCGGGAC'}    {'> HL_06059.6  5…'}    {'ACUUUUAAU'}    {'> HL_06059.6  3…'}    {'ACUGAAAAU'}

  Columns 73 through 78

    {'> HL_06059.6  4…'}    {'ACUCAUAAU'}    {'> HL_06059.6  1…'}    {'ACUUUUAAU'}    {'> HL_06059.6  4…'}    {'CUUGAGGUG'}

  Columns 79 through 84

    {'> HL_06059.6  4…'}    {'CUUGCCAAG'}    {'> HL_06059.6  1…'}    {'CUUGAGGUG'}    {'> HL_06059.6  4…'}    {'AUUGAAAAU'}

  Columns 85 through 90

    {'> HL_06059.6  1…'}    {'GCUGCGAAC'}    {'> HL_06059.6  1…'}    {'CCUCUCAAG'}    {'> HL_06059.6  3…'}    {'ACUUCAAAU'}

  Columns 91 through 96

    {'> HL_06059.6  5…'}    {'ACUUUUAAU'}    {'> HL_06059.6  7…'}    {'UCAAGCCUAG'}    {'> HL_06059.6  4…'}    {'ACUGUAAAU'}

  Columns 97 through 102

    {'> HL_06059.6  1…'}    {'AUUGCAAAU'}    {'> HL_06059.6  4…'}    {'CUCGACACG'}    {'> HL_06059.6  5…'}    {'ACUUUUAAU'}

pCalculateTransitions:  processing HL_06226.4
  Columns 1 through 6

    {'> HL_06226.4  8…'}    {'CCUGAGAAACGG'}    {'> HL_06226.4  8…'}    {'CCUGAGAAACGG'}    {'> HL_06226.4  5…'}    {'GAUCAGAAUGC'}

  Columns 7 through 8

    {'> HL_06226.4  4…'}    {'GAUCAGCCAUGC'}

pCalculateTransitions:  processing HL_07480.2
    {'> HL_07480.2  1…'}    {'AAAGCGGUUAU'}    {'> HL_07480.2  9…'}    {'AAAGCGGUUAU'}    {'> HL_07480.2  1…'}    {'AAAGCGGUUAU'}

pCalculateTransitions:  processing HL_07583.1
    {'> HL_07583.1  4WSM U   11…'}    {'UGGAAUUGGUAGACA'}    {'> HL_07583.1  9IWF A   15…'}    {'AUUAAUACGGUUU'}

pCalculateTransitions:  processing HL_07886.3
  Columns 1 through 6

    {'> HL_07886.3  8…'}    {'CGGAAAGG'}    {'> HL_07886.3  8…'}    {'CGGAAAGG'}    {'> HL_07886.3  2…'}    {'GAUAUGGC'}

  Columns 7 through 12

    {'> HL_07886.3  5…'}    {'AUUUU'}    {'> HL_07886.3  8…'}    {'UGAAGGA'}    {'> HL_07886.3  9…'}    {'UGAAGGA'}

pCalculateTransitions:  processing HL_07903.1
    {'> HL_07903.1  1A9N G    4 C   18'}    {'GUAUUGCAGUACCUC'}

pCalculateTransitions:  processing HL_07951.3
  Columns 1 through 6

    {'> HL_07951.3  1…'}    {'CAGCGGAAG'}    {'> HL_07951.3  3…'}    {'CAGCGGGAG'}    {'> HL_07951.3  4…'}    {'CAGCUGGUUAG'}

  Columns 7 through 8

    {'> HL_07951.3  9…'}    {'UCAUCUCCAA'}

pCalculateTransitions:  processing HL_08100.1
  Columns 1 through 6

    {'> HL_08100.1  5…'}    {'CCUCGCG'}    {'> HL_08100.1  8…'}    {'CCUUGUG'}    {'> HL_08100.1  5…'}    {'CUUUAAG'}

  Columns 7 through 8

    {'> HL_08100.1  5…'}    {'CUUUUGG'}

pCalculateTransitions:  processing HL_08510.1
    {'> HL_08510.1  2QUS A   18…'}    {'AUGUGCUUU'}    {'> HL_08510.1  2QUW A   18…'}    {'AUGUGCUUU'}

pCalculateTransitions:  processing HL_08602.1
    {'> HL_08602.1  4WFL C   42 G   54'}    {'CAAUCCGCUCUAG'}

pCalculateTransitions:  processing HL_09260.2
    {'> HL_09260.2  5…'}    {'CAGCCUGGGAG'}    {'> HL_09260.2  7…'}    {'UAGCCUGGUUAG'}    {'> HL_09260.2  3…'}    {'UAGCCAGGUCAG'}

pCalculateTransitions:  processing HL_09452.1
    {'> HL_09452.1  2…'}    {'UAGGGGCUA'}    {'> HL_09452.1  5…'}    {'UAGGGGCUA'}    {'> HL_09452.1  5…'}    {'GCUUAGGC'}

pCalculateTransitions:  processing HL_10453.3
  Columns 1 through 6

    {'> HL_10453.3  6…'}    {'GCUGCGAAC'}    {'> HL_10453.3  6…'}    {'GCUGCGAAC'}    {'> HL_10453.3  8…'}    {'ACUUUGACU'}

  Columns 7 through 12

    {'> HL_10453.3  8…'}    {'ACUUUGACU'}    {'> HL_10453.3  6…'}    {'GCGAUCAC'}    {'> HL_10453.3  3…'}    {'GUUUAAUC'}

  Columns 13 through 18

    {'> HL_10453.3  2…'}    {'GCACCGUC'}    {'> HL_10453.3  5…'}    {'GCUCAAC'}    {'> HL_10453.3  4…'}    {'GCUCAAC'}

pCalculateTransitions:  processing HL_10456.1
    {'> HL_10456.1  3D0U C   35…'}    {'CAUCAGGGGAGGAAUCGG'}    {'> HL_10456.1  3DIL C   38…'}    {'CAUCAGGGGAGGAAUCGG'}

pCalculateTransitions:  processing HL_10540.1
    {'> HL_10540.1  5JEA C  -38…'}    {'CCGAAGG'}    {'> HL_10540.1  5Y58 U  297…'}    {'UGGCUAAAA'}

pCalculateTransitions:  processing HL_11542.1
    {'> HL_11542.1  4WZD C   12 G   24'}    {'CGAGCGGCCAAAG'}

pCalculateTransitions:  processing HL_12758.3
    {'> HL_12758.3  8U5Z C    6…'}    {'CGAAGGUGAGGAGAGGCGAGGAAGAG'}    {'> HL_12758.3  5V3F C    4…'}    {'CGAAGGGACGGUGCGGAGAGGAGAG'}

pCalculateTransitions:  processing HL_12870.1
    {'> HL_12870.1  2ZY6 G   12 C   24'}    {'GUCCUUGGGAAAC'}

pCalculateTransitions:  processing HL_13189.1
    {'> HL_13189.1  8P9A C  543…'}    {'CCUCGG'}    {'> HL_13189.1  5D0B U   33…'}    {'UGUAA'}

pCalculateTransitions:  processing HL_13529.1
    {'> HL_13529.1  5J7L U  641…'}    {'UUAACUG'}    {'> HL_13529.1  5U3G G   68…'}    {'GAAAAAAGC'}

pCalculateTransitions:  processing HL_13963.3
  Columns 1 through 6

    {'> HL_13963.3  3…'}    {'GGCGAC'}    {'> HL_13963.3  3…'}    {'GGCGAC'}    {'> HL_13963.3  2…'}    {'GCCUAGGAC'}

  Columns 7 through 8

    {'> HL_13963.3  5…'}    {'GCUUAUGC'}

pCalculateTransitions:  processing HL_13971.1
    {'> HL_13971.1  8P9A U   32…'}    {'UUCCCGUCCGAUCA'}    {'> HL_13971.1  8OI5 U   32…'}    {'UCCCCGUUCGAUCA'}

pCalculateTransitions:  processing HL_14757.1
    {'> HL_14757.1  6RTI C   15 G   32'}    {'CCUGACUUCUAUACUAAG'}

pCalculateTransitions:  processing HL_15118.1
    {'> HL_15118.1  3IWN C   57 G   68'}    {'CAUUGCACUCCG'}

pCalculateTransitions:  processing HL_15574.1
    {'> HL_15574.1  4R4V G  670…'}    {'GAAACAC'}    {'> HL_15574.1  6VMY G  253…'}    {'GUAAAAGC'}

pCalculateTransitions:  processing HL_15802.1
    {'> HL_15802.1  3AL0 A   31 U   39'}    {'ACUCUGGAU'}

pCalculateTransitions:  processing HL_16398.2
    {'> HL_16398.2  8…'}    {'GAAGAAUACGACC'}    {'> HL_16398.2  3…'}    {'GAAGAAUACGACC'}    {'> HL_16398.2  1…'}    {'GACCUAGAUCACCC'}

pCalculateTransitions:  processing HL_16991.1
    {'> HL_16991.1  8EYU U   26 A   37'}    {'UGUGGAGGAGUA'}

pCalculateTransitions:  processing HL_18423.1
    {'> HL_18423.1  3HJW U   23 G   33'}    {'UGAUCAAUGAG'}

pCalculateTransitions:  processing HL_18565.1
    {'> HL_18565.1  2ZZN A   31…'}    {'ACUGCAGAU'}    {'> HL_18565.1  5WT1 A   31…'}    {'ACUGAAGAU'}

pCalculateTransitions:  processing HL_18978.1
    {'> HL_18978.1  9FN3 C   18 G   27'}    {'CUGUUCGCAG'}

pCalculateTransitions:  processing HL_19210.3
  Columns 1 through 6

    {'> HL_19210.3  1…'}    {'CUUAGAAGCAG'}    {'> HL_19210.3  5…'}    {'CUUAGAAGCAG'}    {'> HL_19210.3  6…'}    {'CUUAGAAGCAG'}

  Columns 7 through 12

    {'> HL_19210.3  5…'}    {'CUUAGAAGCAG'}    {'> HL_19210.3  8…'}    {'CAUGGAAGUCG'}    {'> HL_19210.3  8…'}    {'CAUGGAAGUCG'}

  Columns 13 through 14

    {'> HL_19210.3  7…'}    {'GUUCGAUUCC'}

pCalculateTransitions:  processing HL_20167.2
  Columns 1 through 6

    {'> HL_20167.2  7…'}    {'GGUAAGUUC'}    {'> HL_20167.2  9…'}    {'GGUAAGUUC'}    {'> HL_20167.2  4…'}    {'GGUAAGUUC'}

  Columns 7 through 12

    {'> HL_20167.2  5…'}    {'GGUAAGUUC'}    {'> HL_20167.2  4…'}    {'CAUCAGUAG'}    {'> HL_20167.2  8…'}    {'UCUAAUUAG'}

  Columns 13 through 18

    {'> HL_20167.2  8…'}    {'UCUAAUUAG'}    {'> HL_20167.2  1…'}    {'GGUAAGAGC'}    {'> HL_20167.2  3…'}    {'GUUCGAAUC'}

  Columns 19 through 20

    {'> HL_20167.2  4…'}    {'AUGAGAAUU'}

pCalculateTransitions:  processing HL_20535.2
    {'> HL_20535.2  5…'}    {'GAUAAUAC'}    {'> HL_20535.2  8…'}    {'UCCUUGUGG'}    {'> HL_20535.2  6…'}    {'GUUCGACUC'}

pCalculateTransitions:  processing HL_20743.5
  Columns 1 through 6

    {'> HL_20743.5  5…'}    {'GGAUAUGGC'}    {'> HL_20743.5  1…'}    {'GGAUAUGGC'}    {'> HL_20743.5  3…'}    {'GGAUAUAGC'}

  Columns 7 through 12

    {'> HL_20743.5  6…'}    {'AAAUAUGGU'}    {'> HL_20743.5  4…'}    {'GGAUAUGGC'}    {'> HL_20743.5  3…'}    {'CAUAAUGGG'}

  Columns 13 through 14

    {'> HL_20743.5  3…'}    {'CAUAAUGGG'}

pCalculateTransitions:  processing HL_20751.2
    {'> HL_20751.2  3…'}    {'CAGGGGAGGAAUCG'}    {'> HL_20751.2  3…'}    {'CAGGGGAGGAAUCG'}    {'> HL_20751.2  3…'}    {'GACGGGGAGUUGU'}

pCalculateTransitions:  processing HL_20781.1
    {'> HL_20781.1  5XWP C    9 G   19'}    {'CAAAAAUGAAG'}

pCalculateTransitions:  processing HL_20811.4
  Columns 1 through 6

    {'> HL_20811.4  1…'}    {'CAGUUGGUAG'}    {'> HL_20811.4  7…'}    {'CAGUCGGUAG'}    {'> HL_20811.4  5…'}    {'CAGUUGGGAG'}

  Columns 7 through 12

    {'> HL_20811.4  5…'}    {'CAAUUGGAUAG'}    {'> HL_20811.4  7…'}    {'CAGUCGGUAG'}    {'> HL_20811.4  2…'}    {'CAAUGGUAG'}

  Columns 13 through 18

    {'> HL_20811.4  8…'}    {'CAGUCGGUAG'}    {'> HL_20811.4  6…'}    {'CAGUGGUAG'}    {'> HL_20811.4  3…'}    {'UAACGGUAG'}

  Columns 19 through 24

    {'> HL_20811.4  1…'}    {'CAGUCGGUAG'}    {'> HL_20811.4  4…'}    {'CAGCCGGUAG'}    {'> HL_20811.4  7…'}    {'CAGUGGUAG'}

  Columns 25 through 28

    {'> HL_20811.4  7…'}    {'CAGCUGGGAG'}    {'> HL_20811.4  5…'}    {'CUGAAG'}

pCalculateTransitions:  processing HL_21372.1
    {'> HL_21372.1  1KOG U   82…'}    {'UUUCGUGUG'}    {'> HL_21372.1  1QF6 A   31…'}    {'AUUCGUAAU'}

pCalculateTransitions:  processing HL_21400.1
    {'> HL_21400.1  8EYU A   16 U   38'}    {'AGGUGGGUGGUGUGGAGGAGUAU'}

pCalculateTransitions:  processing HL_22135.1
    {'> HL_22135.1  6FQ3 U    5 A    9'}    {'UCCAA'}

pCalculateTransitions:  processing HL_22584.6
  Columns 1 through 6

    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}

  Columns 7 through 12

    {'> HL_22584.6  6…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}

  Columns 13 through 18

    {'> HL_22584.6  4…'}    {'GAAACAC'}    {'> HL_22584.6  9…'}    {'GAAACAC'}    {'> HL_22584.6  9…'}    {'GAAACAC'}

  Columns 19 through 24

    {'> HL_22584.6  9…'}    {'GAAACAC'}    {'> HL_22584.6  9…'}    {'GAAACAC'}    {'> HL_22584.6  9…'}    {'GAAACAC'}

  Columns 25 through 30

    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  3…'}    {'GAAACAC'}    {'> HL_22584.6  9…'}    {'GAAACAC'}

  Columns 31 through 36

    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}

  Columns 37 through 42

    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  6…'}    {'GAAACAC'}    {'> HL_22584.6  7…'}    {'GAAACAC'}

  Columns 43 through 48

    {'> HL_22584.6  7…'}    {'GAAACAC'}    {'> HL_22584.6  8…'}    {'GAAACAC'}    {'> HL_22584.6  6…'}    {'GAACCCC'}

  Columns 49 through 52

    {'> HL_22584.6  3…'}    {'CGAACG'}    {'> HL_22584.6  9…'}    {'CUCCAG'}

pCalculateTransitions:  processing HL_22622.1
    {'> HL_22622.1  5J7L C 1451…'}    {'CGACGGUUG'}    {'> HL_22622.1  9DFE C 1451…'}    {'CAUGGACG'}

pCalculateTransitions:  processing HL_23010.1
    {'> HL_23010.1  4V7M C   12 G   22'}    {'CAAGCGGUAAG'}

pCalculateTransitions:  processing HL_23115.1
    {'> HL_23115.1  6UFG C   13…'}    {'CAGGCGGUUAG'}    {'> HL_23115.1  6UFH C   13…'}    {'CAGGCGGUUAG'}

pCalculateTransitions:  processing HL_23509.1
    {'> HL_23509.1  8P9A G 2534 C 2545'}    {'GAAUUCAUUUUC'}

pCalculateTransitions:  processing HL_24792.1
    {'> HL_24792.1  6XJQ G   26 C   35'}    {'GCCCGUUAUC'}

pCalculateTransitions:  processing HL_25061.1
    {'> HL_25061.1  6MWN U  624…'}    {'UGUGAGAGG'}    {'> HL_25061.1  8CRE C 1343…'}    {'CUGUUUUGACG'}

pCalculateTransitions:  processing HL_25847.2
    {'> HL_25847.2  9…'}    {'GUAACUAUAAC'}    {'> HL_25847.2  8…'}    {'GUAACUAUGAC'}    {'> HL_25847.2  5…'}    {'GUAACUAUAAC'}

pCalculateTransitions:  processing HL_25967.2
    {'> HL_25967.2  8…'}    {'GUUUAUC'}    {'> HL_25967.2  8…'}    {'GUUUAUC'}    {'> HL_25967.2  8…'}    {'CACCUUUG'}

pCalculateTransitions:  processing HL_26631.1
    {'> HL_26631.1  3SNP C   14…'}    {'CAGUG'}    {'> HL_26631.1  3SN2 C   14…'}    {'CAGUG'}

pCalculateTransitions:  processing HL_26934.1
    {'> HL_26934.1  3IVN G   37 C   44'}    {'GUGUCUAC'}

pCalculateTransitions:  processing HL_27483.1
    {'> HL_27483.1  8CRE G  539…'}    {'GCUUCUGC'}    {'> HL_27483.1  1KH6 C   42…'}    {'CGUG'}

pCalculateTransitions:  processing HL_27670.2
  Columns 1 through 6

    {'> HL_27670.2  5…'}    {'GUGACAGCC'}    {'> HL_27670.2  4…'}    {'GUGACAACC'}    {'> HL_27670.2  9…'}    {'GUGAAAGCC'}

  Columns 7 through 12

    {'> HL_27670.2  4…'}    {'GUAAUAAUC'}    {'> HL_27670.2  8…'}    {'GUGAGAAUC'}    {'> HL_27670.2  8…'}    {'GUGAGAAUC'}

  Columns 13 through 18

    {'> HL_27670.2  6…'}    {'GUAUAGUC'}    {'> HL_27670.2  4…'}    {'GUUAUACUC'}    {'> HL_27670.2  3…'}    {'GUAUAGUC'}

  Columns 19 through 24

    {'> HL_27670.2  4…'}    {'GUUAUACUC'}    {'> HL_27670.2  6…'}    {'GUAGAGUC'}    {'> HL_27670.2  3…'}    {'GUAGAGUC'}

  Columns 25 through 26

    {'> HL_27670.2  7…'}    {'GUGAGAGUC'}

pCalculateTransitions:  processing HL_28075.1
  Columns 1 through 6

    {'> HL_28075.1  6…'}    {'AUGUCGUUU'}    {'> HL_28075.1  8…'}    {'GAUUUUUC'}    {'> HL_28075.1  7…'}    {'CCGAAUAG'}

  Columns 7 through 8

    {'> HL_28075.1  8…'}    {'CUUUUUAG'}

pCalculateTransitions:  processing HL_28252.8
  Columns 1 through 6

    {'> HL_28252.8  4…'}    {'GUUCAAGUC'}    {'> HL_28252.8  6…'}    {'GUUCGAGUC'}    {'> HL_28252.8  2…'}    {'GUUCAAAUC'}

  Columns 7 through 12

    {'> HL_28252.8  3…'}    {'GUUCAAAUC'}    {'> HL_28252.8  7…'}    {'GUUCAAAUC'}    {'> HL_28252.8  6…'}    {'GUUCGAGUC'}

  Columns 13 through 18

    {'> HL_28252.8  5…'}    {'GUUCAAGUC'}    {'> HL_28252.8  7…'}    {'GUUCAAGUC'}    {'> HL_28252.8  4…'}    {'GUUCAAAUC'}

  Columns 19 through 24

    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}    {'> HL_28252.8  2…'}    {'GUUCAAAUC'}    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}

  Columns 25 through 30

    {'> HL_28252.8  5…'}    {'GUUCGAAUC'}    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}    {'> HL_28252.8  7…'}    {'GUUCGAAUC'}

  Columns 31 through 36

    {'> HL_28252.8  3…'}    {'GUUCAAUUC'}    {'> HL_28252.8  9…'}    {'GUUCGACUC'}    {'> HL_28252.8  2…'}    {'GUUCAAGUC'}

  Columns 37 through 42

    {'> HL_28252.8  1…'}    {'GUUCAAAUC'}    {'> HL_28252.8  3…'}    {'GUUCGAGUC'}    {'> HL_28252.8  1…'}    {'GUUCGAAUC'}

  Columns 43 through 48

    {'> HL_28252.8  6…'}    {'GUUCGAGUC'}    {'> HL_28252.8  8…'}    {'GUUCAAAUC'}    {'> HL_28252.8  4…'}    {'GUUCGAUUC'}

  Columns 49 through 54

    {'> HL_28252.8  8…'}    {'GUUCAAUUC'}    {'> HL_28252.8  5…'}    {'GUUCAAAUC'}    {'> HL_28252.8  4…'}    {'GUUCGAGUC'}

  Columns 55 through 60

    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}    {'> HL_28252.8  7…'}    {'GUUCAAGUC'}    {'> HL_28252.8  9…'}    {'GUUCAAAUC'}

  Columns 61 through 66

    {'> HL_28252.8  4…'}    {'GUUCGAGUC'}    {'> HL_28252.8  3…'}    {'GUUCAAGUC'}    {'> HL_28252.8  5…'}    {'GUUCGAAUC'}

  Columns 67 through 72

    {'> HL_28252.8  7…'}    {'GUUCGAGUC'}    {'> HL_28252.8  3…'}    {'GUUCGAUUC'}    {'> HL_28252.8  4…'}    {'GUUCGAAUC'}

  Columns 73 through 78

    {'> HL_28252.8  5…'}    {'GUUCAAAUC'}    {'> HL_28252.8  2…'}    {'GUUCGAAUC'}    {'> HL_28252.8  5…'}    {'GUUCGAUCC'}

  Columns 79 through 84

    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}    {'> HL_28252.8  2…'}    {'GUUCAAAUC'}    {'> HL_28252.8  4…'}    {'GUUCGAGUC'}

  Columns 85 through 90

    {'> HL_28252.8  4…'}    {'GUUCGAGCC'}    {'> HL_28252.8  4…'}    {'GUUCGAUUC'}    {'> HL_28252.8  7…'}    {'GUUCGAGUC'}

  Columns 91 through 96

    {'> HL_28252.8  4…'}    {'GUGCAACUC'}    {'> HL_28252.8  8…'}    {'GUUCAAUUC'}    {'> HL_28252.8  4…'}    {'GUUCAAAUC'}

  Columns 97 through 102

    {'> HL_28252.8  4…'}    {'GUUCAAAUC'}    {'> HL_28252.8  8…'}    {'GUUCAAAUC'}    {'> HL_28252.8  1…'}    {'GUUCGAAUC'}

  Columns 103 through 108

    {'> HL_28252.8  7…'}    {'GUUCGAUCC'}    {'> HL_28252.8  2…'}    {'GUUCGAAUC'}    {'> HL_28252.8  3…'}    {'GUUCAAUUC'}

  Columns 109 through 114

    {'> HL_28252.8  7…'}    {'GUUCGAUCC'}    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}

  Columns 115 through 120

    {'> HL_28252.8  3…'}    {'GUUCGAUUC'}    {'> HL_28252.8  6…'}    {'GUGCAACUC'}    {'> HL_28252.8  5…'}    {'GUUAGAUUC'}

  Columns 121 through 126

    {'> HL_28252.8  5…'}    {'GUUCGAAUC'}    {'> HL_28252.8  4…'}    {'GUUCGAGUC'}    {'> HL_28252.8  2…'}    {'GUUCGACUC'}

  Columns 127 through 132

    {'> HL_28252.8  3…'}    {'GUUCGAAUC'}    {'> HL_28252.8  2…'}    {'GUUCGAAUC'}    {'> HL_28252.8  5…'}    {'GUUCAAAUC'}

  Columns 133 through 138

    {'> HL_28252.8  4…'}    {'GUUCGACUC'}    {'> HL_28252.8  1…'}    {'GUUCGACUC'}    {'> HL_28252.8  3…'}    {'GUGAGAGUC'}

  Columns 139 through 144

    {'> HL_28252.8  1…'}    {'GUUCGAUUC'}    {'> HL_28252.8  8…'}    {'GUUCAAGUC'}    {'> HL_28252.8  6…'}    {'GUUCAAGUC'}

  Columns 145 through 150

    {'> HL_28252.8  7…'}    {'GUUCGAGUC'}    {'> HL_28252.8  2…'}    {'GUUCGAUUC'}    {'> HL_28252.8  6…'}    {'GUUCGAGAC'}

  Columns 151 through 156

    {'> HL_28252.8  1…'}    {'GUUCGAAUC'}    {'> HL_28252.8  3…'}    {'GUUCAAGUC'}    {'> HL_28252.8  3…'}    {'GUUCGAUCC'}

  Columns 157 through 162

    {'> HL_28252.8  3…'}    {'GUUCGAUUC'}    {'> HL_28252.8  4…'}    {'GUUCAAAUC'}    {'> HL_28252.8  6…'}    {'GUGAGAAUC'}

  Columns 163 through 168

    {'> HL_28252.8  6…'}    {'GUGAGAAUC'}    {'> HL_28252.8  6…'}    {'GUGAGAAUC'}    {'> HL_28252.8  3…'}    {'GUUCGAUUC'}

  Columns 169 through 174

    {'> HL_28252.8  6…'}    {'GUUCGAAUC'}    {'> HL_28252.8  2…'}    {'GUUCGAGUC'}    {'> HL_28252.8  8…'}    {'GUUCGAGUC'}

  Columns 175 through 180

    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}    {'> HL_28252.8  5…'}    {'GUUCGAUUC'}    {'> HL_28252.8  7…'}    {'GUUCGAGUC'}

  Columns 181 through 186

    {'> HL_28252.8  3…'}    {'GUUCGAUCC'}    {'> HL_28252.8  3…'}    {'GUUCGAUUC'}    {'> HL_28252.8  4…'}    {'GUUCGAAUC'}

  Columns 187 through 192

    {'> HL_28252.8  3…'}    {'GUUCGAGUC'}    {'> HL_28252.8  4…'}    {'GUUCGAAUC'}    {'> HL_28252.8  8…'}    {'GUUCGAAUC'}

  Columns 193 through 198

    {'> HL_28252.8  5…'}    {'GUUCGAAUC'}    {'> HL_28252.8  1…'}    {'GUUCAAUUC'}    {'> HL_28252.8  6…'}    {'GUUCAAGUC'}

  Columns 199 through 204

    {'> HL_28252.8  4…'}    {'GUUCGAUUC'}    {'> HL_28252.8  5…'}    {'GUUCAAAUC'}    {'> HL_28252.8  1…'}    {'GUUCGACUC'}

  Columns 205 through 210

    {'> HL_28252.8  6…'}    {'GUUCAAAUC'}    {'> HL_28252.8  1…'}    {'GUUCGACUC'}    {'> HL_28252.8  5…'}    {'GUGCAAGUC'}

  Columns 211 through 216

    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}    {'> HL_28252.8  2…'}    {'GUUCGACUC'}    {'> HL_28252.8  7…'}    {'GUUCGAUUC'}

  Columns 217 through 222

    {'> HL_28252.8  9…'}    {'GUGAGAAUC'}    {'> HL_28252.8  5…'}    {'GUUCGAAUC'}    {'> HL_28252.8  5…'}    {'GUGAAAAGC'}

  Columns 223 through 228

    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}    {'> HL_28252.8  4…'}    {'UUUUGAAAAA'}    {'> HL_28252.8  1…'}    {'GUUCAGAUC'}

  Columns 229 through 234

    {'> HL_28252.8  8…'}    {'AUGAGAACU'}    {'> HL_28252.8  5…'}    {'GUUCGAUCC'}    {'> HL_28252.8  7…'}    {'GUGAGAAUC'}

  Columns 235 through 240

    {'> HL_28252.8  2…'}    {'GUUCGACUC'}    {'> HL_28252.8  5…'}    {'GUGCAAGCC'}    {'> HL_28252.8  4…'}    {'UUUUGUAGAA'}

  Columns 241 through 246

    {'> HL_28252.8  4…'}    {'GUUCGAAUC'}    {'> HL_28252.8  5…'}    {'UUUUGUAUAA'}    {'> HL_28252.8  8…'}    {'AUGAGAACU'}

  Columns 247 through 252

    {'> HL_28252.8  4…'}    {'GUGAGAAUC'}    {'> HL_28252.8  1…'}    {'GUUCAAGUC'}    {'> HL_28252.8  6…'}    {'GUUCGAAUC'}

  Columns 253 through 258

    {'> HL_28252.8  4…'}    {'GUGCAAGUC'}    {'> HL_28252.8  7…'}    {'UAUUGAAGCA'}    {'> HL_28252.8  8…'}    {'UCUUGAAACA'}

  Columns 259 through 264

    {'> HL_28252.8  4…'}    {'GUUCAAGUC'}    {'> HL_28252.8  9…'}    {'UAUUGAAGCA'}    {'> HL_28252.8  2…'}    {'GUGAAACUC'}

  Columns 265 through 270

    {'> HL_28252.8  8…'}    {'UCUUGAAACA'}    {'> HL_28252.8  4…'}    {'GUGAGAACC'}    {'> HL_28252.8  4…'}    {'GUUCAAGUC'}

  Columns 271 through 276

    {'> HL_28252.8  4…'}    {'GUUCGAAUC'}    {'> HL_28252.8  8…'}    {'GUUCAAAUC'}    {'> HL_28252.8  6…'}    {'GUUCGAGUC'}

  Columns 277 through 280

    {'> HL_28252.8  1…'}    {'GUUCGAUUC'}    {'> HL_28252.8  6…'}    {'GUUCGAAUC'}

pCalculateTransitions:  processing HL_28791.1
    {'> HL_28791.1  2Y9H C   11 G   16'}    {'CGCGUG'}

pCalculateTransitions:  processing HL_29129.3
    {'> HL_29129.3  5…'}    {'UUUGGGGAAAG'}    {'> HL_29129.3  7…'}    {'UUUGGGGAAAG'}    {'> HL_29129.3  8…'}    {'GUUGGGGAUC'}

pCalculateTransitions:  processing HL_29762.1
    {'> HL_29762.1  8P9A U 1347 G 1357'}    {'UUGAUAUGAUG'}

pCalculateTransitions:  processing HL_29958.1
    {'> HL_29958.1  2NZ4 A   31 U   43'}    {'AGGUGGGGUUUAU'}

pCalculateTransitions:  processing HL_29966.1
    {'> HL_29966.1  6IV9 A  -21 U  -16'}    {'AAAUUU'}

pCalculateTransitions:  processing HL_30068.2
  Columns 1 through 6

    {'> HL_30068.2  8…'}    {'UAAGCAUA'}    {'> HL_30068.2  8…'}    {'UAAGCAUA'}    {'> HL_30068.2  4…'}    {'GAAACAUC'}

  Columns 7 through 12

    {'> HL_30068.2  5…'}    {'GAAACAUC'}    {'> HL_30068.2  4…'}    {'GAAACAUC'}    {'> HL_30068.2  7…'}    {'GAAACAUC'}

  Columns 13 through 18

    {'> HL_30068.2  9…'}    {'GAAACAUC'}    {'> HL_30068.2  4…'}    {'CUGUUCG'}    {'> HL_30068.2  5…'}    {'CUGUUCG'}

  Columns 19 through 24

    {'> HL_30068.2  9…'}    {'CUGUUCG'}    {'> HL_30068.2  8…'}    {'UUGUUCA'}    {'> HL_30068.2  8…'}    {'UUGUUCA'}

  Columns 25 through 30

    {'> HL_30068.2  7…'}    {'CUGUUCG'}    {'> HL_30068.2  3…'}    {'GGAAUAC'}    {'> HL_30068.2  4…'}    {'UUGUUCG'}

pCalculateTransitions:  processing HL_30680.3
  Columns 1 through 6

    {'> HL_30680.3  5…'}    {'GACUGGC'}    {'> HL_30680.3  4…'}    {'GACUGGC'}    {'> HL_30680.3  6…'}    {'GCUGGAC'}

  Columns 7 through 12

    {'> HL_30680.3  4…'}    {'GACUGGC'}    {'> HL_30680.3  3…'}    {'GACUGGC'}    {'> HL_30680.3  6…'}    {'GUCCCGC'}

  Columns 13 through 18

    {'> HL_30680.3  5…'}    {'UUUCCAG'}    {'> HL_30680.3  3…'}    {'GUGGCAGC'}    {'> HL_30680.3  4…'}    {'GGACCAUC'}

  Columns 19 through 24

    {'> HL_30680.3  3…'}    {'GUGGCAGC'}    {'> HL_30680.3  9…'}    {'GGACCACC'}    {'> HL_30680.3  5…'}    {'GGACCAUC'}

  Columns 25 through 30

    {'> HL_30680.3  7…'}    {'GGACCACC'}    {'> HL_30680.3  4…'}    {'GACGGACAC'}    {'> HL_30680.3  1…'}    {'ACUCAAGAU'}

pCalculateTransitions:  processing HL_31581.6
    {'> HL_31581.6  4…'}    {'CAUUGCACUCCG'}    {'> HL_31581.6  4…'}    {'CAUUGCACUCCG'}    {'> HL_31581.6  6…'}    {'UAUUGCAGUACCG'}

pCalculateTransitions:  processing HL_31585.4
  Columns 1 through 6

    {'> HL_31585.4  4…'}    {'GUUUCUAC'}    {'> HL_31585.4  1…'}    {'GUUUCUAC'}    {'> HL_31585.4  4…'}    {'GUUUCUAC'}

  Columns 7 through 12

    {'> HL_31585.4  1…'}    {'GUUUCUAC'}    {'> HL_31585.4  4…'}    {'GCUUCCAC'}    {'> HL_31585.4  3…'}    {'GUUUCUAC'}

  Columns 13 through 18

    {'> HL_31585.4  9…'}    {'GUUUCGAC'}    {'> HL_31585.4  3…'}    {'GCUUCCAC'}    {'> HL_31585.4  7…'}    {'CUGCGUG'}

  Columns 19 through 24

    {'> HL_31585.4  4…'}    {'GUUUUAC'}    {'> HL_31585.4  5…'}    {'UUCGGGGA'}    {'> HL_31585.4  6…'}    {'GGUUGGCC'}

  Columns 25 through 30

    {'> HL_31585.4  9…'}    {'UGAAGAAG'}    {'> HL_31585.4  6…'}    {'GCUAAAAC'}    {'> HL_31585.4  4…'}    {'UGCAGAAG'}

  Columns 31 through 36

    {'> HL_31585.4  7…'}    {'UGAAGAAG'}    {'> HL_31585.4  5…'}    {'UGAAGUAG'}    {'> HL_31585.4  4…'}    {'UGUAGUCG'}

  Columns 37 through 40

    {'> HL_31585.4  8…'}    {'AGCAGAAU'}    {'> HL_31585.4  8…'}    {'AGCAGAAU'}

pCalculateTransitions:  processing HL_32346.4
  Columns 1 through 7

    {'> HL_32346.4  9…'}    {'CGGAUG'}    {'> HL_32346.4  9…'}    {'CAAUG'}    {'> HL_32346.4  8…'}    {'CUUCG'}    {'> HL_32346.4  6…'}

  Columns 8 through 14

    {'CGUG'}    {'> HL_32346.4  6…'}    {'UUCA'}    {'> HL_32346.4  8…'}    {'CAUUG'}    {'> HL_32346.4  2…'}    {'GGUC'}

  Columns 15 through 18

    {'> HL_32346.4  5…'}    {'UUUUA'}    {'> HL_32346.4  5…'}    {'CUCG'}

pCalculateTransitions:  processing HL_32392.1
    {'> HL_32392.1  5B2P U   82…'}    {'UUUGA'}    {'> HL_32392.1  5J7L U  137…'}    {'UUUCGA'}

pCalculateTransitions:  processing HL_32735.2
  Columns 1 through 6

    {'> HL_32735.2  5…'}    {'AGUUCAUAU'}    {'> HL_32735.2  8…'}    {'CGUUCAUAG'}    {'> HL_32735.2  4…'}    {'AGUUCACAU'}

  Columns 7 through 12

    {'> HL_32735.2  9…'}    {'CGUCCACAG'}    {'> HL_32735.2  7…'}    {'AGUCCAUAU'}    {'> HL_32735.2  8…'}    {'CGUUCAUAG'}

  Columns 13 through 14

    {'> HL_32735.2  4…'}    {'AGCACAUAU'}

pCalculateTransitions:  processing HL_33074.4
  Columns 1 through 6

    {'> HL_33074.4  4…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  8…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  2…'}    {'CAUUGCACUCCG'}

  Columns 7 through 12

    {'> HL_33074.4  5…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  1…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  5…'}    {'CAUUGCACUCCG'}

  Columns 13 through 18

    {'> HL_33074.4  6…'}    {'CAUUGCACCUCG'}    {'> HL_33074.4  7…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  7…'}    {'CAUUGCACUCCG'}

  Columns 19 through 24

    {'> HL_33074.4  6…'}    {'CAUUGCACCUCG'}    {'> HL_33074.4  8…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  4…'}    {'CAUUGCACUCCG'}

  Columns 25 through 30

    {'> HL_33074.4  1…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  8…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  3…'}    {'CAUUGCACUCCG'}

  Columns 31 through 36

    {'> HL_33074.4  3…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  7…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  7…'}    {'CAUUGCACUCCG'}

  Columns 37 through 42

    {'> HL_33074.4  5…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  3…'}    {'CAUUGCACUCCG'}    {'> HL_33074.4  5…'}    {'CAUUGCACUCCG'}

  Columns 43 through 44

    {'> HL_33074.4  6…'}    {'CAUUGCACUCCG'}

pCalculateTransitions:  processing HL_33983.1
    {'> HL_33983.1  8WND C   31 G   39'}    {'CCUGAUAAG'}

pCalculateTransitions:  processing HL_34617.5
  Columns 1 through 6

    {'> HL_34617.5  5…'}    {'CUUCGG'}    {'> HL_34617.5  9…'}    {'GUUCGC'}    {'> HL_34617.5  5…'}    {'CUUCGG'}

  Columns 7 through 12

    {'> HL_34617.5  5…'}    {'CUUCGG'}    {'> HL_34617.5  8…'}    {'GUUCGC'}    {'> HL_34617.5  6…'}    {'CUUCGG'}

  Columns 13 through 18

    {'> HL_34617.5  8…'}    {'AUUCGU'}    {'> HL_34617.5  8…'}    {'CUUCGG'}    {'> HL_34617.5  9…'}    {'CUUCGG'}

  Columns 19 through 24

    {'> HL_34617.5  7…'}    {'GUUCGC'}    {'> HL_34617.5  4…'}    {'CUUCGG'}    {'> HL_34617.5  4…'}    {'CUUCGG'}

  Columns 25 through 30

    {'> HL_34617.5  4…'}    {'CUUCGG'}    {'> HL_34617.5  6…'}    {'CUUCGG'}    {'> HL_34617.5  5…'}    {'CUUCGG'}

  Columns 31 through 36

    {'> HL_34617.5  4…'}    {'CUUCGG'}    {'> HL_34617.5  2…'}    {'CUUCGG'}    {'> HL_34617.5  8…'}    {'CCAAGG'}

  Columns 37 through 42

    {'> HL_34617.5  4…'}    {'CUUCGG'}    {'> HL_34617.5  1…'}    {'CUACGG'}    {'> HL_34617.5  4…'}    {'CUACGG'}

  Columns 43 through 48

    {'> HL_34617.5  4…'}    {'CUACGG'}    {'> HL_34617.5  6…'}    {'CUUCGG'}    {'> HL_34617.5  5…'}    {'CUUCGG'}

  Columns 49 through 54

    {'> HL_34617.5  5…'}    {'CUUCGG'}    {'> HL_34617.5  8…'}    {'CUUCGG'}    {'> HL_34617.5  7…'}    {'CUUCGG'}

  Columns 55 through 60

    {'> HL_34617.5  7…'}    {'GUACGC'}    {'> HL_34617.5  4…'}    {'CUUCGG'}    {'> HL_34617.5  8…'}    {'CUUCGG'}

  Columns 61 through 66

    {'> HL_34617.5  1…'}    {'CUUCGG'}    {'> HL_34617.5  1…'}    {'CUUCGG'}    {'> HL_34617.5  3…'}    {'CUCCGG'}

  Columns 67 through 72

    {'> HL_34617.5  8…'}    {'CUUCGG'}    {'> HL_34617.5  6…'}    {'AUUCGU'}    {'> HL_34617.5  8…'}    {'CCAAGG'}

  Columns 73 through 78

    {'> HL_34617.5  5…'}    {'CUACGG'}    {'> HL_34617.5  1…'}    {'CUUCGG'}    {'> HL_34617.5  4…'}    {'CUUCGG'}

  Columns 79 through 84

    {'> HL_34617.5  6…'}    {'CUUCGG'}    {'> HL_34617.5  6…'}    {'AUUUGU'}    {'> HL_34617.5  3…'}    {'GUUCGC'}

  Columns 85 through 90

    {'> HL_34617.5  7…'}    {'CUUCGG'}    {'> HL_34617.5  5…'}    {'CUACGG'}    {'> HL_34617.5  8…'}    {'UCACGG'}

  Columns 91 through 96

    {'> HL_34617.5  7…'}    {'CUUCGG'}    {'> HL_34617.5  1…'}    {'CUUCGG'}    {'> HL_34617.5  6…'}    {'CUUCGG'}

  Columns 97 through 102

    {'> HL_34617.5  6…'}    {'CUUCGG'}    {'> HL_34617.5  7…'}    {'GUUCGC'}    {'> HL_34617.5  4…'}    {'CGUGAG'}

  Columns 103 through 108

    {'> HL_34617.5  5…'}    {'CGCUAG'}    {'> HL_34617.5  5…'}    {'CUUCGG'}    {'> HL_34617.5  7…'}    {'ACAGAUU'}

  Columns 109 through 114

    {'> HL_34617.5  3…'}    {'CUUCGG'}    {'> HL_34617.5  4…'}    {'CGCCAG'}    {'> HL_34617.5  3…'}    {'CGUGAG'}

pCalculateTransitions:  processing HL_34964.1
    {'> HL_34964.1  2DU3 A  912…'}    {'AGAGGGGCUUU'}    {'> HL_34964.1  4YYE G   30…'}    {'GUUUUGUAAUC'}

pCalculateTransitions:  processing HL_35354.1
    {'> HL_35354.1  6E8S A    8 U   31'}    {'AGGAAGGAUUGGUAUGUGGUAUAU'}

pCalculateTransitions:  processing HL_35677.3
  Columns 1 through 6

    {'> HL_35677.3  2…'}    {'UGAUUUGCUA'}    {'> HL_35677.3  7…'}    {'UGAUUUGCUA'}    {'> HL_35677.3  2…'}    {'UGAUUUGCUA'}

  Columns 7 through 12

    {'> HL_35677.3  5…'}    {'UGCUAAUCUG'}    {'> HL_35677.3  6…'}    {'CGGCUUCCUG'}    {'> HL_35677.3  6…'}    {'CGGCUUCCUG'}

  Columns 13 through 14

    {'> HL_35677.3  2…'}    {'CUUCCUGCG'}

pCalculateTransitions:  processing HL_35941.1
    {'> HL_35941.1  4O26 C  186 G  190'}    {'CUCGG'}

pCalculateTransitions:  processing HL_36335.1
    {'> HL_36335.1  5W1H C  -19…'}    {'CAAGAAAGAG'}    {'> HL_36335.1  5WLH C  -19…'}    {'CAAGAAAGAG'}

pCalculateTransitions:  processing HL_36684.4
  Columns 1 through 6

    {'> HL_36684.4  5…'}    {'GACUUUUAAUC'}    {'> HL_36684.4  7…'}    {'GCUUGAGAACC'}    {'> HL_36684.4  4…'}    {'GAUUGUGAUUC'}

  Columns 7 through 12

    {'> HL_36684.4  4…'}    {'GGUUCGGCGUC'}    {'> HL_36684.4  6…'}    {'GGCUACGAACC'}    {'> HL_36684.4  6…'}    {'CCUUGGUAAGG'}

  Columns 13 through 14

    {'> HL_36684.4  4…'}    {'CCUUGAGGUGG'}

pCalculateTransitions:  processing HL_37344.1
    {'> HL_37344.1  8P9A C 2567…'}    {'CCAUUCGG'}    {'> HL_37344.1  5J7L C  840…'}    {'CCUUGAG'}

pCalculateTransitions:  processing HL_37369.2
  Columns 1 through 6

    {'> HL_37369.2  9…'}    {'CGGCGAG'}    {'> HL_37369.2  7…'}    {'CGGCGAG'}    {'> HL_37369.2  8…'}    {'CGGCGAG'}

  Columns 7 through 12

    {'> HL_37369.2  8…'}    {'CGGCGAG'}    {'> HL_37369.2  5…'}    {'CGGCGAG'}    {'> HL_37369.2  4…'}    {'CGGCGAG'}

  Columns 13 through 18

    {'> HL_37369.2  4…'}    {'CCGCGAG'}    {'> HL_37369.2  8…'}    {'UUUCAAG'}    {'> HL_37369.2  8…'}    {'UUUCAAG'}

pCalculateTransitions:  processing HL_37824.7
  Columns 1 through 6

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAAAG'}

  Columns 7 through 12

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'CGAAAG'}

  Columns 13 through 18

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGAAAG'}

  Columns 19 through 24

    {'> HL_37824.7  8…'}    {'UGAAAA'}    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 25 through 30

    {'> HL_37824.7  2…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'GGAAAC'}    {'> HL_37824.7  1…'}    {'CGAAAG'}

  Columns 31 through 36

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'GGAAAC'}

  Columns 37 through 42

    {'> HL_37824.7  5…'}    {'UGAAAA'}    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'CGAAAG'}

  Columns 43 through 48

    {'> HL_37824.7  3…'}    {'GGAAAC'}    {'> HL_37824.7  1…'}    {'CGAAAG'}    {'> HL_37824.7  7…'}    {'CGAAAG'}

  Columns 49 through 54

    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGGGAG'}

  Columns 55 through 60

    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'UGAAAG'}

  Columns 61 through 66

    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGAAAG'}

  Columns 67 through 72

    {'> HL_37824.7  2…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'GGAAAC'}

  Columns 73 through 78

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'UGAAAA'}

  Columns 79 through 84

    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'GGAAAC'}    {'> HL_37824.7  8…'}    {'CGAAAG'}

  Columns 85 through 90

    {'> HL_37824.7  4…'}    {'UGAAAA'}    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'UGAAAA'}

  Columns 91 through 96

    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'AGAAAU'}

  Columns 97 through 102

    {'> HL_37824.7  9…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'GGAGAC'}    {'> HL_37824.7  5…'}    {'AGAAAU'}

  Columns 103 through 108

    {'> HL_37824.7  4…'}    {'UGAAAA'}    {'> HL_37824.7  4…'}    {'UGAAAG'}    {'> HL_37824.7  7…'}    {'CGAAAG'}

  Columns 109 through 114

    {'> HL_37824.7  5…'}    {'CGAGAG'}    {'> HL_37824.7  7…'}    {'UGAAAA'}    {'> HL_37824.7  8…'}    {'CGAAAG'}

  Columns 115 through 120

    {'> HL_37824.7  9…'}    {'CGAGAG'}    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'GGAAAC'}

  Columns 121 through 126

    {'> HL_37824.7  5…'}    {'UGAAAA'}    {'> HL_37824.7  4…'}    {'CGUAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 127 through 132

    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  1…'}    {'UGAAAG'}

  Columns 133 through 138

    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 139 through 144

    {'> HL_37824.7  1…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CUCACG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}

  Columns 145 through 150

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'GGAAAC'}

  Columns 151 through 156

    {'> HL_37824.7  1…'}    {'CGCAAG'}    {'> HL_37824.7  5…'}    {'AGAAAU'}    {'> HL_37824.7  1…'}    {'UGAGAA'}

  Columns 157 through 162

    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAGAG'}

  Columns 163 through 168

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'CGAAAG'}

  Columns 169 through 174

    {'> HL_37824.7  9…'}    {'CGUAAG'}    {'> HL_37824.7  5…'}    {'UGAAAG'}    {'> HL_37824.7  4…'}    {'GGAAAC'}

  Columns 175 through 180

    {'> HL_37824.7  8…'}    {'GGUGAC'}    {'> HL_37824.7  4…'}    {'CGAGAG'}    {'> HL_37824.7  3…'}    {'CCAAAG'}

  Columns 181 through 186

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'UGAAAG'}    {'> HL_37824.7  7…'}    {'CGAGAG'}

  Columns 187 through 192

    {'> HL_37824.7  8…'}    {'CGCAAG'}    {'> HL_37824.7  5…'}    {'UGAAAG'}    {'> HL_37824.7  1…'}    {'GGAAAC'}

  Columns 193 through 198

    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  3…'}    {'GGAAAC'}    {'> HL_37824.7  5…'}    {'CGCAAG'}

  Columns 199 through 204

    {'> HL_37824.7  5…'}    {'CGCAAG'}    {'> HL_37824.7  7…'}    {'CGCAAG'}    {'> HL_37824.7  3…'}    {'GGAAAC'}

  Columns 205 through 210

    {'> HL_37824.7  7…'}    {'GGAAAC'}    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  7…'}    {'UGAAAA'}

  Columns 211 through 216

    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  2…'}    {'CGAAAG'}

  Columns 217 through 222

    {'> HL_37824.7  7…'}    {'AGAAAU'}    {'> HL_37824.7  7…'}    {'UGAAAA'}    {'> HL_37824.7  6…'}    {'GGAAAC'}

  Columns 223 through 228

    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'CGAGAG'}

  Columns 229 through 234

    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  9…'}    {'CGGGAG'}    {'> HL_37824.7  9…'}    {'CGAAAG'}

  Columns 235 through 240

    {'> HL_37824.7  8…'}    {'CGCAAG'}    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  3…'}    {'CGAAAG'}

  Columns 241 through 246

    {'> HL_37824.7  1…'}    {'GGUAAC'}    {'> HL_37824.7  8…'}    {'AGAAAU'}    {'> HL_37824.7  8…'}    {'GGAGAC'}

  Columns 247 through 252

    {'> HL_37824.7  3…'}    {'CGGAAG'}    {'> HL_37824.7  3…'}    {'CGGAAG'}    {'> HL_37824.7  1…'}    {'GGAAAC'}

  Columns 253 through 258

    {'> HL_37824.7  8…'}    {'CGCAAG'}    {'> HL_37824.7  8…'}    {'GGAAAC'}    {'> HL_37824.7  7…'}    {'CGAAAG'}

  Columns 259 through 264

    {'> HL_37824.7  5…'}    {'UGAAAA'}    {'> HL_37824.7  2…'}    {'CGUAGG'}    {'> HL_37824.7  8…'}    {'CGAGAG'}

  Columns 265 through 270

    {'> HL_37824.7  5…'}    {'AGUGAU'}    {'> HL_37824.7  3…'}    {'CGUAAG'}    {'> HL_37824.7  4…'}    {'CGAGAG'}

  Columns 271 through 276

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'UGAAAA'}    {'> HL_37824.7  4…'}    {'CGCAAG'}

  Columns 277 through 282

    {'> HL_37824.7  4…'}    {'CUAACG'}    {'> HL_37824.7  7…'}    {'GGAAAC'}    {'> HL_37824.7  5…'}    {'UGAGAG'}

  Columns 283 through 288

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  7…'}    {'AGAAAU'}

  Columns 289 through 294

    {'> HL_37824.7  4…'}    {'AAAAAU'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGUAAG'}

  Columns 295 through 300

    {'> HL_37824.7  1…'}    {'AGAAAU'}    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'GGAAAC'}

  Columns 301 through 306

    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGCAAG'}    {'> HL_37824.7  7…'}    {'GGAAAC'}

  Columns 307 through 312

    {'> HL_37824.7  9…'}    {'GGAAAC'}    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'AGAAAU'}

  Columns 313 through 318

    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'GGCAAC'}    {'> HL_37824.7  3…'}    {'UUAGCG'}

  Columns 319 through 324

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'AGAAAU'}    {'> HL_37824.7  8…'}    {'UGAAAG'}

  Columns 325 through 330

    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'GGUAAGC'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 331 through 336

    {'> HL_37824.7  7…'}    {'AGAAAU'}    {'> HL_37824.7  1…'}    {'GGAAAC'}    {'> HL_37824.7  9…'}    {'CGUGAG'}

  Columns 337 through 342

    {'> HL_37824.7  4…'}    {'CGCGAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'CUAACG'}

  Columns 343 through 348

    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'GGUAAC'}    {'> HL_37824.7  4…'}    {'GGAGAC'}

  Columns 349 through 354

    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'AGAAAU'}    {'> HL_37824.7  6…'}    {'UGAAAA'}

  Columns 355 through 360

    {'> HL_37824.7  7…'}    {'GGAAAC'}    {'> HL_37824.7  8…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'CGCAAG'}

  Columns 361 through 366

    {'> HL_37824.7  2…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGCAAG'}    {'> HL_37824.7  4…'}    {'CGGAAG'}

  Columns 367 through 372

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGAGAG'}    {'> HL_37824.7  4…'}    {'UGAGAG'}

  Columns 373 through 378

    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  7…'}    {'CGGGAG'}    {'> HL_37824.7  5…'}    {'AGAAAU'}

  Columns 379 through 384

    {'> HL_37824.7  5…'}    {'AGCGAU'}    {'> HL_37824.7  8…'}    {'AGAAAU'}    {'> HL_37824.7  7…'}    {'AGCUAACU'}

  Columns 385 through 390

    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGAGAG'}    {'> HL_37824.7  2…'}    {'GGUGAC'}

  Columns 391 through 396

    {'> HL_37824.7  9…'}    {'CGAUAACG'}    {'> HL_37824.7  7…'}    {'UGCAAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}

  Columns 397 through 402

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'AGAAAGU'}

  Columns 403 through 408

    {'> HL_37824.7  7…'}    {'UGAAAA'}    {'> HL_37824.7  4…'}    {'CGUAAG'}    {'> HL_37824.7  8…'}    {'GGUAAGC'}

  Columns 409 through 414

    {'> HL_37824.7  5…'}    {'CGUGAG'}    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'CGAGAG'}

  Columns 415 through 420

    {'> HL_37824.7  7…'}    {'AGCAAU'}    {'> HL_37824.7  8…'}    {'GGUAAGC'}    {'> HL_37824.7  8…'}    {'AGAAAGU'}

  Columns 421 through 426

    {'> HL_37824.7  4…'}    {'GGAAAC'}    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  9…'}    {'UGCAAG'}

  Columns 427 through 432

    {'> HL_37824.7  6…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'CGUGAG'}

  Columns 433 through 438

    {'> HL_37824.7  8…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'CGUGAG'}

  Columns 439 through 444

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'CGGCGAG'}

  Columns 445 through 450

    {'> HL_37824.7  6…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'GGUAAC'}    {'> HL_37824.7  4…'}    {'GGCAAC'}

  Columns 451 through 456

    {'> HL_37824.7  5…'}    {'CGUGAG'}    {'> HL_37824.7  8…'}    {'CGUGAG'}    {'> HL_37824.7  9…'}    {'CGCGAG'}

  Columns 457 through 462

    {'> HL_37824.7  8…'}    {'UGAAAG'}    {'> HL_37824.7  5…'}    {'UGACGG'}    {'> HL_37824.7  5…'}    {'UGAAAA'}

  Columns 463 through 468

    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  7…'}    {'GGAAAC'}    {'> HL_37824.7  4…'}    {'CGGAACG'}

  Columns 469 through 474

    {'> HL_37824.7  4…'}    {'GGAAAC'}    {'> HL_37824.7  7…'}    {'CGUGAG'}    {'> HL_37824.7  7…'}    {'CGCAGG'}

  Columns 475 through 480

    {'> HL_37824.7  4…'}    {'UGUGAA'}    {'> HL_37824.7  4…'}    {'CGAGAG'}    {'> HL_37824.7  5…'}    {'UGAAAA'}

  Columns 481 through 486

    {'> HL_37824.7  8…'}    {'AGUGAU'}    {'> HL_37824.7  5…'}    {'CGAAGG'}    {'> HL_37824.7  8…'}    {'AGUGAU'}

  Columns 487 through 492

    {'> HL_37824.7  3…'}    {'CGAGAG'}    {'> HL_37824.7  9…'}    {'CGCGAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 493 through 498

    {'> HL_37824.7  8…'}    {'AGUGAU'}    {'> HL_37824.7  8…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGUGAG'}

  Columns 499 through 504

    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'CGAAGG'}    {'> HL_37824.7  4…'}    {'CGAAGG'}

  Columns 505 through 510

    {'> HL_37824.7  3…'}    {'GGCGAC'}    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  7…'}    {'CGUGAG'}

  Columns 511 through 516

    {'> HL_37824.7  4…'}    {'CGCGAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}

  Columns 517 through 522

    {'> HL_37824.7  4…'}    {'UGAAAG'}    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'GGAAAC'}

  Columns 523 through 528

    {'> HL_37824.7  1…'}    {'CGAAGG'}    {'> HL_37824.7  4…'}    {'UGAUAAGG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}

  Columns 529 through 534

    {'> HL_37824.7  9…'}    {'CGUGAG'}    {'> HL_37824.7  7…'}    {'GGAAAUC'}    {'> HL_37824.7  4…'}    {'CGCGAG'}

  Columns 535 through 540

    {'> HL_37824.7  7…'}    {'GGUGAC'}    {'> HL_37824.7  9…'}    {'GGCGAC'}    {'> HL_37824.7  8…'}    {'CGAGAG'}

  Columns 541 through 546

    {'> HL_37824.7  7…'}    {'AGAAAU'}    {'> HL_37824.7  4…'}    {'CGAGAG'}    {'> HL_37824.7  9…'}    {'CGAAAG'}

  Columns 547 through 552

    {'> HL_37824.7  2…'}    {'GGCGAC'}    {'> HL_37824.7  4…'}    {'GGUGAC'}    {'> HL_37824.7  3…'}    {'CGCAAG'}

  Columns 553 through 558

    {'> HL_37824.7  4…'}    {'CGGAAG'}    {'> HL_37824.7  2…'}    {'CGUAUAG'}    {'> HL_37824.7  4…'}    {'CUGAAG'}

  Columns 559 through 564

    {'> HL_37824.7  4…'}    {'CGUAUAG'}    {'> HL_37824.7  6…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'AGUGAU'}

  Columns 565 through 570

    {'> HL_37824.7  4…'}    {'CGUGAG'}    {'> HL_37824.7  1…'}    {'GGAAAC'}    {'> HL_37824.7  5…'}    {'UGUGAA'}

  Columns 571 through 576

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  5…'}    {'UGAAGAA'}    {'> HL_37824.7  4…'}    {'CGUGAG'}

  Columns 577 through 582

    {'> HL_37824.7  5…'}    {'CGCGAG'}    {'> HL_37824.7  5…'}    {'CGCACAG'}    {'> HL_37824.7  7…'}    {'CGCAAG'}

  Columns 583 through 588

    {'> HL_37824.7  8…'}    {'CGUAAG'}    {'> HL_37824.7  6…'}    {'UGAAAA'}    {'> HL_37824.7  8…'}    {'UGUAAA'}

  Columns 589 through 594

    {'> HL_37824.7  6…'}    {'UGCAUAA'}    {'> HL_37824.7  7…'}    {'CGCAUAG'}    {'> HL_37824.7  8…'}    {'GGUAAC'}

  Columns 595 through 600

    {'> HL_37824.7  2…'}    {'CGCAAG'}    {'> HL_37824.7  3…'}    {'CGAAAG'}    {'> HL_37824.7  3…'}    {'GGAAUAC'}

  Columns 601 through 606

    {'> HL_37824.7  4…'}    {'CGAAAG'}    {'> HL_37824.7  1…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CGAGAG'}

  Columns 607 through 612

    {'> HL_37824.7  8…'}    {'GGCAAC'}    {'> HL_37824.7  5…'}    {'AGAGAAU'}    {'> HL_37824.7  5…'}    {'UGUGAG'}

  Columns 613 through 618

    {'> HL_37824.7  8…'}    {'GAAGCU'}    {'> HL_37824.7  8…'}    {'GAAGCU'}    {'> HL_37824.7  5…'}    {'UGCUAACG'}

  Columns 619 through 624

    {'> HL_37824.7  4…'}    {'CGUAAG'}    {'> HL_37824.7  9…'}    {'CGAAAG'}    {'> HL_37824.7  6…'}    {'UGAACAA'}

  Columns 625 through 630

    {'> HL_37824.7  1…'}    {'GGAGUAC'}    {'> HL_37824.7  4…'}    {'UUAACG'}    {'> HL_37824.7  3…'}    {'CUUCGG'}

  Columns 631 through 636

    {'> HL_37824.7  1…'}    {'GGGAGC'}    {'> HL_37824.7  4…'}    {'CGACGAG'}    {'> HL_37824.7  1…'}    {'CAAACG'}

  Columns 637 through 642

    {'> HL_37824.7  5…'}    {'CGAAAG'}    {'> HL_37824.7  8…'}    {'UCACCG'}    {'> HL_37824.7  9…'}    {'CGAACAG'}

  Columns 643 through 648

    {'> HL_37824.7  1…'}    {'GGGAGC'}    {'> HL_37824.7  4…'}    {'UCAGAAG'}    {'> HL_37824.7  4…'}    {'GCAACUC'}

  Columns 649 through 654

    {'> HL_37824.7  5…'}    {'CAGCCG'}    {'> HL_37824.7  5…'}    {'GGGAAC'}    {'> HL_37824.7  8…'}    {'GUGAAC'}

  Columns 655 through 660

    {'> HL_37824.7  4…'}    {'CGGAAG'}    {'> HL_37824.7  7…'}    {'CGGAAG'}    {'> HL_37824.7  8…'}    {'CGAAAUG'}

  Columns 661 through 666

    {'> HL_37824.7  1…'}    {'GGGAGC'}    {'> HL_37824.7  7…'}    {'CGAAAG'}    {'> HL_37824.7  4…'}    {'CAGCCG'}

  Columns 667 through 672

    {'> HL_37824.7  4…'}    {'UGAAUAG'}    {'> HL_37824.7  8…'}    {'GUGAAC'}    {'> HL_37824.7  4…'}    {'UUCAAG'}

  Columns 673 through 678

    {'> HL_37824.7  9…'}    {'UGAUGAG'}    {'> HL_37824.7  8…'}    {'UUAACAG'}    {'> HL_37824.7  4…'}    {'CGACAG'}

  Columns 679 through 684

    {'> HL_37824.7  8…'}    {'GUAAUUC'}    {'> HL_37824.7  8…'}    {'UAAGGG'}    {'> HL_37824.7  3…'}    {'UGGAGG'}

  Columns 685 through 690

    {'> HL_37824.7  7…'}    {'CGAACG'}    {'> HL_37824.7  8…'}    {'UGAACAG'}    {'> HL_37824.7  7…'}    {'AGAAAU'}

  Columns 691 through 696

    {'> HL_37824.7  5…'}    {'UGCAUA'}    {'> HL_37824.7  8…'}    {'GUAAUUC'}    {'> HL_37824.7  5…'}    {'CGCAAG'}

  Columns 697 through 698

    {'> HL_37824.7  1…'}    {'GUAACGC'}

pCalculateTransitions:  processing HL_38046.1
    {'> HL_38046.1  7A0S A 2188 U 2196'}    {'AAAAUCACU'}

pCalculateTransitions:  processing HL_38168.1
    {'> HL_38168.1  8J72 C    4…'}    {'CAAAG'}    {'> HL_38168.1  9H1K C 2551…'}    {'CUGUUCG'}

pCalculateTransitions:  processing HL_38649.1
  Columns 1 through 6

    {'> HL_38649.1  3…'}    {'GGAACACUAUAC'}    {'> HL_38649.1  3…'}    {'GGAACACUAUAC'}    {'> HL_38649.1  2…'}    {'CGGCGCAUGCAG'}

  Columns 7 through 10

    {'> HL_38649.1  7…'}    {'GUGCAGCCCGUC'}    {'> HL_38649.1  4…'}    {'CUGACCGAUAUG'}

pCalculateTransitions:  processing HL_38808.1
  Columns 1 through 6

    {'> HL_38808.1  4…'}    {'AUUCCCAUU'}    {'> HL_38808.1  5…'}    {'AUUCCCAUU'}    {'> HL_38808.1  2…'}    {'ACUGCAGAU'}

  Columns 7 through 8

    {'> HL_38808.1  6…'}    {'CUAAUUAGUG'}

pCalculateTransitions:  processing HL_38901.2
  Columns 1 through 6

    {'> HL_38901.2  3…'}    {'UUGGUA'}    {'> HL_38901.2  3…'}    {'CUGGUG'}    {'> HL_38901.2  3…'}    {'GUGGUC'}

  Columns 7 through 13

    {'> HL_38901.2  3…'}    {'GUGGUC'}    {'> HL_38901.2  5…'}    {'GAGUC'}    {'> HL_38901.2  8…'}    {'CAUUUG'}    {'> HL_38901.2  4…'}

  Column 14

    {'GGAAAC'}

pCalculateTransitions:  processing HL_39243.1
    {'> HL_39243.1  3BT7 G   53…'}    {'GUUCGAUCC'}    {'> HL_39243.1  7A0S G 1508…'}    {'GAAAAUC'}

pCalculateTransitions:  processing HL_40252.4
  Columns 1 through 6

    {'> HL_40252.4  4…'}    {'CAAGCGGUAAG'}    {'> HL_40252.4  8…'}    {'CGAGCGGUUGAAG'}    {'> HL_40252.4  1…'}    {'CCAAUGGUCACG'}

  Columns 7 through 10

    {'> HL_40252.4  9…'}    {'CGAGUGGCUGAAG'}    {'> HL_40252.4  1…'}    {'CAAGCGGUAAG'}

pCalculateTransitions:  processing HL_41464.2
  Columns 1 through 6

    {'> HL_41464.2  8…'}    {'GUGUAAAAC'}    {'> HL_41464.2  8…'}    {'GUGUAAAAC'}    {'> HL_41464.2  3…'}    {'CUGUUCGCAG'}

  Columns 7 through 8

    {'> HL_41464.2  6…'}    {'GGUGAAUGAC'}

pCalculateTransitions:  processing HL_41543.1
    {'> HL_41543.1  7MKY G    9…'}    {'GUGCAGCCCGUC'}    {'> HL_41543.1  5X2G G   54…'}    {'GUUUGCGGGAC'}

pCalculateTransitions:  processing HL_41902.1
    {'> HL_41902.1  6QN3 U   32…'}    {'UAGGGAACGGGA'}    {'> HL_41902.1  6QN3 U   32…'}    {'UAGGGAACGGGA'}

pCalculateTransitions:  processing HL_42046.2
  Columns 1 through 6

    {'> HL_42046.2  5…'}    {'CGUUCUAG'}    {'> HL_42046.2  5…'}    {'CGUUCUAG'}    {'> HL_42046.2  5…'}    {'CGUUUUAG'}

  Columns 7 through 10

    {'> HL_42046.2  5…'}    {'CGUUUUAG'}    {'> HL_42046.2  9…'}    {'CGUUGAG'}

pCalculateTransitions:  processing HL_42998.2
  Columns 1 through 6

    {'> HL_42998.2  5…'}    {'GAAACAAC'}    {'> HL_42998.2  4…'}    {'GAAACAGC'}    {'> HL_42998.2  7…'}    {'GAAACAAC'}

  Columns 7 through 12

    {'> HL_42998.2  9…'}    {'GGAACAAC'}    {'> HL_42998.2  4…'}    {'GGAACAAC'}    {'> HL_42998.2  8…'}    {'GGAUGAAC'}

  Columns 13 through 14

    {'> HL_42998.2  8…'}    {'GGAUGAAC'}

pCalculateTransitions:  processing HL_43517.1
    {'> HL_43517.1  2OZB G   35…'}    {'GUUUAUC'}    {'> HL_43517.1  8XZL C   28…'}    {'CUUCG'}

pCalculateTransitions:  processing HL_45175.1
  Columns 1 through 6

    {'> HL_45175.1  3…'}    {'CAGUUGGUAG'}    {'> HL_45175.1  3…'}    {'CAGUCGGUAG'}    {'> HL_45175.1  3…'}    {'CAGUGGUAG'}

  Columns 7 through 10

    {'> HL_45175.1  5…'}    {'CAGGGGUAG'}    {'> HL_45175.1  1…'}    {'UAAUGGUCAG'}

pCalculateTransitions:  processing HL_45785.1
    {'> HL_45785.1  8FZA G    5…'}    {'GUUCCCUCACC'}    {'> HL_45785.1  8FZA G    5…'}    {'GUUCCCUCACC'}

pCalculateTransitions:  processing HL_46501.1
    {'> HL_46501.1  3DD2 C   11…'}    {'CUGAAG'}    {'> HL_46501.1  4M4O C   32…'}    {'CUUAG'}

pCalculateTransitions:  processing HL_47732.1
    {'> HL_47732.1  4Z7K C   17…'}    {'CAAAAUAACAAG'}    {'> HL_47732.1  4Z7L C   17…'}    {'CAAAAUAACAAG'}

pCalculateTransitions:  processing HL_47787.2
  Columns 1 through 6

    {'> HL_47787.2  4…'}    {'CAUCCCG'}    {'> HL_47787.2  9…'}    {'CAUUCCG'}    {'> HL_47787.2  5…'}    {'CAUGCCG'}

  Columns 7 through 12

    {'> HL_47787.2  1…'}    {'CAUGCCG'}    {'> HL_47787.2  8…'}    {'CGUUCG'}    {'> HL_47787.2  4…'}    {'CAUGCCG'}

  Columns 13 through 18

    {'> HL_47787.2  8…'}    {'CGUCCG'}    {'> HL_47787.2  7…'}    {'CAUGCCG'}    {'> HL_47787.2  6…'}    {'CAUUUUGG'}

  Columns 19 through 20

    {'> HL_47787.2  7…'}    {'UGAAAA'}

pCalculateTransitions:  processing HL_47854.1
    {'> HL_47854.1  4Z0C G    4 C   11'}    {'GAAAGACC'}

pCalculateTransitions:  processing HL_48417.5
  Columns 1 through 6

    {'> HL_48417.5  6…'}    {'CAUGUGG'}    {'> HL_48417.5  5…'}    {'CAUGUAG'}    {'> HL_48417.5  6…'}    {'CAUGUGG'}

  Columns 7 through 12

    {'> HL_48417.5  7…'}    {'CGAUUUG'}    {'> HL_48417.5  2…'}    {'GAUUAC'}    {'> HL_48417.5  2…'}    {'GAUUAC'}

  Columns 13 through 18

    {'> HL_48417.5  5…'}    {'UAGUGUA'}    {'> HL_48417.5  5…'}    {'GAUCAC'}    {'> HL_48417.5  7…'}    {'CAACAG'}

  Columns 19 through 24

    {'> HL_48417.5  4…'}    {'CAGUUGGUUAG'}    {'> HL_48417.5  1…'}    {'GAUCAC'}    {'> HL_48417.5  4…'}    {'CCUUGG'}

  Columns 25 through 30

    {'> HL_48417.5  9…'}    {'GAGUUAC'}    {'> HL_48417.5  3…'}    {'ACCUAU'}    {'> HL_48417.5  8…'}    {'CGACACG'}

  Columns 31 through 36

    {'> HL_48417.5  3…'}    {'ACCUAU'}    {'> HL_48417.5  6…'}    {'CUGGG'}    {'> HL_48417.5  6…'}    {'CUUUUUG'}

  Columns 37 through 42

    {'> HL_48417.5  2…'}    {'CGCGUG'}    {'> HL_48417.5  1…'}    {'UUCGGGA'}    {'> HL_48417.5  5…'}    {'CAGUUGGUAG'}

  Columns 43 through 48

    {'> HL_48417.5  5…'}    {'CAUAGG'}    {'> HL_48417.5  8…'}    {'CAUUUG'}    {'> HL_48417.5  8…'}    {'CGUAUUG'}

  Columns 49 through 52

    {'> HL_48417.5  8…'}    {'UAAUUCA'}    {'> HL_48417.5  8…'}    {'AAUUAUU'}

pCalculateTransitions:  processing HL_48778.2
  Columns 1 through 7

    {'> HL_48778.2  8…'}    {'CCGUG'}    {'> HL_48778.2  7…'}    {'CUAG'}    {'> HL_48778.2  6…'}    {'UUUCA'}    {'> HL_48778.2  2…'}

  Columns 8 through 14

    {'UUGA'}    {'> HL_48778.2  7…'}    {'CUAG'}    {'> HL_48778.2  5…'}    {'CUAG'}    {'> HL_48778.2  7…'}    {'CUAG'}

  Columns 15 through 21

    {'> HL_48778.2  7…'}    {'CUAG'}    {'> HL_48778.2  7…'}    {'CAUCG'}    {'> HL_48778.2  8…'}    {'CCUUG'}    {'> HL_48778.2  6…'}

  Columns 22 through 28

    {'GUCAC'}    {'> HL_48778.2  8…'}    {'CACG'}    {'> HL_48778.2  5…'}    {'UAGA'}    {'> HL_48778.2  4…'}    {'CCAUG'}

  Columns 29 through 35

    {'> HL_48778.2  5…'}    {'CUAG'}    {'> HL_48778.2  5…'}    {'CUAG'}    {'> HL_48778.2  7…'}    {'CUAG'}    {'> HL_48778.2  8…'}

  Columns 36 through 42

    {'CUUG'}    {'> HL_48778.2  8…'}    {'CUAG'}    {'> HL_48778.2  7…'}    {'CAUCG'}    {'> HL_48778.2  8…'}    {'CAUUG'}

  Columns 43 through 49

    {'> HL_48778.2  6…'}    {'GUCAC'}    {'> HL_48778.2  8…'}    {'CUAG'}    {'> HL_48778.2  5…'}    {'GUCUC'}    {'> HL_48778.2  7…'}

  Columns 50 through 56

    {'CUUAUG'}    {'> HL_48778.2  8…'}    {'CACG'}    {'> HL_48778.2  5…'}    {'CUAG'}    {'> HL_48778.2  9…'}    {'CAAG'}

  Columns 57 through 63

    {'> HL_48778.2  5…'}    {'UUUCUA'}    {'> HL_48778.2  5…'}    {'CAGG'}    {'> HL_48778.2  6…'}    {'CUCG'}    {'> HL_48778.2  4…'}

  Columns 64 through 70

    {'GUCUC'}    {'> HL_48778.2  7…'}    {'CAAG'}    {'> HL_48778.2  4…'}    {'CUAAG'}    {'> HL_48778.2  4…'}    {'CUUUG'}

  Columns 71 through 77

    {'> HL_48778.2  2…'}    {'CUACGG'}    {'> HL_48778.2  8…'}    {'UUUUUA'}    {'> HL_48778.2  5…'}    {'CUCUG'}    {'> HL_48778.2  8…'}

  Columns 78 through 84

    {'CUUG'}    {'> HL_48778.2  8…'}    {'CUUG'}    {'> HL_48778.2  8…'}    {'CUUUG'}    {'> HL_48778.2  4…'}    {'CCCUG'}

  Columns 85 through 91

    {'> HL_48778.2  4…'}    {'GUGUCC'}    {'> HL_48778.2  8…'}    {'CAUUG'}    {'> HL_48778.2  4…'}    {'CGAG'}    {'> HL_48778.2  4…'}

  Column 92

    {'CUUUG'}

pCalculateTransitions:  processing HL_49922.4
  Columns 1 through 6

    {'> HL_49922.4  6…'}    {'UAGUAA'}    {'> HL_49922.4  5…'}    {'UAGUAA'}    {'> HL_49922.4  7…'}    {'UAGUAA'}

  Columns 7 through 12

    {'> HL_49922.4  4…'}    {'UAGUAA'}    {'> HL_49922.4  9…'}    {'UAGUAA'}    {'> HL_49922.4  7…'}    {'UAGUAA'}

  Columns 13 through 18

    {'> HL_49922.4  7…'}    {'CAAAAUG'}    {'> HL_49922.4  7…'}    {'CAAAAUG'}    {'> HL_49922.4  5…'}    {'GUAAUCC'}

  Columns 19 through 20

    {'> HL_49922.4  4…'}    {'CUUAUCG'}

pCalculateTransitions:  processing HL_49941.1
  Columns 1 through 6

    {'> HL_49941.1  1…'}    {'CAGGUGGUUAG'}    {'> HL_49941.1  1…'}    {'CAGGUGGUUAG'}    {'> HL_49941.1  2…'}    {'CAGCUGGUCAG'}

  Columns 7 through 8

    {'> HL_49941.1  6…'}    {'CAGCCUGGUAG'}

pCalculateTransitions:  processing HL_50006.2
  Columns 1 through 6

    {'> HL_50006.2  5…'}    {'CCUUUCACG'}    {'> HL_50006.2  5…'}    {'CCUUUCACG'}    {'> HL_50006.2  7…'}    {'CGAAAG'}

  Columns 7 through 10

    {'> HL_50006.2  8…'}    {'CUUCGG'}    {'> HL_50006.2  4…'}    {'GAAGGAUC'}

pCalculateTransitions:  processing HL_50318.1
    {'> HL_50318.1  4WF9 C  587 G  594'}    {'CGUUAAUG'}

pCalculateTransitions:  processing HL_50418.1
    {'> HL_50418.1  7…'}    {'GAAGCAGGCAC'}    {'> HL_50418.1  7…'}    {'GAAGCCUCCAC'}    {'> HL_50418.1  7…'}    {'CUGGAGAUACG'}

pCalculateTransitions:  processing HL_50537.6
  Columns 1 through 6

    {'> HL_50537.6  4…'}    {'ACUGUUAAU'}    {'> HL_50537.6  3…'}    {'GCUGUUAAC'}    {'> HL_50537.6  1…'}    {'CUUGUCGCG'}

  Columns 7 through 8

    {'> HL_50537.6  6…'}    {'CCAGUUAG'}

pCalculateTransitions:  processing HL_50779.4
  Columns 1 through 6

    {'> HL_50779.4  4…'}    {'GAAGCAACGC'}    {'> HL_50779.4  5…'}    {'GAUGCAACGC'}    {'> HL_50779.4  8…'}    {'GACUCAACAC'}

  Columns 7 through 8

    {'> HL_50779.4  8…'}    {'GACUCAACAC'}

pCalculateTransitions:  processing HL_50851.1
    {'> HL_50851.1  8UTG G    8 U   19'}    {'GAGGCGGUUGGU'}

pCalculateTransitions:  processing HL_50860.2
  Columns 1 through 6

    {'> HL_50860.2  5…'}    {'GUCGGACAU'}    {'> HL_50860.2  4…'}    {'GACAGAGAC'}    {'> HL_50860.2  9…'}    {'GACGGAAAU'}

  Columns 7 through 12

    {'> HL_50860.2  8…'}    {'AACAGAAAU'}    {'> HL_50860.2  8…'}    {'AACAGAAAU'}    {'> HL_50860.2  7…'}    {'GUUGGAAAU'}

pCalculateTransitions:  processing HL_51447.1
    {'> HL_51447.1  8KAJ C   86 G   92'}    {'CGAGUCG'}

pCalculateTransitions:  processing HL_51921.1
    {'> HL_51921.1  8CRE U   69…'}    {'UGAAUUGCAGAUAUUCGUGAA'}    {'> HL_51921.1  8P9A U   69…'}    {'UGAAUUGCAGAAUUCCGUGAA'}

pCalculateTransitions:  processing HL_52953.3
  Columns 1 through 6

    {'> HL_52953.3  4…'}    {'GGAAAC'}    {'> HL_52953.3  8…'}    {'GGAAAC'}    {'> HL_52953.3  6…'}    {'GAGUAC'}

  Columns 7 through 12

    {'> HL_52953.3  3…'}    {'CGAGUG'}    {'> HL_52953.3  8…'}    {'CAAUGG'}    {'> HL_52953.3  8…'}    {'CAAUGG'}

  Columns 13 through 18

    {'> HL_52953.3  4…'}    {'GGAAAC'}    {'> HL_52953.3  2…'}    {'CGUGAG'}    {'> HL_52953.3  2…'}    {'CGUGAG'}

pCalculateTransitions:  processing HL_53454.2
  Columns 1 through 6

    {'> HL_53454.2  7…'}    {'CGUGUGGAAG'}    {'> HL_53454.2  4…'}    {'CGCAUGGAAG'}    {'> HL_53454.2  9…'}    {'CGUGUGGAAG'}

  Columns 7 through 12

    {'> HL_53454.2  5…'}    {'UGAAUGGAAG'}    {'> HL_53454.2  7…'}    {'UAUCGGUUAGAG'}    {'> HL_53454.2  7…'}    {'UAUCGGUUAGAG'}

pCalculateTransitions:  processing HL_53504.3
    {'> HL_53504.3  1NBS C   96…'}    {'CGAAGUCAUAAG'}    {'> HL_53504.3  2A64 G  288…'}    {'GGAAAUGAAC'}

pCalculateTransitions:  processing HL_53890.2
  Columns 1 through 6

    {'> HL_53890.2  7…'}    {'AGAAUU'}    {'> HL_53890.2  9…'}    {'AGAAAU'}    {'> HL_53890.2  4…'}    {'AAAAUU'}

  Columns 7 through 12

    {'> HL_53890.2  8…'}    {'CAACAG'}    {'> HL_53890.2  8…'}    {'CAACCG'}    {'> HL_53890.2  2…'}    {'CGCAAG'}

  Columns 13 through 18

    {'> HL_53890.2  8…'}    {'CACAUUG'}    {'> HL_53890.2  7…'}    {'UGAAAAG'}    {'> HL_53890.2  8…'}    {'CACAUUG'}

  Columns 19 through 24

    {'> HL_53890.2  8…'}    {'CCUUUG'}    {'> HL_53890.2  4…'}    {'UGUAAG'}    {'> HL_53890.2  6…'}    {'CCAAGCG'}

  Columns 25 through 30

    {'> HL_53890.2  8…'}    {'CUUCGG'}    {'> HL_53890.2  8…'}    {'CCACGUG'}    {'> HL_53890.2  1…'}    {'CUUCGG'}

pCalculateTransitions:  processing HL_55195.3
  Columns 1 through 6

    {'> HL_55195.3  9…'}    {'UUUAGG'}    {'> HL_55195.3  5…'}    {'UUUAGG'}    {'> HL_55195.3  4…'}    {'UUUAGG'}

  Columns 7 through 12

    {'> HL_55195.3  7…'}    {'UUGAGG'}    {'> HL_55195.3  4…'}    {'UCGAAG'}    {'> HL_55195.3  8…'}    {'GGUAC'}

pCalculateTransitions:  processing HL_55305.1
    {'> HL_55305.1  3TS2 U    5…'}    {'UCUAUGAUACCA'}    {'> HL_55305.1  3TS2 U    5…'}    {'UCUAUGAUACCA'}

pCalculateTransitions:  processing HL_55436.1
  Columns 1 through 6

    {'> HL_55436.1  2…'}    {'GGUCCCAGAC'}    {'> HL_55436.1  6…'}    {'UCUGCGAGGA'}    {'> HL_55436.1  3…'}    {'ACGGGGAGUU'}

  Columns 7 through 8

    {'> HL_55436.1  1…'}    {'UCAGAGGACA'}

pCalculateTransitions:  processing HL_56131.2
  Columns 1 through 6

    {'> HL_56131.2  1…'}    {'GCUGCGAAC'}    {'> HL_56131.2  2…'}    {'CCUCCUAAG'}    {'> HL_56131.2  4…'}    {'UACUAUA'}

  Columns 7 through 12

    {'> HL_56131.2  4…'}    {'UACUAUA'}    {'> HL_56131.2  2…'}    {'GGUC'}    {'> HL_56131.2  3…'}    {'UUGCG'}

pCalculateTransitions:  processing HL_56334.1
  Columns 1 through 7

    {'> HL_56334.1  4…'}    {'UCUAA'}    {'> HL_56334.1  6…'}    {'UGGAAA'}    {'> HL_56334.1  8…'}    {'CAUUG'}    {'> HL_56334.1  6…'}

  Columns 8 through 14

    {'AUAUU'}    {'> HL_56334.1  6…'}    {'AUAUU'}    {'> HL_56334.1  4…'}    {'CUGUG'}    {'> HL_56334.1  8…'}    {'UCCUUA'}

  Columns 15 through 21

    {'> HL_56334.1  6…'}    {'UGGAAA'}    {'> HL_56334.1  4…'}    {'UUUUCA'}    {'> HL_56334.1  4…'}    {'CUGUG'}    {'> HL_56334.1  4…'}

  Columns 22 through 28

    {'CUGUG'}    {'> HL_56334.1  4…'}    {'UUUUCA'}    {'> HL_56334.1  4…'}    {'CUGUG'}    {'> HL_56334.1  1…'}    {'UUUUCA'}

  Columns 29 through 32

    {'> HL_56334.1  4…'}    {'GAGUCC'}    {'> HL_56334.1  5…'}    {'GAGUCC'}

pCalculateTransitions:  processing HL_56676.1
    {'> HL_56676.1  8HNT U  103…'}    {'UGUAAG'}    {'> HL_56676.1  6DLR C   27…'}    {'CUUCGG'}

pCalculateTransitions:  processing HL_57176.2
  Columns 1 through 6

    {'> HL_57176.2  4…'}    {'GCUGAUC'}    {'> HL_57176.2  4…'}    {'GCUCGUC'}    {'> HL_57176.2  7…'}    {'GGUCGUC'}

  Columns 7 through 12

    {'> HL_57176.2  9…'}    {'GGUCGUC'}    {'> HL_57176.2  5…'}    {'GCAAAUC'}    {'> HL_57176.2  5…'}    {'GUUAAUC'}

  Columns 13 through 18

    {'> HL_57176.2  8…'}    {'AGCAGUU'}    {'> HL_57176.2  9…'}    {'GCAAAUC'}    {'> HL_57176.2  8…'}    {'AGCAGUU'}

  Columns 19 through 24

    {'> HL_57176.2  5…'}    {'GACGAC'}    {'> HL_57176.2  7…'}    {'UCAAUG'}    {'> HL_57176.2  5…'}    {'GACGAC'}

  Columns 25 through 28

    {'> HL_57176.2  5…'}    {'GACGAC'}    {'> HL_57176.2  9…'}    {'CAAGAG'}

pCalculateTransitions:  processing HL_57863.1
    {'> HL_57863.1  5BJO G    9…'}    {'GAAGGAGGUC'}    {'> HL_57863.1  5BJO G   20…'}    {'GAGGAGGUC'}

pCalculateTransitions:  processing HL_57875.1
  Columns 1 through 6

    {'> HL_57875.1  2…'}    {'GGUUUC'}    {'> HL_57875.1  6…'}    {'GUGAAGC'}    {'> HL_57875.1  3…'}    {'UGUAGG'}

  Columns 7 through 10

    {'> HL_57875.1  8…'}    {'CAUUAG'}    {'> HL_57875.1  8…'}    {'AAUUAUU'}

pCalculateTransitions:  processing HL_58224.1
    {'> HL_58224.1  5CCB C   13 G   22'}    {'CAGUCGGUAG'}

pCalculateTransitions:  processing HL_58539.1
    {'> HL_58539.1  3Q3Z U   31 G   46'}    {'UUAAAUUGGGCACUUG'}

pCalculateTransitions:  processing HL_59330.1
    {'> HL_59330.1  2W2H U   10 G   17'}    {'UUCUGCGG'}

pCalculateTransitions:  processing HL_59564.1
    {'> HL_59564.1  4PLX U   47 A   66'}    {'UGGCCUUUCUUAAAAAAAAA'}

pCalculateTransitions:  processing HL_59735.5
    {'> HL_59735.5  4WSM C   49…'}    {'CAAUAGG'}    {'> HL_59735.5  8CRE U 1019…'}    {'UGAAAUG'}

pCalculateTransitions:  processing HL_59843.1
    {'> HL_59843.1  9C2K U   19…'}    {'UCAAUGA'}    {'> HL_59843.1  1F1T C   14…'}    {'CGAGAG'}

pCalculateTransitions:  processing HL_60266.1
    {'> HL_60266.1  6DME G   78…'}    {'GGAUAAAAGAC'}    {'> HL_60266.1  7A0S G 1767…'}    {'GUUUACCAAAAUC'}

pCalculateTransitions:  processing HL_60293.1
    {'> HL_60293.1  5DEA U    8…'}    {'UGUGGAAGGAGUGGCUGGGUUG'}    {'> HL_60293.1  5DE8 U    8…'}    {'UGUGGAAGGAGUGGCUGGGUUG'}

pCalculateTransitions:  processing HL_60914.1
    {'> HL_60914.1  6CYT C   30 G   34'}    {'CUGGG'}

pCalculateTransitions:  processing HL_61996.2
  Columns 1 through 6

    {'> HL_61996.2  5…'}    {'GUGAAGAUGC'}    {'> HL_61996.2  4…'}    {'GUGAAGAUGC'}    {'> HL_61996.2  9…'}    {'GUGAAGAUGC'}

  Columns 7 through 12

    {'> HL_61996.2  4…'}    {'GUGCGGAGUC'}    {'> HL_61996.2  7…'}    {'GUAAAGAUGC'}    {'> HL_61996.2  8…'}    {'GGGAACGGGC'}

  Columns 13 through 16

    {'> HL_61996.2  8…'}    {'GGGAACGGGC'}    {'> HL_61996.2  5…'}    {'GUUCGAAUC'}

pCalculateTransitions:  processing HL_62934.1
    {'> HL_62934.1  8K0K C   42…'}    {'CGCAUAG'}    {'> HL_62934.1  5J7L C  225…'}    {'CAACCG'}

pCalculateTransitions:  processing HL_63355.1
    {'> HL_63355.1  7A0S G 1074 C 1087'}    {'GCUUAGAAGCAGCC'}

pCalculateTransitions:  processing HL_64292.1
    {'> HL_64292.1  8P9A G  486…'}    {'GGGCCCAUUCGGGUCU'}    {'> HL_64292.1  2ANN C    5…'}    {'CGGAUCAGUCACCCAAG'}

pCalculateTransitions:  processing HL_64690.6
  Columns 1 through 6

    {'> HL_64690.6  5…'}    {'GAAGACGAC'}    {'> HL_64690.6  7…'}    {'GAAGACCAC'}    {'> HL_64690.6  8…'}    {'GCAUACGAC'}

  Columns 7 through 12

    {'> HL_64690.6  9…'}    {'GAAGACCAC'}    {'> HL_64690.6  4…'}    {'AAAGAUGAU'}    {'> HL_64690.6  8…'}    {'GUAUACGAC'}

  Columns 13 through 18

    {'> HL_64690.6  4…'}    {'GUACAAGAC'}    {'> HL_64690.6  2…'}    {'CCUUUCACG'}    {'> HL_64690.6  8…'}    {'CCCUUUUGG'}

pCalculateTransitions:  processing HL_65313.1
    {'> HL_65313.1  8CRE C  762 G  767'}    {'CCUUUG'}

pCalculateTransitions:  processing HL_65794.5
  Columns 1 through 6

    {'> HL_65794.5  8…'}    {'UGAUCA'}    {'> HL_65794.5  8…'}    {'UGAUCA'}    {'> HL_65794.5  4…'}    {'CGAGAG'}

  Columns 7 through 12

    {'> HL_65794.5  7…'}    {'UACCAA'}    {'> HL_65794.5  5…'}    {'UGCCAA'}    {'> HL_65794.5  6…'}    {'GGAAAC'}

  Columns 13 through 18

    {'> HL_65794.5  4…'}    {'UGCCAA'}    {'> HL_65794.5  1…'}    {'CGCCCG'}    {'> HL_65794.5  3…'}    {'UGGUUG'}

  Columns 19 through 24

    {'> HL_65794.5  4…'}    {'CGCCGAG'}    {'> HL_65794.5  4…'}    {'GUCCCGC'}    {'> HL_65794.5  8…'}    {'GCAAUAC'}

  Columns 25 through 28

    {'> HL_65794.5  8…'}    {'GCACGGC'}    {'> HL_65794.5  7…'}    {'UUGCCAA'}

pCalculateTransitions:  processing HL_66103.1
    {'> HL_66103.1  3SIU C   40…'}    {'CGCAUAG'}    {'> HL_66103.1  6WBR C   56…'}    {'CUUCGUG'}

pCalculateTransitions:  processing HL_66482.1
    {'> HL_66482.1  6D3P C   12 G   29'}    {'CCAUCCGAGUUGCAAGAG'}

pCalculateTransitions:  processing HL_66853.7
  Columns 1 through 6

    {'> HL_66853.7  8…'}    {'CAGUCGGUAG'}    {'> HL_66853.7  8…'}    {'CAGUCGGUAG'}    {'> HL_66853.7  8…'}    {'CAGUCGGUAG'}

  Columns 7 through 12

    {'> HL_66853.7  4…'}    {'CAGUCGGUAG'}    {'> HL_66853.7  6…'}    {'CAAUGGUAG'}    {'> HL_66853.7  4…'}    {'CAGUCGGUAG'}

  Columns 13 through 18

    {'> HL_66853.7  4…'}    {'CAGUGGUAG'}    {'> HL_66853.7  4…'}    {'CAAUUGGUAG'}    {'> HL_66853.7  6…'}    {'CAGUCGGUUAG'}

  Columns 19 through 22

    {'> HL_66853.7  7…'}    {'CAGUGGUAG'}    {'> HL_66853.7  7…'}    {'CAGUGGUAG'}

pCalculateTransitions:  processing HL_67079.1
  Columns 1 through 6

    {'> HL_67079.1  4…'}    {'GGUUCGAAUCC'}    {'> HL_67079.1  4…'}    {'CAACUCUACCG'}    {'> HL_67079.1  8…'}    {'AUUGUAAUUAUU'}

  Columns 7 through 8

    {'> HL_67079.1  8…'}    {'AUUGUAAUUGUU'}

pCalculateTransitions:  processing HL_67407.5
  Columns 1 through 6

    {'> HL_67407.5  9…'}    {'CGACCGUCUGG'}    {'> HL_67407.5  4…'}    {'CGCCCGCCUGG'}    {'> HL_67407.5  4…'}    {'CGACCGCCUGG'}

  Columns 7 through 12

    {'> HL_67407.5  8…'}    {'CGCCCGCCUGG'}    {'> HL_67407.5  4…'}    {'GAGGUGCACAC'}    {'> HL_67407.5  7…'}    {'GAAGCUCGCAC'}

  Columns 13 through 18

    {'> HL_67407.5  5…'}    {'CGACCGUCUGG'}    {'> HL_67407.5  7…'}    {'GAAGCAGGCAC'}    {'> HL_67407.5  7…'}    {'GAAGCCUCCAC'}

  Columns 19 through 20

    {'> HL_67407.5  7…'}    {'GAAGCUCGCAC'}

pCalculateTransitions:  processing HL_67667.2
    {'> HL_67667.2  7…'}    {'CUGUUCG'}    {'> HL_67667.2  7…'}    {'CUGUUCG'}    {'> HL_67667.2  3…'}    {'CUGUUCG'}

pCalculateTransitions:  processing HL_68257.1
    {'> HL_68257.1  7A0S A  253…'}    {'AAACGCUUGCGUUU'}    {'> HL_68257.1  5J7L U  158…'}    {'UGAAUCCAUAG'}

pCalculateTransitions:  processing HL_68572.1
    {'> HL_68572.1  4…'}    {'CGGAGCGGCUGAAG'}    {'> HL_68572.1  7…'}    {'UCAGUCUGGCAGAG'}    {'> HL_68572.1  4…'}    {'CUCAGCAGGUAGAG'}

pCalculateTransitions:  processing HL_68767.1
    {'> HL_68767.1  3…'}    {'GGAAUCGGUAGAC'}    {'> HL_68767.1  2…'}    {'GGAAUGGGUAGAC'}    {'> HL_68767.1  5…'}    {'GAAAUCGGUAAAC'}

pCalculateTransitions:  processing HL_69139.1
    {'> HL_69139.1  8CRE U 1040…'}    {'UCUUUUAUUG'}    {'> HL_69139.1  4WF9 A  427…'}    {'AGCACGUGAAAUU'}

pCalculateTransitions:  processing HL_69752.2
  Columns 1 through 6

    {'> HL_69752.2  8…'}    {'CUAAGUG'}    {'> HL_69752.2  5…'}    {'CUAAGUG'}    {'> HL_69752.2  5…'}    {'CUAAGUG'}

  Columns 7 through 12

    {'> HL_69752.2  8…'}    {'CUAAGUG'}    {'> HL_69752.2  5…'}    {'CUGUUG'}    {'> HL_69752.2  8…'}    {'CUGUUG'}

  Columns 13 through 14

    {'> HL_69752.2  4…'}    {'CUUAG'}

pCalculateTransitions:  processing HL_70658.1
    {'> HL_70658.1  4LVW A   33…'}    {'AAUGGGAUGUCGU'}    {'> HL_70658.1  8P9A A 2252…'}    {'AGUAACUAUGACU'}

pCalculateTransitions:  processing HL_70751.1
    {'> HL_70751.1  5WTK C    7 G   17'}    {'CAAUAUCGAAG'}

pCalculateTransitions:  processing HL_70782.2
  Columns 1 through 6

    {'> HL_70782.2  8…'}    {'CCUCAG'}    {'> HL_70782.2  8…'}    {'CCUCAG'}    {'> HL_70782.2  4…'}    {'GUGUCC'}

  Columns 7 through 8

    {'> HL_70782.2  6…'}    {'UUUAA'}

pCalculateTransitions:  processing HL_71391.1
    {'> HL_71391.1  9DFE G  139…'}    {'GGGAAC'}    {'> HL_71391.1  3D2V G   17…'}    {'GUUCAC'}

pCalculateTransitions:  processing HL_72628.1
    {'> HL_72628.1  3PDR C   99 G  107'}    {'CGACAUAAG'}

pCalculateTransitions:  processing HL_73183.1
    {'> HL_73183.1  6ZDU C 1297…'}    {'CGAAAAAAUUGGAAGUAG'}    {'> HL_73183.1  3IGI U   47…'}    {'UGAAGGCAGAAGUAA'}

pCalculateTransitions:  processing HL_73247.1
  Columns 1 through 5

    {'> HL_73247.1  7…'}    {'CAUACACGAGUUGCAAG'}    {'> HL_73247.1  7…'}    {'CAUACACGAGUUGCAAG'}    {'> HL_73247.1  6…'}

  Column 6

    {'CAUCCGAGUUGCAAG'}

pCalculateTransitions:  processing HL_73255.1
    {'> HL_73255.1  5AOX C   32…'}    {'CAGCACUUUG'}    {'> HL_73255.1  1E8O C  131…'}    {'CAGCUACUCG'}

pCalculateTransitions:  processing HL_73266.9
  Columns 1 through 6

    {'> HL_73266.9  5…'}    {'GCCUUAAAC'}    {'> HL_73266.9  3…'}    {'GCCUUAAAC'}    {'> HL_73266.9  4…'}    {'ACCGUAAAU'}

  Columns 7 through 12

    {'> HL_73266.9  4…'}    {'GCCUUAAAC'}    {'> HL_73266.9  1…'}    {'ACCGUAAAU'}    {'> HL_73266.9  4…'}    {'GCCUUAAAC'}

  Columns 13 through 18

    {'> HL_73266.9  1…'}    {'GCCUUAAAC'}    {'> HL_73266.9  7…'}    {'GCCUUAAAC'}    {'> HL_73266.9  5…'}    {'ACCGUAAAU'}

  Columns 19 through 24

    {'> HL_73266.9  3…'}    {'ACUGUAAAU'}    {'> HL_73266.9  8…'}    {'ACCACAAAU'}    {'> HL_73266.9  9…'}    {'ACCCUAAAU'}

  Columns 25 through 26

    {'> HL_73266.9  6…'}    {'UCUUUAAAA'}

pCalculateTransitions:  processing HL_73916.1
    {'> HL_73916.1  4WT8 A    7 U   46'}    {'AUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUUCCGAGU'}

pCalculateTransitions:  processing HL_74055.2
  Columns 1 through 5

    {'> HL_74055.2  5…'}    {'CUGAAAGCAUCUAAG'}    {'> HL_74055.2  4…'}    {'CUGAACGCAUCUAAG'}    {'> HL_74055.2  9…'}

  Columns 6 through 10

    {'CUGAAAGCAUCUAAG'}    {'> HL_74055.2  4…'}    {'CUGAAAGCAUCUAAG'}    {'> HL_74055.2  8…'}    {'CUGAACGCCUCUAAG'}

  Columns 11 through 14

    {'> HL_74055.2  8…'}    {'CUGAACGCCUCUAAG'}    {'> HL_74055.2  7…'}    {'CUGAAAGCAUCUAAG'}

pCalculateTransitions:  processing HL_74292.1
    {'> HL_74292.1  4FRN G   90 C   99'}    {'GCAAGGAGAC'}

pCalculateTransitions:  processing HL_74379.3
    {'> HL_74379.3  8JY0 G   42…'}    {'GCAAGGUUAACC'}    {'> HL_74379.3  9DXL G   26…'}    {'GCAAGGUUAACC'}

pCalculateTransitions:  processing HL_75293.5
  Columns 1 through 6

    {'> HL_75293.5  8…'}    {'AGGUGAAAUU'}    {'> HL_75293.5  5…'}    {'CGGUGAAAUG'}    {'> HL_75293.5  4…'}    {'CGGUGAAAUG'}

  Columns 7 through 12

    {'> HL_75293.5  8…'}    {'AGGUGAAAUU'}    {'> HL_75293.5  8…'}    {'GAUCAGAUACC'}    {'> HL_75293.5  5…'}    {'GAUUAGAUACC'}

  Columns 13 through 18

    {'> HL_75293.5  8…'}    {'GAUCAGAUACC'}    {'> HL_75293.5  4…'}    {'GAUUAGAUACC'}    {'> HL_75293.5  4…'}    {'CCUUGGUAAG'}

  Columns 19 through 22

    {'> HL_75293.5  5…'}    {'GCGUAAUAGC'}    {'> HL_75293.5  4…'}    {'CCCAAUAGGG'}

pCalculateTransitions:  processing HL_75660.5
  Columns 1 through 7

    {'> HL_75660.5  8…'}    {'CACAG'}    {'> HL_75660.5  8…'}    {'CAUAG'}    {'> HL_75660.5  4…'}    {'GAUAC'}    {'> HL_75660.5  8…'}

  Columns 8 through 14

    {'GUGGUC'}    {'> HL_75660.5  5…'}    {'GAUAC'}    {'> HL_75660.5  5…'}    {'CGAAAG'}    {'> HL_75660.5  9…'}    {'CAGAG'}

  Columns 15 through 21

    {'> HL_75660.5  7…'}    {'CUCAG'}    {'> HL_75660.5  4…'}    {'CAAAG'}    {'> HL_75660.5  4…'}    {'GGAAAC'}    {'> HL_75660.5  7…'}

  Columns 22 through 28

    {'CUGAUG'}    {'> HL_75660.5  8…'}    {'GGUGGC'}    {'> HL_75660.5  2…'}    {'CGAAUAG'}    {'> HL_75660.5  2…'}    {'CGCGUG'}

  Columns 29 through 35

    {'> HL_75660.5  1…'}    {'CGUAGG'}    {'> HL_75660.5  8…'}    {'CUCUG'}    {'> HL_75660.5  8…'}    {'GAGUC'}    {'> HL_75660.5  4…'}

  Columns 36 through 38

    {'GAAUC'}    {'> HL_75660.5  8…'}    {'AAUUUU'}

pCalculateTransitions:  processing HL_76094.1
    {'> HL_76094.1  9E7E C   20 G   24'}    {'CAAUG'}

pCalculateTransitions:  processing HL_77082.1
  Columns 1 through 6

    {'> HL_77082.1  9…'}    {'CCGAAAAG'}    {'> HL_77082.1  5…'}    {'ACUCUAAAU'}    {'> HL_77082.1  4…'}    {'ACUCAUACU'}

  Columns 7 through 12

    {'> HL_77082.1  1…'}    {'UCUGUAAAA'}    {'> HL_77082.1  7…'}    {'GUUUCGAC'}    {'> HL_77082.1  6…'}    {'GCCAUCAC'}

  Columns 13 through 16

    {'> HL_77082.1  8…'}    {'GUUAUCUUU'}    {'> HL_77082.1  8…'}    {'GUUAUCUUU'}

pCalculateTransitions:  processing HL_77436.5
  Columns 1 through 6

    {'> HL_77436.5  8…'}    {'CUUAAUUG'}    {'> HL_77436.5  8…'}    {'CUUAAUUG'}    {'> HL_77436.5  8…'}    {'CUUAAUUG'}

  Columns 7 through 12

    {'> HL_77436.5  8…'}    {'CUUAAUUG'}    {'> HL_77436.5  4…'}    {'GUUAAGUC'}    {'> HL_77436.5  5…'}    {'GUUAAGUC'}

  Columns 13 through 18

    {'> HL_77436.5  8…'}    {'UUUGGGAAUG'}    {'> HL_77436.5  8…'}    {'UUUGGGAAUG'}    {'> HL_77436.5  3…'}    {'AUUGAGUU'}

  Columns 19 through 24

    {'> HL_77436.5  3…'}    {'GAUAAUGC'}    {'> HL_77436.5  7…'}    {'GAUAAUGC'}    {'> HL_77436.5  3…'}    {'GGUAAUGC'}

  Columns 25 through 30

    {'> HL_77436.5  8…'}    {'GAUGAUUC'}    {'> HL_77436.5  8…'}    {'GAUGAUUC'}    {'> HL_77436.5  4…'}    {'CGUAAUG'}

  Columns 31 through 36

    {'> HL_77436.5  3…'}    {'GUUAAAAC'}    {'> HL_77436.5  1…'}    {'AUUCUGAUU'}    {'> HL_77436.5  4…'}    {'UUUUUGAUA'}

  Columns 37 through 42

    {'> HL_77436.5  4…'}    {'CAGUAAAUG'}    {'> HL_77436.5  4…'}    {'CGUACAAG'}    {'> HL_77436.5  2…'}    {'GCUUUGGAC'}

  Columns 43 through 46

    {'> HL_77436.5  5…'}    {'GUUCAAGUC'}    {'> HL_77436.5  7…'}    {'CGUAAUAG'}

pCalculateTransitions:  processing HL_77600.2
  Columns 1 through 6

    {'> HL_77600.2  8…'}    {'GGUAAAUUCC'}    {'> HL_77600.2  8…'}    {'GGUAAAUUCC'}    {'> HL_77600.2  4…'}    {'GAUGAGGCCC'}

  Columns 7 through 12

    {'> HL_77600.2  4…'}    {'UACUCCUUCG'}    {'> HL_77600.2  7…'}    {'GAACCAUCC'}    {'> HL_77600.2  7…'}    {'GGAUGGUUC'}

  Columns 13 through 18

    {'> HL_77600.2  5…'}    {'ACUGCAGAU'}    {'> HL_77600.2  4…'}    {'UGUAAGUAA'}    {'> HL_77600.2  9…'}    {'CGGUAGCGG'}

  Columns 19 through 20

    {'> HL_77600.2  7…'}    {'UCAAGCCUAG'}

pCalculateTransitions:  processing HL_78197.1
  Columns 1 through 6

    {'> HL_78197.1  6…'}    {'GGUUGGCC'}    {'> HL_78197.1  6…'}    {'GGUGAGCC'}    {'> HL_78197.1  6…'}    {'GCGAUCAC'}

  Columns 7 through 10

    {'> HL_78197.1  5…'}    {'CGUUGAAAAG'}    {'> HL_78197.1  9…'}    {'UUAUCUUA'}

pCalculateTransitions:  processing HL_78284.1
    {'> HL_78284.1  5J7L U 1009…'}    {'UUCAGAGAUGAG'}    {'> HL_78284.1  1EC6 G    4…'}    {'GACCUAGAUCACCC'}

pCalculateTransitions:  processing HL_78347.4
  Columns 1 through 6

    {'> HL_78347.4  5…'}    {'UAGAGGCCCAG'}    {'> HL_78347.4  5…'}    {'UAGAGGCCCAG'}    {'> HL_78347.4  2…'}    {'UAGAGGCCCAG'}

  Columns 7 through 12

    {'> HL_78347.4  1…'}    {'UAGCGGUUAG'}    {'> HL_78347.4  6…'}    {'CCUUCGUGG'}    {'> HL_78347.4  1…'}    {'CCUGAUAAG'}

  Columns 13 through 18

    {'> HL_78347.4  1…'}    {'CCUGAUAAG'}    {'> HL_78347.4  8…'}    {'UGUUUG'}    {'> HL_78347.4  3…'}    {'GGUCUC'}

pCalculateTransitions:  processing HL_78677.1
    {'> HL_78677.1  2CZJ U   26…'}    {'UUCG'}    {'> HL_78677.1  8CRE G 2088…'}    {'GGUAC'}

pCalculateTransitions:  processing HL_80008.1
    {'> HL_80008.1  2R8S C  166 G  174'}    {'CUUGCAAAG'}

pCalculateTransitions:  processing HL_80241.1
    {'> HL_80241.1  8V1I U   22…'}    {'UGGUUUCCA'}    {'> HL_80241.1  5J7L U   87…'}    {'UGAUAUGAA'}

pCalculateTransitions:  processing HL_80362.1
    {'> HL_80362.1  1GAX C  930 G  938'}    {'CCUCACACG'}

pCalculateTransitions:  processing HL_80411.1
    {'> HL_80411.1  1H4S C   13 G   22'}    {'CAGCCCGGUAG'}

pCalculateTransitions:  processing HL_80599.2
    {'> HL_80599.2  8…'}    {'UUCAGUGUG'}    {'> HL_80599.2  8…'}    {'UUCAGUGUG'}    {'> HL_80599.2  1…'}    {'CCUUACGAG'}

pCalculateTransitions:  processing HL_80709.3
  Columns 1 through 7

    {'> HL_80709.3  4…'}    {'CGCAG'}    {'> HL_80709.3  9…'}    {'CGCAG'}    {'> HL_80709.3  7…'}    {'CGCAG'}    {'> HL_80709.3  4…'}

  Columns 8 through 14

    {'CGCAG'}    {'> HL_80709.3  5…'}    {'CGAAG'}    {'> HL_80709.3  4…'}    {'GGAAAC'}    {'> HL_80709.3  3…'}    {'CGAAG'}

  Columns 15 through 21

    {'> HL_80709.3  3…'}    {'CGAAG'}    {'> HL_80709.3  5…'}    {'CUGUUG'}    {'> HL_80709.3  5…'}    {'CUCUUG'}    {'> HL_80709.3  5…'}

  Column 22

    {'CUCUUG'}

pCalculateTransitions:  processing HL_80922.2
    {'> HL_80922.2  4…'}    {'GAGUAUC'}    {'> HL_80922.2  2…'}    {'ACUACGGAU'}    {'> HL_80922.2  5…'}    {'CGAAUAG'}

pCalculateTransitions:  processing HL_81100.2
    {'> HL_81100.2  2…'}    {'CGCGUG'}    {'> HL_81100.2  2…'}    {'CGCGUG'}    {'> HL_81100.2  4…'}    {'GCUUGC'}

pCalculateTransitions:  processing HL_81205.3
    {'> HL_81205.3  4LFB C  320…'}    {'CACUGAGACACGGG'}    {'> HL_81205.3  5J7L A  320…'}    {'AACUGAGACACGGU'}

pCalculateTransitions:  processing HL_81312.1
    {'> HL_81312.1  8P9A C   70…'}    {'CAAUUUAUACAG'}    {'> HL_81312.1  8CRE C   70…'}    {'CAAUUUAUACAG'}

pCalculateTransitions:  processing HL_81538.2
  Columns 1 through 6

    {'> HL_81538.2  5…'}    {'GGUAACAC'}    {'> HL_81538.2  8…'}    {'UGUAACAA'}    {'> HL_81538.2  5…'}    {'CGUAACAG'}

  Columns 7 through 12

    {'> HL_81538.2  1…'}    {'CGUAACAG'}    {'> HL_81538.2  6…'}    {'CGUAAUAG'}    {'> HL_81538.2  8…'}    {'UGUAACAA'}

  Columns 13 through 18

    {'> HL_81538.2  3…'}    {'GUUAAAAC'}    {'> HL_81538.2  5…'}    {'GGUGGCUC'}    {'> HL_81538.2  9…'}    {'GGUGAGAC'}

  Columns 19 through 24

    {'> HL_81538.2  4…'}    {'AGUUAUGU'}    {'> HL_81538.2  1…'}    {'GGUGGCGC'}    {'> HL_81538.2  8…'}    {'AUUGAGAGCU'}

  Columns 25 through 30

    {'> HL_81538.2  4…'}    {'CUCGAACAG'}    {'> HL_81538.2  4…'}    {'CGGCGAAAG'}    {'> HL_81538.2  8…'}    {'AUUGAGAGCU'}

  Columns 31 through 32

    {'> HL_81538.2  5…'}    {'GUUAAUACC'}

pCalculateTransitions:  processing HL_81545.2
  Columns 1 through 6

    {'> HL_81545.2  4…'}    {'GUUAAUAUUC'}    {'> HL_81545.2  5…'}    {'GUUAAUAUUC'}    {'> HL_81545.2  4…'}    {'GUUGAUAUUC'}

  Columns 7 through 12

    {'> HL_81545.2  8…'}    {'GUUAAGAUUC'}    {'> HL_81545.2  8…'}    {'GUUAAAAUUC'}    {'> HL_81545.2  9…'}    {'GUUAAUAUUC'}

  Columns 13 through 14

    {'> HL_81545.2  7…'}    {'GUCAAGAUUC'}

pCalculateTransitions:  processing HL_82710.2
  Columns 1 through 6

    {'> HL_82710.2  9…'}    {'GGGAAC'}    {'> HL_82710.2  5…'}    {'GGAAAC'}    {'> HL_82710.2  7…'}    {'GGAAAC'}

  Columns 7 through 8

    {'> HL_82710.2  1…'}    {'GAACUC'}

pCalculateTransitions:  processing HL_83632.1
  Columns 1 through 6

    {'> HL_83632.1  2…'}    {'ACUCCAGAU'}    {'> HL_83632.1  6…'}    {'CCUGUCACG'}    {'> HL_83632.1  1…'}    {'ACUGUAGAU'}

  Columns 7 through 12

    {'> HL_83632.1  2…'}    {'ACUCUAAAU'}    {'> HL_83632.1  4…'}    {'CUUGCCAAG'}    {'> HL_83632.1  2…'}    {'ACUGAAAAU'}

pCalculateTransitions:  processing HL_83808.4
    {'> HL_83808.4  3…'}    {'CUCCUCGCG'}    {'> HL_83808.4  4…'}    {'CUCCUCGCUG'}    {'> HL_83808.4  4…'}    {'CUCCUCGCUG'}

pCalculateTransitions:  processing HL_84299.4
  Columns 1 through 6

    {'> HL_84299.4  8…'}    {'GAUAGUGGC'}    {'> HL_84299.4  8…'}    {'GAUAGUGGC'}    {'> HL_84299.4  4…'}    {'GGUAAUGGC'}

  Columns 7 through 12

    {'> HL_84299.4  5…'}    {'GGUAACGGC'}    {'> HL_84299.4  4…'}    {'GUUGACUAC'}    {'> HL_84299.4  5…'}    {'GAUAAAAGC'}

  Columns 13 through 18

    {'> HL_84299.4  7…'}    {'GAUAAAAGC'}    {'> HL_84299.4  6…'}    {'GAUAGAAGC'}    {'> HL_84299.4  2…'}    {'GGUAAGUUC'}

pCalculateTransitions:  processing HL_84847.1
    {'> HL_84847.1  7REX G    5 C   18'}    {'GUUCGCAACCAUCC'}

pCalculateTransitions:  processing HL_85367.2
  Columns 1 through 6

    {'> HL_85367.2  4…'}    {'CUGGGGCGG'}    {'> HL_85367.2  5…'}    {'CUGGGGCGG'}    {'> HL_85367.2  8…'}    {'CUGGGGCGG'}

  Columns 7 through 12

    {'> HL_85367.2  7…'}    {'CUGGGGCGG'}    {'> HL_85367.2  8…'}    {'CUGGGGCGG'}    {'> HL_85367.2  9…'}    {'CUGGGGCGG'}

  Columns 13 through 18

    {'> HL_85367.2  4…'}    {'CUGGGGCGG'}    {'> HL_85367.2  4…'}    {'UUAAGUGG'}    {'> HL_85367.2  4…'}    {'UUAGGUAG'}

  Columns 19 through 22

    {'> HL_85367.2  8…'}    {'UGUUCAAAG'}    {'> HL_85367.2  8…'}    {'UGUUCAAAG'}

pCalculateTransitions:  processing HL_85434.1
    {'> HL_85434.1  8VM9 G   15 C   24'}    {'GGUAUCCCAC'}

pCalculateTransitions:  processing HL_85461.1
    {'> HL_85461.1  8CRE G  701 C  720'}    {'GGUAGCCAUUUAUGGCGAAC'}

pCalculateTransitions:  processing HL_85993.1
    {'> HL_85993.1  1S03 A   22 U   29'}    {'AGGCAAUU'}

pCalculateTransitions:  processing HL_86012.1
    {'> HL_86012.1  1ZL3 G  408…'}    {'GUUCGAUCC'}    {'> HL_86012.1  1R3E G  408…'}    {'GUUCGAUCC'}

pCalculateTransitions:  processing HL_86109.1
    {'> HL_86109.1  4…'}    {'GGGCGGUGGGAGC'}    {'> HL_86109.1  4…'}    {'GGGCGGUGGGAGC'}    {'> HL_86109.1  4…'}    {'GGAUAGUGAAAGC'}

pCalculateTransitions:  processing HL_86769.4
  Columns 1 through 6

    {'> HL_86769.4  4…'}    {'AGGGUCAU'}    {'> HL_86769.4  6…'}    {'AGGGUCAU'}    {'> HL_86769.4  1…'}    {'CACCUCAG'}

  Columns 7 through 10

    {'> HL_86769.4  4…'}    {'GACGAUAU'}    {'> HL_86769.4  3…'}    {'GGCUCAUAACC'}

pCalculateTransitions:  processing HL_86870.2
  Columns 1 through 6

    {'> HL_86870.2  8…'}    {'GUGUUC'}    {'> HL_86870.2  8…'}    {'GUCUUC'}    {'> HL_86870.2  2…'}    {'ACGCGUGU'}

  Columns 7 through 8

    {'> HL_86870.2  9…'}    {'CAAUG'}

pCalculateTransitions:  processing HL_86883.1
    {'> HL_86883.1  8P9A G  124…'}    {'GUAUUC'}    {'> HL_86883.1  8CRE G  124…'}    {'GUAUUC'}

pCalculateTransitions:  processing HL_87463.1
    {'> HL_87463.1  4V9F G  390 C  399'}    {'GUUGGAUAUC'}

pCalculateTransitions:  processing HL_87553.1
  Columns 1 through 6

    {'> HL_87553.1  8…'}    {'GCGAAAGAC'}    {'> HL_87553.1  8…'}    {'GCGAAAGAC'}    {'> HL_87553.1  6…'}    {'ACUUCGGU'}

  Columns 7 through 12

    {'> HL_87553.1  9…'}    {'CCCACCAG'}    {'> HL_87553.1  5…'}    {'GCGCCAGC'}    {'> HL_87553.1  4…'}    {'UCAUCGA'}

  Columns 13 through 14

    {'> HL_87553.1  2…'}    {'UCUCAUAAG'}

pCalculateTransitions:  processing HL_87954.2
  Columns 1 through 6

    {'> HL_87954.2  5…'}    {'UGAAAGG'}    {'> HL_87954.2  9…'}    {'UGAAAAG'}    {'> HL_87954.2  4…'}    {'UGAAAGG'}

  Columns 7 through 12

    {'> HL_87954.2  4…'}    {'AGAAAUU'}    {'> HL_87954.2  5…'}    {'GUCCGGC'}    {'> HL_87954.2  4…'}    {'CUUCGCG'}

  Columns 13 through 14

    {'> HL_87954.2  4…'}    {'GUUCGGC'}

pCalculateTransitions:  processing HL_88205.2
  Columns 1 through 6

    {'> HL_88205.2  8…'}    {'ACGUGCAAAU'}    {'> HL_88205.2  8…'}    {'ACGUGCAAAU'}    {'> HL_88205.2  4…'}    {'UCCUACAAUA'}

  Columns 7 through 12

    {'> HL_88205.2  9…'}    {'GGAUGCAAAC'}    {'> HL_88205.2  7…'}    {'UGCUGAAACA'}    {'> HL_88205.2  4…'}    {'CGUUGAAAAG'}

  Columns 13 through 14

    {'> HL_88205.2  5…'}    {'UGUUGAAAAA'}

pCalculateTransitions:  processing HL_88364.2
  Columns 1 through 5

    {'> HL_88364.2  4…'}    {'UACUUAUUUCCUUUGA'}    {'> HL_88364.2  5…'}    {'UACUUAUUUCCUUUGA'}    {'> HL_88364.2  8…'}

  Column 6

    {'AUUUUGUUGGUUUCU'}

pCalculateTransitions:  processing HL_88558.1
    {'> HL_88558.1  2A64 C   97 G  108'}    {'CGAAUCCAUAAG'}

pCalculateTransitions:  processing HL_89199.2
  Columns 1 through 6

    {'> HL_89199.2  2…'}    {'CUGAUG'}    {'> HL_89199.2  2…'}    {'CUGAUG'}    {'> HL_89199.2  5…'}    {'CUGAUG'}

  Columns 7 through 10

    {'> HL_89199.2  2…'}    {'CUGAUG'}    {'> HL_89199.2  8…'}    {'CUGAUG'}

pCalculateTransitions:  processing HL_89346.1
    {'> HL_89346.1  8P9A A 1691…'}    {'AGAAGGGGGCAACUCCAUCU'}    {'> HL_89346.1  6ZDU C 1268…'}    {'CUUCCCGAAUUGUGGAUAG'}

pCalculateTransitions:  processing HL_89567.2
  Columns 1 through 6

    {'> HL_89567.2  5…'}    {'CGACACAG'}    {'> HL_89567.2  4…'}    {'CGACACAG'}    {'> HL_89567.2  7…'}    {'CGACACAG'}

  Columns 7 through 12

    {'> HL_89567.2  9…'}    {'CGACACAG'}    {'> HL_89567.2  4…'}    {'CGACACAG'}    {'> HL_89567.2  8…'}    {'CGCAGCAG'}

  Columns 13 through 16

    {'> HL_89567.2  8…'}    {'CGCAGCAG'}    {'> HL_89567.2  1…'}    {'AGGCAAUU'}

pCalculateTransitions:  processing HL_89881.5
  Columns 1 through 6

    {'> HL_89881.5  4…'}    {'UUUGAUCCUGG'}    {'> HL_89881.5  5…'}    {'UUUGAUCAUGG'}    {'> HL_89881.5  8…'}    {'GUUGAUCCUGC'}

  Columns 7 through 8

    {'> HL_89881.5  8…'}    {'GUUGAUCCUGC'}

pCalculateTransitions:  processing HL_89893.1
    {'> HL_89893.1  4RUM C   27 G   33'}    {'CAGAGCG'}

pCalculateTransitions:  processing HL_90620.1
    {'> HL_90620.1  6P2H A   59…'}    {'AACCGUAAAAU'}    {'> HL_90620.1  3IVN A   49…'}    {'AACCGUAAAAU'}

pCalculateTransitions:  processing HL_91503.7
    {'> HL_91503.7  9…'}    {'GUUCGUGGAGC'}    {'> HL_91503.7  7…'}    {'GUUCGUGAAAC'}    {'> HL_91503.7  5…'}    {'ACACGUGGUAU'}

pCalculateTransitions:  processing HL_91641.1
    {'> HL_91641.1  2QWY A   24 U   40'}    {'AGUCGCGUGAUAAAUGU'}

pCalculateTransitions:  processing HL_91939.2
  Columns 1 through 6

    {'> HL_91939.2  4…'}    {'CUAAAAGGUAACG'}    {'> HL_91939.2  5…'}    {'CUAAAGAGUAACG'}    {'> HL_91939.2  9…'}    {'CUAAAAGGUAACG'}

  Columns 7 through 12

    {'> HL_91939.2  4…'}    {'CGAAAAGAUAUCG'}    {'> HL_91939.2  8…'}    {'UUAAACGAUAACG'}    {'> HL_91939.2  8…'}    {'UUAAACGAUAACG'}

  Columns 13 through 16

    {'> HL_91939.2  7…'}    {'CCAAAAUGUAACG'}    {'> HL_91939.2  4…'}    {'UUCCCAACGAG'}

pCalculateTransitions:  processing HL_92488.1
    {'> HL_92488.1  4UYK G   43 C   58'}    {'GAAACCGCCGAUAUGC'}

pCalculateTransitions:  processing HL_93135.1
    {'> HL_93135.1  7A0S C 1466 G 1476'}    {'CUAUGGCUAUG'}

pCalculateTransitions:  processing HL_93324.4
  Columns 1 through 6

    {'> HL_93324.4  4…'}    {'UUACUUGA'}    {'> HL_93324.4  6…'}    {'GUUCGGGC'}    {'> HL_93324.4  6…'}    {'GUUUGAGC'}

  Columns 7 through 12

    {'> HL_93324.4  5…'}    {'GUUAGGGC'}    {'> HL_93324.4  9…'}    {'CGCAAGGG'}    {'> HL_93324.4  2…'}    {'CCUGGGAG'}

  Columns 13 through 18

    {'> HL_93324.4  8…'}    {'CAAAAGGG'}    {'> HL_93324.4  7…'}    {'CGCAAAGG'}    {'> HL_93324.4  3…'}    {'GACCCCGC'}

  Columns 19 through 24

    {'> HL_93324.4  8…'}    {'CAAAAGGG'}    {'> HL_93324.4  4…'}    {'UGUAAAGG'}    {'> HL_93324.4  3…'}    {'GACCCCGC'}

  Columns 25 through 30

    {'> HL_93324.4  4…'}    {'UGCAAGAG'}    {'> HL_93324.4  5…'}    {'UGCAAUGG'}    {'> HL_93324.4  4…'}    {'GGCAUCGAC'}

  Columns 31 through 36

    {'> HL_93324.4  8…'}    {'CGGAAUUUG'}    {'> HL_93324.4  3…'}    {'UUCCUCCCG'}    {'> HL_93324.4  2…'}    {'GUUCAUCAC'}

  Columns 37 through 42

    {'> HL_93324.4  8…'}    {'CGGAAUUUG'}    {'> HL_93324.4  3…'}    {'UUCCUCCCG'}    {'> HL_93324.4  4…'}    {'GCUUGAUGC'}

  Columns 43 through 48

    {'> HL_93324.4  6…'}    {'UACCUUCUG'}    {'> HL_93324.4  4…'}    {'CGCACGGAG'}    {'> HL_93324.4  3…'}    {'UGCAUAACAA'}

pCalculateTransitions:  processing HL_93383.1
    {'> HL_93383.1  5K7D G   33…'}    {'GCCCUAAGC'}    {'> HL_93383.1  6UFJ G   33…'}    {'GCUCAAAGC'}

pCalculateTransitions:  processing HL_93438.2
  Columns 1 through 6

    {'> HL_93438.2  7…'}    {'CGAUUACCUG'}    {'> HL_93438.2  4…'}    {'UGCCAAGCUG'}    {'> HL_93438.2  4…'}    {'UUACUAACGA'}

  Columns 7 through 12

    {'> HL_93438.2  9…'}    {'UGGCUACCUG'}    {'> HL_93438.2  8…'}    {'CAGCGAAAUG'}    {'> HL_93438.2  8…'}    {'CAGCGAAAUG'}

pCalculateTransitions:  processing HL_93535.1
  Columns 1 through 6

    {'> HL_93535.1  8…'}    {'CAGCCG'}    {'> HL_93535.1  8…'}    {'CAGCCG'}    {'> HL_93535.1  5…'}    {'UGAUAAA'}

  Columns 7 through 12

    {'> HL_93535.1  7…'}    {'CGAACAG'}    {'> HL_93535.1  7…'}    {'CGUAAG'}    {'> HL_93535.1  8…'}    {'UAAGGG'}

pCalculateTransitions:  processing HL_93616.2
  Columns 1 through 6

    {'> HL_93616.2  5…'}    {'CAGCCCGGUAG'}    {'> HL_93616.2  9…'}    {'CAGCCUGGUAG'}    {'> HL_93616.2  6…'}    {'CAGCCUGGUAG'}

  Columns 7 through 12

    {'> HL_93616.2  4…'}    {'CAGCCUGGUAG'}    {'> HL_93616.2  1…'}    {'CAGCCUGGUAG'}    {'> HL_93616.2  4…'}    {'CAGCCUGGUAG'}

  Columns 13 through 16

    {'> HL_93616.2  2…'}    {'UAGCCAGGACAG'}    {'> HL_93616.2  4…'}    {'CAGCCUGGUAG'}

pCalculateTransitions:  processing HL_94376.1
    {'> HL_94376.1  1…'}    {'GAAGUGCACAC'}    {'> HL_94376.1  1…'}    {'GAAGUGCACAC'}    {'> HL_94376.1  4…'}    {'UAGUCUCUUUCG'}

pCalculateTransitions:  processing HL_94980.1
    {'> HL_94980.1  8CRE C  274 G  277'}    {'CUUG'}

pCalculateTransitions:  processing HL_97733.1
    {'> HL_97733.1  5NWQ C   20 G   29'}    {'CCCGGUCAGG'}

pCalculateTransitions:  processing HL_97756.2
  Columns 1 through 5

    {'> HL_97756.2  4…'}    {'UACCCAUCCCGAACA'}    {'> HL_97756.2  9…'}    {'UUCCCAUUCCGAACA'}    {'> HL_97756.2  5…'}

  Columns 6 through 10

    {'ACCCCAUGCCGAACU'}    {'> HL_97756.2  4…'}    {'UUCCCAUGCCGAACA'}    {'> HL_97756.2  5…'}    {'ACCCCAUGCCGAACU'}

  Columns 11 through 12

    {'> HL_97756.2  1…'}    {'ACCCCAUGCCGAACU'}

pCalculateTransitions:  processing HL_97917.2
    {'> HL_97917.2  3…'}    {'CUUCAACG'}    {'> HL_97917.2  4…'}    {'GGAGGAC'}    {'> HL_97917.2  8…'}    {'UUUUUUAAUG'}

pCalculateTransitions:  processing HL_97983.1
    {'> HL_97983.1  3TRZ A    5 U   13'}    {'AGGGAUUUU'}

pCalculateTransitions:  processing HL_98252.1
    {'> HL_98252.1  5K36 A    2 U   12'}    {'AUUAUUUAUUU'}

pCalculateTransitions:  processing HL_98864.1
  Columns 1 through 6

    {'> HL_98864.1  4…'}    {'GUCCCAAGCC'}    {'> HL_98864.1  4…'}    {'GUCCUAAGCC'}    {'> HL_98864.1  4…'}    {'GUCCCAAGCC'}

  Columns 7 through 8

    {'> HL_98864.1  8…'}    {'GUAGGUAGUC'}

pCalculateTransitions:  processing HL_98870.1
    {'> HL_98870.1  6DU4 C    7…'}    {'CGUAGGCUACAGAGAAG'}    {'> HL_98870.1  6DU5 U    7…'}    {'UGUGGUACAGAGAAG'}

pCalculateTransitions:  processing HL_99040.1
    {'> HL_99040.1  8S95 U   92 G   97'}    {'UUGCGG'}

pCalculateTransitions:  processing HL_99324.1
    {'> HL_99324.1  6XKO C    4…'}    {'CAACUUAGGAUUUUAGG'}    {'> HL_99324.1  8CRE U  813…'}    {'UAUUUUGUUGGUUUCUA'}

pCalculateTransitions:  processing HL_99748.1
    {'> HL_99748.1  4P5J C    7 G   14'}    {'CCAGUUAG'}

pCalculateTransitions:  processing HL_99769.3
  Columns 1 through 6

    {'> HL_99769.3  5…'}    {'GUAGUGGUAUC'}    {'> HL_99769.3  4…'}    {'GUAGUGGUAUC'}    {'> HL_99769.3  2…'}    {'GUAGUGGUAAUC'}

  Columns 7 through 12

    {'> HL_99769.3  6…'}    {'CCCGAAUUGUGG'}    {'> HL_99769.3  7…'}    {'AACGCUUGCGUU'}    {'> HL_99769.3  4…'}    {'CAAGCUUGCUUG'}

pCalculateTransitions:  processing HL_99867.1
  Columns 1 through 6

    {'> HL_99867.1  3…'}    {'GAAGUGCAAC'}    {'> HL_99867.1  3…'}    {'GAUGCUUGUC'}    {'> HL_99867.1  3…'}    {'AUUAGGUAGU'}

  Columns 7 through 10

    {'> HL_99867.1  6…'}    {'GCUGGCGGUC'}    {'> HL_99867.1  4…'}    {'GUUCGGGGAC'}

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

cWW_M =

    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

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

initial_M =

    0.2039
    0.1141
    0.3525
    0.3295

pCalculateTransitions:  initial transition matrix is

initialTransition_M =

    0.1341    0.2683    0.3293    0.2683
    0.2418    0.0853    0.4182    0.2546
    0.1980    0.1007    0.2492    0.4521
    0.1597    0.1255    0.4297    0.2852

pCalculateTransitions:  interior transition matrix is

transition_M =

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

Timestamp 18-Jul-2025 22:26:24
pMakeSCFGModels: Making JAR3D model for motif group HL_00317.1, number 1 of 253
pMakeSCFGModels: Loaded C:\Users\zirbel\Documents\JAR3D\Motifs\HL_3.98\mat\HL_00317.1.mat, looks like:
Search = 

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

         motif_id: 'HL_00317.1'
       Candidates: [1 2 3 4 5 6 7 8 9 10 11 12 14 15 16 17 18 19 20 1]
    consensusEdge: [19×19 double]
     bp_signature: 'cWW-F-cSS-F-F-F-F-F-F-F-F-F-F-F-F-F-F'
        Signature: 'cWW-F-cSS-F-F-F-F-F-F-F-F-F-F-F-F-F-F'
       chainbreak: []
         loop_ids: {'HL_6SVS_002'}
         Truncate: [0×1 double]
            Query: [1×1 struct]
       MaxDiffMat: [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]
             File: [1×1 struct]
         NumFixed: 0


ans = 

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

         Backbone: [20×20 double]
    BasePhosphate: [20×20 double]
       BaseRibose: [20×20 double]
       BestChains: {{1×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [20×20 double]
         Covalent: [20×20 double]
         Crossing: [20×20 double]
         Distance: []
             Edge: [20×20 double]
         Filename: '6SVS'
            Flank: [20×20 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [1 79]
         Modified: 0
               NT: [1×20 struct]
            NumNT: 20
      PDBFilename: '6SVS.pdb'
            PDBID: '6SVS'
            Range: [20×20 double]
        Redundant: [20×20 double]


ans = 

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

         Backbone: [20×20 double]
    BasePhosphate: [20×20 double]
       BaseRibose: [20×20 double]
       BestChains: {{1×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [20×20 double]
         Covalent: [20×20 double]
         Crossing: [20×20 double]
         Distance: []
             Edge: [20×20 double]
         Filename: '6SVS'
            Flank: [20×20 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [1 79]
         Modified: 0
               NT: [1×20 struct]
            NumNT: 20
      PDBFilename: '6SVS.pdb'
            PDBID: '6SVS'
            Range: [20×20 double]
        Redundant: [20×20 double]

pMakeNodes starting loop:     a=6SVS|1|A|U|50 B=6SVS|1|A|A|69
  2 Basepair    50   69 UA cWW 
pMakeNodes probe for inserts:  a=6SVS|1|A|G|51 B=6SVS|1|A|A|68
    Insertion on left  6SVS|1|A|G|51
    Insertion on left  6SVS|1|A|G|52
pMakeNodesProbeForInsertions:  a 6SVS|1|A|C|53 interacts with 6SVS|1|A|A|68
pMakeNodesProbeForInsertions:  B 6SVS|1|A|A|68 interacts with 6SVS|1|A|C|53
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6SVS|1|A|A|68 interacts with 6SVS|1|A|C|53
pMakeNodes probed for insert:  a=6SVS|1|A|C|53 B=6SVS|1|A|A|68
  3 Basepair    53   68 CA cSS 
pMakeNodes adding hairpin:     a=6SVS|1|A|C|54 B=6SVS|1|A|A|67
    Right strand conserved insertion C  54 at right strand position 1
    Right strand conserved insertion U  55 at right strand position 2
    Right strand conserved insertion U  56 at right strand position 3
    Right strand conserved insertion U  57 at right strand position 4
    Right strand conserved insertion C  58 at right strand position 5
    Right strand conserved insertion U  59 at right strand position 6
    Right strand conserved insertion U  60 at right strand position 7
    Right strand conserved insertion A  61 at right strand position 8
    Right strand conserved insertion A  63 at right strand position 9
    Right strand conserved insertion A  64 at right strand position 10
    Right strand conserved insertion A  65 at right strand position 11
    Right strand conserved insertion A  66 at right strand position 12
    Right strand conserved insertion A  67 at right strand position 13
  4 Hairpin   54:67 CUUUCUUAAAAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right 18
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right 17
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6SVS|1|A|G|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6SVS|1|A|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 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: []
              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: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGG'
           RightLetter: 'A'
               Comment: ' // Basepair U50 - A69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6SVS|1|A|G|51'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'CUUUCUUAAAAAA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6SVS|1|A|G|52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 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: 'A'
               Comment: ' // Basepair C53 - A68 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUUCUUAAAAAA'
           RightLetter: ''
               Comment: ' // Hairpin node C54:A67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 18
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 18
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 18
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 18
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right 18
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right 17
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_00317.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.1580

Timestamp 18-Jul-2025 22:26:26
pMakeSCFGModels: Making JAR3D model for motif group HL_00914.1, number 2 of 253
pMakeNodes starting loop:     a=8CRE|1|1|G|2514 B=8CRE|1|1|C|2521
  2 Basepair  2514 2521 GC cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|G|2515 B=8CRE|1|1|A|2520
    Right strand conserved insertion G2515 at right strand position 1
    Right strand conserved insertion U2516 at right strand position 2
    Right strand conserved insertion A2519 at right strand position 3
    Right strand conserved insertion A2520 at right strand position 4
  3 Hairpin   2515:2520 GUAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2514 - C2521 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUAA'
           RightLetter: ''
               Comment: ' // Hairpin node G2515:A2520'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_00914.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4881

Timestamp 18-Jul-2025 22:26:26
pMakeSCFGModels: Making JAR3D model for motif group HL_01255.1, number 3 of 253
pMakeNodes starting loop:     a=8Y03|1|G|C|25 B=8Y03|1|G|G|36
  2 Basepair    25   36 CG cWW 
pMakeNodes adding hairpin:     a=8Y03|1|G|A|26 B=8Y03|1|G|A|35
    Right strand conserved insertion A  26 at right strand position 1
    Right strand conserved insertion U  27 at right strand position 2
    Right strand conserved insertion A  30 at right strand position 3
    Right strand conserved insertion A  33 at right strand position 4
    Right strand conserved insertion A  34 at right strand position 5
    Right strand conserved insertion A  35 at right strand position 6
  3 Hairpin   26:35 AUAAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C25 - G36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUAAAA'
           RightLetter: ''
               Comment: ' // Hairpin node A26:A35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_01255.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3341

Timestamp 18-Jul-2025 22:26:26
pMakeSCFGModels: Making JAR3D model for motif group HL_01609.3, number 4 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|305 B=5J7L|1|DA|G|312
  2 Basepair   305  312 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|306 B=5J7L|1|DA|A|310
  3 Basepair   306  310 UA tWH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|G|307 B=5J7L|1|DA|A|309
    Right strand conserved insertion G 307 at right strand position 1
    Right strand conserved insertion G 308 at right strand position 2
    Right strand conserved insertion A 309 at right strand position 3
  4 Hairpin   307:309 GGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C305 - G312 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U306 - A310 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGA'
           RightLetter: ''
               Comment: ' // Hairpin node G307:A309'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_01609.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0310
   -6.0310
   -5.8346
   -5.6729
   -5.6729
   -4.7594
   -8.6596
   -6.6284
   -5.6729
   -6.0310
   -5.6729
   -5.6729
   -6.3688
   -6.3688
   -6.1028
  -11.3841
  -15.8511
  -10.2578

Timestamp 18-Jul-2025 22:26:26
pMakeSCFGModels: Making JAR3D model for motif group HL_01962.2, number 5 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|U|1777 B=5J7L|1|DA|A|1787
  2 Basepair  1777 1787 UA cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|1778 B=5J7L|1|DA|A|1785
  3 Basepair  1778 1785 UA tWH 
No need to probe because of interaction between a=5J7L|1|DA|U|1779 B=5J7L|1|DA|A|1784
  4 Basepair  1779 1784 UA tWH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|1783 B=5J7L|1|DA|A|1783
    Right strand conserved insertion A1783 at right strand position 1
  5 Hairpin   1783:1783 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1777 - A1787 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U1778 - A1785 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1779 - A1784 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A1783:A1783'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1783'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_01962.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6529
   -7.8910
   -8.2957
   -7.2719
   -7.6703
   -7.6703

Timestamp 18-Jul-2025 22:26:27
pMakeSCFGModels: Making JAR3D model for motif group HL_02483.1, number 6 of 253
pMakeNodes starting loop:     a=4PKD|1|V|U|92 B=4PKD|1|V|G|103
  2 Basepair    92  103 UG cWW 
pMakeNodes probe for inserts:  a=4PKD|1|V|A|94 B=4PKD|1|V|G|102
    Insertion on right 4PKD|1|V|G|102
pMakeNodesProbeForInsertions:  a 4PKD|1|V|A|94 interacts with 4PKD|1|V|A|101
pMakeNodesProbeForInsertions:  B 4PKD|1|V|A|101 interacts with 4PKD|1|V|A|94
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4PKD|1|V|A|101 interacts with 4PKD|1|V|A|94
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4PKD|1|V|A|94 B=4PKD|1|V|A|101
  3 Basepair    94  101 AA tWH 
pMakeNodes adding hairpin:     a=4PKD|1|V|U|95 B=4PKD|1|V|A|100
    Right strand conserved insertion C  98 at right strand position 3
    Right strand conserved insertion G  99 at right strand position 4
    Right strand conserved insertion A 100 at right strand position 5
  4 Hairpin   95:100 UCCGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4PKD|1|V|A|100
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'GG'
               Comment: ' // Basepair U92 - G103 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4PKD|1|V|A|100'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UCCGA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A94 - A101 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCCGA'
           RightLetter: ''
               Comment: ' // Hairpin node U95:A100'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_02483.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7782

Timestamp 18-Jul-2025 22:26:27
pMakeSCFGModels: Making JAR3D model for motif group HL_02581.1, number 7 of 253
pMakeNodes starting loop:     a=1WZ2|1|D|C|912 B=1WZ2|1|D|G|926
  2 Basepair   912  926 CG cWW 
No need to probe because of interaction between a=1WZ2|1|D|G|913 B=1WZ2|1|D|A|925
  3 Basepair   913  925 GA tSH 
No need to probe because of interaction between a=1WZ2|1|D|A|914 B=1WZ2|1|D|A|924
  4 Basepair   914  924 AA cWS 
No need to probe because of interaction between a=1WZ2|1|D|G|915 B=1WZ2|1|D|C|922
  5 Basepair   915  922 GC tSW 
pMakeNodes adding hairpin:     a=1WZ2|1|D|C|916 B=1WZ2|1|D|U|918
    Right strand conserved insertion C 916 at right strand position 1
    Right strand conserved insertion C 917 at right strand position 2
    Right strand conserved insertion U 918 at right strand position 3
  6 Hairpin   916:918 CCU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              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 C912 - G926 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G913 - A925 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A914 - A924 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G915 - C922 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCU'
           RightLetter: ''
               Comment: ' // Hairpin node C916:U918'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_02581.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5501
   -9.5274

Timestamp 18-Jul-2025 22:26:27
pMakeSCFGModels: Making JAR3D model for motif group HL_02817.2, number 8 of 253
pMakeNodes starting loop:     a=8SYK|1|A|C|32 B=8SYK|1|A|G|39
  2 Basepair    32   39 CG cWW 
pMakeNodes adding hairpin:     a=8SYK|1|A|C|33 B=8SYK|1|A|A|38
    Right strand conserved insertion C  33 at right strand position 1
    Right strand conserved insertion A  34 at right strand position 2
    Right strand conserved insertion U  37 at right strand position 3
    Right strand conserved insertion A  38 at right strand position 4
  3 Hairpin   33:38 CAUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C32 - G39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAUA'
           RightLetter: ''
               Comment: ' // Hairpin node C33:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_02817.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7906
   -4.7906
   -7.0412

Timestamp 18-Jul-2025 22:26:27
pMakeSCFGModels: Making JAR3D model for motif group HL_02887.3, number 9 of 253
pMakeNodes starting loop:     a=4LFB|1|A|C|1314 B=4LFB|1|A|G|1323
  2 Basepair  1314 1323 CG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|U|1315 B=4LFB|1|A|C|1322
    Insertion on right 4LFB|1|A|C|1322
    Insertion on right 4LFB|1|A|C|1321
    Insertion on right 4LFB|1|A|C|1320
pMakeNodesProbeForInsertions:  a 4LFB|1|A|U|1315 interacts with 4LFB|1|A|A|1319
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|1319 interacts with 4LFB|1|A|U|1315
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|1319 interacts with 4LFB|1|A|U|1315
pMakeNodes probed for insert:  a=4LFB|1|A|U|1315 B=4LFB|1|A|A|1319
  3 Basepair  1315 1319 UA tWH 
pMakeNodes adding hairpin:     a=4LFB|1|A|G|1316 B=4LFB|1|A|A|1318
    Right strand conserved insertion G1316 at right strand position 1
    Right strand conserved insertion C1317 at right strand position 2
    Right strand conserved insertion A1318 at right strand position 3
  4 Hairpin   1316:1318 GCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1322
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1321
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1320
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'CCCG'
               Comment: ' // Basepair C1314 - G1323 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|1322'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|1321'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|1320'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 2
            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 U1315 - A1319 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // Hairpin node G1316:A1318'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_02887.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3391
   -5.3391

Timestamp 18-Jul-2025 22:26:27
pMakeSCFGModels: Making JAR3D model for motif group HL_04171.7, number 10 of 253
pMakeNodes starting loop:     a=4LX6|1|A|A|30 B=4LX6|1|A|U|40
  2 Basepair    30   40 AU cWW 
No need to probe because of interaction between a=4LX6|1|A|U|31 B=4LX6|1|A|U|39
  3 Basepair    31   39 UU cWW 
pMakeNodes probe for inserts:  a=4LX6|1|A|G|32 B=4LX6|1|A|G|38
    Insertion on left  4LX6|1|A|G|32
    Insertion on right 4LX6|1|A|G|38
pMakeNodesProbeForInsertions:  a 4LX6|1|A|A|33 interacts with 4LX6|1|A|G|37
pMakeNodesProbeForInsertions:  B 4LX6|1|A|G|37 interacts with 4LX6|1|A|A|33
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LX6|1|A|G|37 interacts with 4LX6|1|A|U|34
pMakeNodes probed for insert:  a=4LX6|1|A|A|33 B=4LX6|1|A|G|37
pMakeNodes checking on making a cluster a=4LX6|1|A|A|33 B=4LX6|1|A|G|37
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 0
pMakeNodesCluster: Cluster goes from 4 to 5 and then 7 to 7
aa is 5 bb is 7
  4 Cluster   4LX6|1|A|A|33:4LX6|1|A|U|34 4LX6|1|A|G|37:4LX6|1|A|G|37
    LR Inter  4LX6|1|A|A|33 4LX6|1|A|G|37 cSS 
    LR Inter  4LX6|1|A|U|34 4LX6|1|A|G|37 cSS 
pMakeNodesCluster a=6 B=6 at the end
pMakeNodesCluster a=6 B=6 at the end
pMakeNodes adding hairpin:     a=4LX6|1|A|A|35 B=4LX6|1|A|A|35
    Right strand conserved insertion A  35 at right strand position 1
  5 Hairpin   35:35 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Cluster Left  4  5 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LX6|1|A|G|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LX6|1|A|G|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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A30 - U40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'GU'
               Comment: ' // Basepair U31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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 4LX6|1|A|G|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2640

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 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 4LX6|1|A|G|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 6
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A35'}
      JunctionDeletion: []
          InterIndices: [6 6]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Cluster'
              nextnode: 9
             LeftIndex: [4 5]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AU'
           RightLetter: 'G'
               Comment: ' // Cluster node 4LX6|1|A|A|33:4LX6|1|A|U|34 and 4LX6|1|A|G|37:4LX6|1|A|G|37'
              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: 0.2640

Node 9

ans = 

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

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

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A35:A35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 6
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A35'}
      JunctionDeletion: []
          InterIndices: [6 6]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8   Cluster Left  4  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  6
pNextNodeJunction: Found a hairpin at node 10
pUpdateModelWithSSF: HL_04171.7 allow insertions from initial node 9?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.0055    0.9887    0.0055    0.0003


ans =

    0.0455    0.0455    0.0455    0.8636         0

pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04171.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2298
   -5.2298
   -5.2298
   -5.2298
   -5.2298
   -5.2298
   -5.2298
   -6.3284
   -9.8727

Timestamp 18-Jul-2025 22:26:28
pMakeSCFGModels: Making JAR3D model for motif group HL_04259.3, number 11 of 253
pMakeNodes starting loop:     a=4WF9|1|X|C|2382 B=4WF9|1|X|G|2389
  2 Basepair  2382 2389 CG cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|C|2383 B=4WF9|1|X|A|2388
    Insertion on left  4WF9|1|X|C|2383
    Insertion on right 4WF9|1|X|A|2388
pMakeNodesProbeForInsertions:  a 4WF9|1|X|U|2384 interacts with 4WF9|1|X|A|2387
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|2387 interacts with 4WF9|1|X|U|2384
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|2387 interacts with 4WF9|1|X|U|2384
pMakeNodes probed for insert:  a=4WF9|1|X|U|2384 B=4WF9|1|X|A|2387
  3 Basepair  2384 2387 UA tSH 
pMakeNodes adding hairpin:     a=4WF9|1|X|A|2385 B=4WF9|1|X|C|2386
    Right strand conserved insertion A2385 at right strand position 1
    Right strand conserved insertion C2386 at right strand position 2
  4 Hairpin   2385:2386 AC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|2383
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|A|2388
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'AG'
               Comment: ' // Basepair C2382 - G2389 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|C|2383'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'AC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2385'  ' // Hairpin conserved non-basepairing position C2386'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 4WF9|1|X|A|2388'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2384 - A2387 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: ''
               Comment: ' // Hairpin node A2385:C2386'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2385'  ' // Hairpin conserved non-basepairing position C2386'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04259.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5743
   -7.1621
   -7.5437
   -8.3393
   -6.7298
   -9.8874
   -8.4126

Timestamp 18-Jul-2025 22:26:28
pMakeSCFGModels: Making JAR3D model for motif group HL_04641.1, number 12 of 253
pMakeNodes starting loop:     a=7OS0|1|F|C|16 B=7OS0|1|F|G|25
  2 Basepair    16   25 CG cWW 
pMakeNodes adding hairpin:     a=7OS0|1|F|A|17 B=7OS0|1|F|A|23
    Right strand conserved insertion A  17 at right strand position 1
    Right strand conserved insertion A  18 at right strand position 2
    Right strand conserved insertion A  20 at right strand position 3
    Right strand conserved insertion G  22 at right strand position 4
    Right strand conserved insertion A  23 at right strand position 5
  3 Hairpin   17:23 AAAGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C16 - G25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAAGA'
           RightLetter: ''
               Comment: ' // Hairpin node A17:A23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04641.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4541

Timestamp 18-Jul-2025 22:26:28
pMakeSCFGModels: Making JAR3D model for motif group HL_04642.1, number 13 of 253
pMakeNodes starting loop:     a=6UFM|1|A|C|13 B=6UFM|1|A|G|23
  2 Basepair    13   23 CG cWW 
No need to probe because of interaction between a=6UFM|1|A|A|14 B=6UFM|1|A|A|22
  3 Basepair    14   22 AA cWS 
pMakeNodes adding hairpin:     a=6UFM|1|A|G|15 B=6UFM|1|A|U|20
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion G  16 at right strand position 2
    Right strand conserved insertion U  20 at right strand position 3
  4 Hairpin   15:20 GGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A22 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGU'
           RightLetter: ''
               Comment: ' // Hairpin node G15:U20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04642.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8711
   -8.3820
   -8.9636

Timestamp 18-Jul-2025 22:26:28
pMakeSCFGModels: Making JAR3D model for motif group HL_04725.1, number 14 of 253
pMakeNodes starting loop:     a=4M4O|1|B|G|28 B=4M4O|1|B|C|39
pMakeNodes checking on making a cluster a=4M4O|1|B|G|28 B=4M4O|1|B|C|39
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 4 and then 5 to 8
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=4M4O|1|B|G|28 B=4M4O|1|B|C|39
  2 Hairpin   28:39 GUACUAGC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Hairpin Left  1 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [1 1 1 1 1 1 1 1]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Hairpin'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUACUAGC'
           RightLetter: ''
               Comment: ' // Hairpin node G28:C39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [1 2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
              NormCons: 0.0623

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Hairpin Left  1 Right  8
pNextNodeJunction: Found a hairpin at node 2
pNextNodeJunction: Found a hairpin at node 2

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04725.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0288
   -5.0288

Timestamp 18-Jul-2025 22:26:28
pMakeSCFGModels: Making JAR3D model for motif group HL_04783.2, number 15 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|1806 B=5J7L|1|DA|G|1811
  2 Basepair  1806 1811 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1807 B=5J7L|1|DA|A|1810
  3 Basepair  1807 1810 GA tSH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|1809 B=5J7L|1|DA|A|1809
    Right strand conserved insertion A1809 at right strand position 1
  4 Hairpin   1809:1809 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1806 - G1811 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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: 'A'
               Comment: ' // Basepair G1807 - A1810 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A1809:A1809'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1809'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_04783.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0967
   -6.1943
   -7.7699
   -9.1818
  -11.5696
  -12.5251
   -8.2379
   -9.7820
   -6.8041

Timestamp 18-Jul-2025 22:26:29
pMakeSCFGModels: Making JAR3D model for motif group HL_05304.3, number 16 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|A|520 B=8P9A|1|sR|U|532
  2 Basepair   520  532 AU cWW 
No need to probe because of interaction between a=8P9A|1|sR|A|521 B=8P9A|1|sR|C|531
  3 Basepair   521  531 AC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|522 B=8P9A|1|sR|C|530
    Insertion on left  8P9A|1|sR|U|522
    Insertion on right 8P9A|1|sR|C|530
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|523 interacts with 8P9A|1|sR|A|529
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|529 interacts with 8P9A|1|sR|G|523
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|529 interacts with 8P9A|1|sR|G|523
pMakeNodes probed for insert:  a=8P9A|1|sR|G|523 B=8P9A|1|sR|A|529
  4 Basepair   523  529 GA tSH 
pMakeNodes adding hairpin:     a=8P9A|1|sR|U|524 B=8P9A|1|sR|U|528
    Right strand conserved insertion U 524 at right strand position 1
    Right strand conserved insertion A 525 at right strand position 2
    Right strand conserved insertion A 526 at right strand position 3
    Right strand conserved insertion A 527 at right strand position 4
    Right strand conserved insertion U 528 at right strand position 5
  5 Hairpin   524:528 UAAAU
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  4 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|522
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|C|530
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A520 - U532 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'CC'
               Comment: ' // Basepair A521 - C531 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|522'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UAAAU'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|C|530'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: '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: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G523 - A529 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAAAU'
           RightLetter: ''
               Comment: ' // Hairpin node U524:U528'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  4 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  9
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_05304.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4004
  -10.4004
  -12.7691
  -16.0549
  -13.8658

Timestamp 18-Jul-2025 22:26:29
pMakeSCFGModels: Making JAR3D model for motif group HL_06059.6, number 17 of 253
pMakeNodes starting loop:     a=7U2I|1|1w|C|31 B=7U2I|1|1w|G|39
  2 Basepair    31   39 CG cWW 
No need to probe because of interaction between a=7U2I|1|1w|U|32 B=7U2I|1|1w|A|38
  3 Basepair    32   38 UA bif 
pMakeNodes adding hairpin:     a=7U2I|1|1w|U|33 B=7U2I|1|1w|A|37
    Right strand conserved insertion U  33 at right strand position 1
    Right strand conserved insertion C  34 at right strand position 2
    Right strand conserved insertion C  35 at right strand position 3
    Right strand conserved insertion C  36 at right strand position 4
    Right strand conserved insertion A  37 at right strand position 5
  4 Hairpin   33:37 UCCCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U32 - A38 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCCCA'
           RightLetter: ''
               Comment: ' // Hairpin node U33:A37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_06059.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9220
   -7.1198
   -4.9266
   -6.1570
   -4.7484
   -6.6176
   -6.6176
   -4.9266
   -6.4333
   -4.9266
   -9.4949
   -4.7484
   -4.9266
   -6.1570
   -9.4949
   -6.7132
   -7.2759
   -7.4442
   -4.9266
   -6.1570
   -4.9266
   -4.9266
   -9.4257
   -6.1560
   -9.4949
  -12.7105
   -9.4257
   -4.8099
   -7.1198
   -4.7484
   -7.4819
   -7.3381
   -4.9818
   -9.4949
   -7.3772
   -4.8099
   -4.9293
   -7.3772
   -9.6334
   -7.7437
   -9.6334
   -6.1570
   -6.4333
   -7.0545
   -6.9565
   -7.3772
  -20.0880
   -6.2523
   -7.1198
  -13.0683
   -7.3772

Timestamp 18-Jul-2025 22:26:29
pMakeSCFGModels: Making JAR3D model for motif group HL_06226.4, number 18 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|C|393 B=8P9A|1|sR|G|404
  2 Basepair   393  404 CG cWW 
No need to probe because of interaction between a=8P9A|1|sR|C|394 B=8P9A|1|sR|A|401
  3 Basepair   394  401 CA tWH 
No need to probe because of interaction between a=8P9A|1|sR|U|395 B=8P9A|1|sR|A|399
  4 Basepair   395  399 UA tWH 
pMakeNodes adding hairpin:     a=8P9A|1|sR|G|396 B=8P9A|1|sR|G|398
    Right strand conserved insertion G 396 at right strand position 1
    Right strand conserved insertion A 397 at right strand position 2
    Right strand conserved insertion G 398 at right strand position 3
  5 Hairpin   396:398 GAG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C393 - G404 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C394 - A401 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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 U395 - A399 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAG'
           RightLetter: ''
               Comment: ' // Hairpin node G396:G398'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  6
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_06226.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0798
   -8.0798
   -9.3812
  -11.5693

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_07480.2, number 19 of 253
pMakeNodes starting loop:     a=1U0B|1|A|A|12 B=1U0B|1|A|U|23
  2 Basepair    12   23 AU cWW 
No need to probe because of interaction between a=1U0B|1|A|A|13 B=1U0B|1|A|A|22
  3 Basepair    13   22 AA tSH 
pMakeNodes adding hairpin:     a=1U0B|1|A|A|14 B=1U0B|1|A|C|16
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion C  16 at right strand position 3
  4 Hairpin   14:16 AGC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A12 - U23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A13 - A22 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGC'
           RightLetter: ''
               Comment: ' // Hairpin node A14:C16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_07480.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2433
   -7.2433
   -7.2433

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_07583.1, number 20 of 253
pMakeNodes starting loop:     a=4WSM|1|1K|U|11 B=4WSM|1|1K|A|25
  2 Basepair    11   25 UA cWW 
No need to probe because of interaction between a=4WSM|1|1K|G|12 B=4WSM|1|1K|C|24
  3 Basepair    12   24 GC cWW 
pMakeNodes probe for inserts:  a=4WSM|1|1K|G|13 B=4WSM|1|1K|A|23
    Insertion on left  4WSM|1|1K|G|13
    Insertion on left  4WSM|1|1K|A|14
    Insertion on right 4WSM|1|1K|A|23
    Insertion on right 4WSM|1|1K|A|21
pMakeNodesProbeForInsertions:  a 4WSM|1|1K|A|15 interacts with 4WSM|1|1K|U|20
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|20 interacts with 4WSM|1|1K|A|15
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WSM|1|1K|U|20 interacts with 4WSM|1|1K|A|15
pMakeNodes probed for insert:  a=4WSM|1|1K|A|15 B=4WSM|1|1K|U|20
  4 Basepair    15   20 AU cSS 
pMakeNodes adding hairpin:     a=4WSM|1|1K|U|16 B=4WSM|1|1K|G|19
    Right strand conserved insertion U  16 at right strand position 1
    Right strand conserved insertion G  19 at right strand position 2
  5 Hairpin   16:19 UG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WSM|1|1K|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WSM|1|1K|A|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WSM|1|1K|U|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WSM|1|1K|G|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: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U11 - A25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGA'
           RightLetter: 'AAC'
               Comment: ' // Basepair G12 - C24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WSM|1|1K|G|13'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U16'  ' // Hairpin conserved non-basepairing position G19'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WSM|1|1K|A|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

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

Node 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WSM|1|1K|U|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WSM|1|1K|G|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A15 - U20 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UG'
           RightLetter: ''
               Comment: ' // Hairpin node U16:G19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U16'  ' // Hairpin conserved non-basepairing position G19'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_07583.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.1298
  -13.2273

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_07886.3, number 21 of 253
pMakeNodes starting loop:     a=8CRE|1|1|C|3205 B=8CRE|1|1|G|3212
  2 Basepair  3205 3212 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|G|3206 B=8CRE|1|1|A|3210
    Right strand conserved insertion G3206 at right strand position 1
    Right strand conserved insertion G3207 at right strand position 2
    Right strand conserved insertion A3210 at right strand position 3
  3 Hairpin   3206:3210 GGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C3205 - G3212 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGA'
           RightLetter: ''
               Comment: ' // Hairpin node G3206:A3210'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_07886.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8319
   -6.8319
   -9.6232
  -10.3675
   -5.4345
   -5.4345

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_07903.1, number 22 of 253
pMakeNodes starting loop:     a=1A9N|1|Q|G|4 B=1A9N|1|Q|C|18
  2 Basepair     4   18 GC cWW 
No need to probe because of interaction between a=1A9N|1|Q|U|5 B=1A9N|1|Q|U|17
  3 Basepair     5   17 UU cWW 
pMakeNodes adding hairpin:     a=1A9N|1|Q|A|6 B=1A9N|1|Q|C|16
    Right strand conserved insertion A   6 at right strand position 1
    Right strand conserved insertion U   7 at right strand position 2
    Right strand conserved insertion U   8 at right strand position 3
    Right strand conserved insertion G   9 at right strand position 4
    Right strand conserved insertion A  11 at right strand position 5
    Right strand conserved insertion G  12 at right strand position 6
    Right strand conserved insertion A  14 at right strand position 7
    Right strand conserved insertion C  15 at right strand position 8
    Right strand conserved insertion C  16 at right strand position 9
  4 Hairpin   6:16 AUUGAGACC
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   Hairpin Left  3 Right 11
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U5 - U17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUGAGACC'
           RightLetter: ''
               Comment: ' // Hairpin node A6:C16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9 10 11]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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   Hairpin Left  3 Right 11
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_07903.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.1715

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_07951.3, number 23 of 253
pMakeNodes starting loop:     a=1GAX|1|D|C|913 B=1GAX|1|D|G|921
  2 Basepair   913  921 CG cWW 
pMakeNodes adding hairpin:     a=1GAX|1|D|A|914 B=1GAX|1|D|G|915
    Right strand conserved insertion A 914 at right strand position 1
    Right strand conserved insertion G 915 at right strand position 2
  3 Hairpin   914:915 AG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C913 - G921 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AG'
           RightLetter: ''
               Comment: ' // Hairpin node A914:G915'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A914'  ' // Hairpin conserved non-basepairing position G915'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_07951.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0436
   -9.7335
  -13.7576
  -14.3061

Timestamp 18-Jul-2025 22:26:30
pMakeSCFGModels: Making JAR3D model for motif group HL_08100.1, number 24 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|1727 B=5J7L|1|DA|G|1733
  2 Basepair  1727 1733 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|1728 B=5J7L|1|DA|G|1731
  3 Basepair  1728 1731 CG cWW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|C|1730 B=5J7L|1|DA|C|1730
    Right strand conserved insertion C1730 at right strand position 1
  4 Hairpin   1730:1730 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1727 - G1733 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            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 C1728 - G1731 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C1730:C1730'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C1730'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_08100.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9430
   -5.0957
   -5.3428
   -6.4601

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_08510.1, number 25 of 253
pMakeNodes starting loop:     a=2QUS|1|A|A|18 B=2QUS|1|A|U|26
  2 Basepair    18   26 AU cWW 
pMakeNodes adding hairpin:     a=2QUS|1|A|U|19 B=2QUS|1|A|U|24
    Right strand conserved insertion U  19 at right strand position 1
    Right strand conserved insertion G  22 at right strand position 4
    Right strand conserved insertion C  23 at right strand position 5
    Right strand conserved insertion U  24 at right strand position 6
  3 Hairpin   19:24 UGUGCU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A18 - U26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGUGCU'
           RightLetter: ''
               Comment: ' // Hairpin node U19:U24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_08510.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3349
   -5.3349

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_08602.1, number 26 of 253
pMakeNodes starting loop:     a=4WFL|1|A|C|42 B=4WFL|1|A|G|54
pMakeNodes checking on making a cluster a=4WFL|1|A|C|42 B=4WFL|1|A|G|54
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 5 and then 11 to 11
aa is 5 bb is 11
  2 Cluster   4WFL|1|A|C|42:4WFL|1|A|C|47 4WFL|1|A|G|54:4WFL|1|A|G|54
    LR Inter  4WFL|1|A|C|42 4WFL|1|A|G|54 cWW 
    LL Inter  4WFL|1|A|C|42 4WFL|1|A|C|47 cSS 
    Left  strand conserved insertion 4WFL|1|A|A|43 at position 2
    Left  strand conserved insertion 4WFL|1|A|A|44 at position 3
    Left  strand conserved insertion 4WFL|1|A|C|46 at position 4
pMakeNodesCluster a=6 B=10 at the end
pMakeNodesCluster a=6 B=10 at the end
pMakeNodes probe for inserts:  a=4WFL|1|A|G|48 B=4WFL|1|A|A|53
    Insertion on left  4WFL|1|A|G|48
pMakeNodesProbeForInsertions:  a 4WFL|1|A|C|49 interacts with 4WFL|1|A|A|53
pMakeNodesProbeForInsertions:  B 4WFL|1|A|A|53 interacts with 4WFL|1|A|C|49
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WFL|1|A|A|53 interacts with 4WFL|1|A|C|49
  3 Initial     48 (1 insertion) and   53 (0 insertion)
pMakeNodes probed for insert:  a=4WFL|1|A|C|49 B=4WFL|1|A|A|53
  4 Basepair    49   53 CA cSS 
pMakeNodes adding hairpin:     a=4WFL|1|A|U|50 B=4WFL|1|A|C|51
    Right strand conserved insertion U  50 at right strand position 1
    Right strand conserved insertion C  51 at right strand position 2
  5 Hairpin   50:51 UC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WFL|1|A|C|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 0 0 0 0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAACC'
           RightLetter: 'G'
               Comment: ' // Cluster node 4WFL|1|A|C|42:4WFL|1|A|C|47 and 4WFL|1|A|G|54:4WFL|1|A|G|54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2499
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 4WFL|1|A|G|48 - 4WFL|1|A|A|53 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WFL|1|A|C|47'
              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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U50'  ' // Hairpin conserved non-basepairing position C51'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000
                  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: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C49 - A53 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

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

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UC'
           RightLetter: ''
               Comment: ' // Hairpin node U50:C51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U50'  ' // Hairpin conserved non-basepairing position C51'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  9
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_08602.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3260

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_09260.2, number 27 of 253
pMakeNodes starting loop:     a=5WT1|1|C|C|13 B=5WT1|1|C|G|22
  2 Basepair    13   22 CG cWW 
pMakeNodes adding hairpin:     a=5WT1|1|C|A|14 B=5WT1|1|C|C|17
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion C  16 at right strand position 3
    Right strand conserved insertion C  17 at right strand position 4
  3 Hairpin   14:17 AGCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCC'
           RightLetter: ''
               Comment: ' // Hairpin node A14:C17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_09260.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2392
  -10.2825
  -11.7825

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_09452.1, number 28 of 253
pMakeNodes starting loop:     a=2ZZN|1|D|U|13 B=2ZZN|1|D|A|22
  2 Basepair    13   22 UA cWW 
pMakeNodes adding hairpin:     a=2ZZN|1|D|A|14 B=2ZZN|1|D|G|16
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion G  16 at right strand position 3
  3 Hairpin   14:16 AGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U13 - A22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGG'
           RightLetter: ''
               Comment: ' // Hairpin node A14:G16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_09452.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7143
   -8.7143
   -9.8381

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_10453.3, number 29 of 253
pMakeNodes starting loop:     a=6MPI|1|X|G|31 B=6MPI|1|X|C|39
  2 Basepair    31   39 GC cWW 
pMakeNodes adding hairpin:     a=6MPI|1|X|RSP|32 B=6MPI|1|X|A|38
    Right strand conserved insertion C  32 at right strand position 1
    Right strand conserved insertion C  35 at right strand position 2
    Right strand conserved insertion G  36 at right strand position 3
    Right strand conserved insertion A  37 at right strand position 4
    Right strand conserved insertion A  38 at right strand position 5
  3 Hairpin   32:38 CCGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G31 - C39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCGAA'
           RightLetter: ''
               Comment: ' // Hairpin node C32:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_10453.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8040
   -7.8040
   -7.4005
   -7.4005
  -10.8196
  -10.9076
  -11.5120
   -5.5959
   -5.5959

Timestamp 18-Jul-2025 22:26:31
pMakeSCFGModels: Making JAR3D model for motif group HL_10456.1, number 30 of 253
pMakeNodes starting loop:     a=3D0U|1|A|C|35 B=3D0U|1|A|G|52
  2 Basepair    35   52 CG cWW 
pMakeNodes probe for inserts:  a=3D0U|1|A|A|36 B=3D0U|1|A|G|51
pMakeNodesProbeForInsertions:  a 3D0U|1|A|A|36 interacts with 3D0U|1|A|C|38
pMakeNodesProbeForInsertions:  B 3D0U|1|A|G|51 interacts with 3D0U|1|A|C|38
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3D0U|1|A|G|51 interacts with 3D0U|1|A|C|38
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3D0U|1|A|A|36 B=3D0U|1|A|G|51
pMakeNodes checking on making a cluster a=3D0U|1|A|A|36 B=3D0U|1|A|G|51
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 4 and then 15 to 16
aa is 4 bb is 15
  3 Cluster   3D0U|1|A|A|36:3D0U|1|A|C|38 3D0U|1|A|U|49:3D0U|1|A|G|51
    LR Inter  3D0U|1|A|U|37 3D0U|1|A|U|49 tWW 
    LR Inter  3D0U|1|A|C|38 3D0U|1|A|G|51 cWW 
    LL Inter  3D0U|1|A|A|36 3D0U|1|A|U|37 cSH 
    LL Inter  3D0U|1|A|A|36 3D0U|1|A|C|38 cSH 
pMakeNodesCluster a=5 B=14 at the end
pMakeNodesCluster a=5 B=14 at the end
pMakeNodes probe for inserts:  a=3D0U|1|A|A|39 B=3D0U|1|A|A|48
    Insertion on right 3D0U|1|A|A|48
pMakeNodesProbeForInsertions:  a 3D0U|1|A|A|39 interacts with 3D0U|1|A|A|47
pMakeNodesProbeForInsertions:  B 3D0U|1|A|A|47 interacts with 3D0U|1|A|A|39
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3D0U|1|A|A|47 interacts with 3D0U|1|A|A|39
  4 Initial     39 (0 insertion) and   48 (1 insertion)
pMakeNodes probed for insert:  a=3D0U|1|A|A|39 B=3D0U|1|A|A|47
  5 Basepair    39   47 AA tHW 
pMakeNodes adding hairpin:     a=3D0U|1|A|G|40 B=3D0U|1|A|G|46
    Right strand conserved insertion G  40 at right strand position 1
    Right strand conserved insertion G  41 at right strand position 2
    Right strand conserved insertion G  42 at right strand position 3
    Right strand conserved insertion G  43 at right strand position 4
    Right strand conserved insertion A  44 at right strand position 5
    Right strand conserved insertion G  45 at right strand position 6
    Right strand conserved insertion G  46 at right strand position 7
  6 Hairpin   40:46 GGGGAGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 15 16
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right 12
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3D0U|1|A|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

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

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 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 C35 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUC'
           RightLetter: 'UG'
               Comment: ' // Cluster node 3D0U|1|A|A|36:3D0U|1|A|C|38 and 3D0U|1|A|U|49:3D0U|1|A|G|51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0226

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 14
             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 3D0U|1|A|A|39 - 3D0U|1|A|A|48 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 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 3D0U|1|A|A|48'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GGGGAGG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [6 7 8 9 10 11 12]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A39 - A47 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]
          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: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGAGG'
           RightLetter: ''
               Comment: ' // Hairpin node G40:G46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [6 7 8 9 10 11 12]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 15 16
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right 12
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_10456.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6384
   -7.6384

Timestamp 18-Jul-2025 22:26:32
pMakeSCFGModels: Making JAR3D model for motif group HL_10540.1, number 31 of 253
pMakeNodes starting loop:     a=5JEA|1|R|C|-38 B=5JEA|1|R|G|-32
  2 Basepair   -38  -32 CG cWW 
No need to probe because of interaction between a=5JEA|1|R|C|-37 B=5JEA|1|R|G|-33
  3 Basepair   -37  -33 CG tSH 
pMakeNodes adding hairpin:     a=5JEA|1|R|G|-36 B=5JEA|1|R|A|-34
    Right strand conserved insertion G -36 at right strand position 1
    Right strand conserved insertion A -35 at right strand position 2
    Right strand conserved insertion A -34 at right strand position 3
  4 Hairpin   -36:-34 GAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C-38 - G-32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C-37 - G-33 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: ''
               Comment: ' // Hairpin node G-36:A-34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_10540.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2067
   -8.3110

Timestamp 18-Jul-2025 22:26:32
pMakeSCFGModels: Making JAR3D model for motif group HL_11542.1, number 32 of 253
pMakeNodes starting loop:     a=4WZD|1|3L|C|12 B=4WZD|1|3L|G|24
  2 Basepair    12   24 CG cWW 
No need to probe because of interaction between a=4WZD|1|3L|G|13 B=4WZD|1|3L|A|23
  3 Basepair    13   23 GA tSH 
No need to probe because of interaction between a=4WZD|1|3L|A|14 B=4WZD|1|3L|A|22
  4 Basepair    14   22 AA cWS 
pMakeNodes adding hairpin:     a=4WZD|1|3L|G|15 B=4WZD|1|3L|A|21
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion C  19 at right strand position 2
    Right strand conserved insertion C  20 at right strand position 3
    Right strand conserved insertion A  21 at right strand position 4
  5 Hairpin   15:21 GCCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C12 - G24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G13 - A23 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A22 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCCA'
           RightLetter: ''
               Comment: ' // Hairpin node G15:A21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  7
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_11542.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5311

Timestamp 18-Jul-2025 22:26:32
pMakeSCFGModels: Making JAR3D model for motif group HL_12758.3, number 33 of 253
pMakeNodes starting loop:     a=8U5Z|1|A|C|6 B=8U5Z|1|A|G|31
  2 Basepair     6   31 CG cWW 
No need to probe because of interaction between a=8U5Z|1|A|G|7 B=8U5Z|1|A|A|30
  3 Basepair     7   30 GA tSH 
pMakeNodes probe for inserts:  a=8U5Z|1|A|A|8 B=8U5Z|1|A|G|29
    Insertion on left  8U5Z|1|A|A|8
    Insertion on left  8U5Z|1|A|A|9
pMakeNodesProbeForInsertions:  a 8U5Z|1|A|G|10 interacts with 8U5Z|1|A|G|25
pMakeNodesProbeForInsertions:  B 8U5Z|1|A|G|29 interacts with 8U5Z|1|A|U|12
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8U5Z|1|A|G|29 interacts with 8U5Z|1|A|G|23
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8U5Z|1|A|G|10 B=8U5Z|1|A|G|29
pMakeNodes checking on making a cluster a=8U5Z|1|A|G|10 B=8U5Z|1|A|G|29
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 0
pMakeNodesCluster: Cluster goes from 5 to 11 and then 12 to 17
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=8U5Z|1|A|G|10 B=8U5Z|1|A|G|29
  4 Hairpin   10:29 GGUGGGGGGAGGG
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   Hairpin Left  5 Right 17
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8U5Z|1|A|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8U5Z|1|A|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: 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: []
              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 C6 - G31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'A'
               Comment: ' // Basepair G7 - A30 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8U5Z|1|A|A|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.4076e-05

Node 5

ans = 

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

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

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8U5Z|1|A|A|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGUGGGGGGAGGG'
           RightLetter: ''
               Comment: ' // Hairpin node G10:G29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.4076e-05

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  4 Right 17
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 17
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right 17
pNextNodeJunction: Found a hairpin at node 8
pUpdateModelWithSSF: HL_12758.3 allow insertions from initial node 7?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

     1


ans =

    0.2500    0.2500    0.2500    0.2500

pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_12758.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.9168
  -10.6766

Timestamp 18-Jul-2025 22:26:32
pMakeSCFGModels: Making JAR3D model for motif group HL_12870.1, number 34 of 253
pMakeNodes starting loop:     a=2ZY6|1|A|G|12 B=2ZY6|1|A|C|24
pMakeNodes checking on making a cluster a=2ZY6|1|A|G|12 B=2ZY6|1|A|C|24
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 1 and then 7 to 12
aa is 1 bb is 7
  2 Cluster   2ZY6|1|A|G|12:2ZY6|1|A|G|12 2ZY6|1|A|G|19:2ZY6|1|A|C|24
    LR Inter  2ZY6|1|A|G|12 2ZY6|1|A|G|19 tHW 
    LR Inter  2ZY6|1|A|G|12 2ZY6|1|A|C|24 cWW 
    Right strand conserved insertion 2ZY6|1|A|G|20 at position 2
    Right strand conserved insertion 2ZY6|1|A|A|21 at position 3
    Right strand conserved insertion 2ZY6|1|A|A|22 at position 4
    Right strand conserved insertion 2ZY6|1|A|A|23 at position 5
pMakeNodesCluster a=2 B=6 at the end
pMakeNodesCluster a=2 B=6 at the end
pMakeNodes adding hairpin:     a=2ZY6|1|A|C|14 B=2ZY6|1|A|G|18
    Right strand conserved insertion C  14 at right strand position 1
    Right strand conserved insertion C  15 at right strand position 2
    Right strand conserved insertion U  16 at right strand position 3
    Right strand conserved insertion U  17 at right strand position 4
    Right strand conserved insertion G  18 at right strand position 5
  3 Hairpin   14:18 CCUUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  7  8  9 10 11 12
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

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

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: [7 8 9 10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'GGAAAC'
               Comment: ' // Cluster node 2ZY6|1|A|G|12:2ZY6|1|A|G|12 and 2ZY6|1|A|G|19:2ZY6|1|A|C|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4 5 6]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3 4 5]
              NormCons: 0.2516

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCUUG'
           RightLetter: ''
               Comment: ' // Hairpin node C14:G18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  7  8  9 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_12870.1 allow insertions from initial node 3?
ans =

    0.0454    0.9070    0.0454    0.0023


ans =

    0.1667    0.1667    0.1667    0.5000         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_12870.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4651

Timestamp 18-Jul-2025 22:26:33
pMakeSCFGModels: Making JAR3D model for motif group HL_13189.1, number 35 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|C|543 B=8P9A|1|AR|G|548
  2 Basepair   543  548 CG cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|C|544 B=8P9A|1|AR|G|547
  3 Hairpin   544:547 CG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C543 - G548 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CG'
           RightLetter: ''
               Comment: ' // Hairpin node C544:G547'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction C544 - G547 cSH '}
      JunctionDeletion: []
          InterIndices: [2 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_13189.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2565
   -5.8431

Timestamp 18-Jul-2025 22:26:33
pMakeSCFGModels: Making JAR3D model for motif group HL_13529.1, number 36 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|U|641 B=5J7L|1|DA|G|647
  2 Basepair   641  647 UG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|642 B=5J7L|1|DA|U|646
    Insertion on right 5J7L|1|DA|U|646
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|U|642 interacts with 5J7L|1|DA|C|645
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|645 interacts with 5J7L|1|DA|U|642
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|645 interacts with 5J7L|1|DA|U|642
pMakeNodes probed for insert:  a=5J7L|1|DA|U|642 B=5J7L|1|DA|C|645
  3 Basepair   642  645 UC tHH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|643 B=5J7L|1|DA|A|644
    Right strand conserved insertion A 643 at right strand position 1
    Right strand conserved insertion A 644 at right strand position 2
  4 Hairpin   643:644 AA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|U|646
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'UG'
               Comment: ' // Basepair U641 - G647 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|U|646'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            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: 'AA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A643'  ' // Hairpin conserved non-basepairing position A644'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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: 'C'
               Comment: ' // Basepair U642 - C645 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: ''
               Comment: ' // Hairpin node A643:A644'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A643'  ' // Hairpin conserved non-basepairing position A644'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_13529.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4438
   -6.6026

Timestamp 18-Jul-2025 22:26:33
pMakeSCFGModels: Making JAR3D model for motif group HL_13963.3, number 37 of 253
pMakeNodes starting loop:     a=361D|1|B|G|86 B=361D|1|B|C|90
  2 Basepair    86   90 GC cWW 
pMakeNodes adding hairpin:     a=361D|1|B|G|87 B=361D|1|B|A|89|||A
    Right strand conserved insertion G  87 at right strand position 1
    Right strand conserved insertion A 89A at right strand position 2
  3 Hairpin   87:89A GA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G86 - C90 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: ''
               Comment: ' // Hairpin node G87:A89A'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G87'  ' // Hairpin conserved non-basepairing position A89A'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_13963.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3650
   -6.3650
  -11.8186
  -12.1310

Timestamp 18-Jul-2025 22:26:33
pMakeSCFGModels: Making JAR3D model for motif group HL_13971.1, number 38 of 253
pMakeNodes starting loop:     a=8P9A|1|AS|U|32 B=8P9A|1|AS|A|45
pMakeNodes checking on making a cluster a=8P9A|1|AS|U|32 B=8P9A|1|AS|A|45
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 4 and then 14 to 14
aa is 4 bb is 14
  2 Cluster   8P9A|1|AS|U|32:8P9A|1|AS|C|35 8P9A|1|AS|A|45:8P9A|1|AS|A|45
    LR Inter  8P9A|1|AS|U|32 8P9A|1|AS|A|45 cWW 
    LR Inter  8P9A|1|AS|C|35 8P9A|1|AS|A|45 cWS 
    Left  strand conserved insertion 8P9A|1|AS|U|33 at position 2
    Left  strand conserved insertion 8P9A|1|AS|C|34 at position 3
pMakeNodesCluster a=5 B=13 at the end
pMakeNodesCluster a=5 B=13 at the end
pMakeNodes probe for inserts:  a=8P9A|1|AS|C|36 B=8P9A|1|AS|C|44
pMakeNodesProbeForInsertions:  a 8P9A|1|AS|C|36 interacts with 8P9A|1|AS|G|41
pMakeNodesProbeForInsertions:  B 8P9A|1|AS|C|44 interacts with 8P9A|1|AS|G|41
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AS|C|44 interacts with 8P9A|1|AS|G|41
  3 Initial     36 (0 insertion) and   44 (0 insertion)
pMakeNodes probed for insert:  a=8P9A|1|AS|C|36 B=8P9A|1|AS|C|44
pMakeNodes checking on making a cluster a=8P9A|1|AS|C|36 B=8P9A|1|AS|C|44
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 5 to 7 and then 10 to 13
aa is 7 bb is 10
  4 Cluster   8P9A|1|AS|C|36:8P9A|1|AS|U|38 8P9A|1|AS|G|41:8P9A|1|AS|C|44
    LR Inter  8P9A|1|AS|C|36 8P9A|1|AS|G|41 cWW 
    LR Inter  8P9A|1|AS|U|38 8P9A|1|AS|A|42 tSH 
    LR Inter  8P9A|1|AS|G|37 8P9A|1|AS|U|43 tSH 
    RR Inter  8P9A|1|AS|G|41 8P9A|1|AS|C|44 tSW 
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
pMakeNodes adding hairpin:     a=8P9A|1|AS|C|39 B=8P9A|1|AS|C|40
    Right strand conserved insertion C  39 at right strand position 1
    Right strand conserved insertion C  40 at right strand position 2
  5 Hairpin   39:40 CC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5   Hairpin Left  8 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: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 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: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCC'
           RightLetter: 'A'
               Comment: ' // Cluster node 8P9A|1|AS|U|32:8P9A|1|AS|C|35 and 8P9A|1|AS|A|45:8P9A|1|AS|A|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2458

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 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 8P9A|1|AS|C|36 - 8P9A|1|AS|C|44 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [5 6 7]
            RightIndex: [10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGU'
           RightLetter: 'GAUC'
               Comment: ' // Cluster node 8P9A|1|AS|C|36:8P9A|1|AS|U|38 and 8P9A|1|AS|G|41:8P9A|1|AS|C|44'
              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]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2526

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: ''
               Comment: ' // Hairpin node C39:C40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C39'  ' // Hairpin conserved non-basepairing position C40'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  9
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: HL_13971.1 allow insertions from initial node 5?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_13971.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3144
   -6.3144

Timestamp 18-Jul-2025 22:26:33
pMakeSCFGModels: Making JAR3D model for motif group HL_14757.1, number 39 of 253
pMakeNodes starting loop:     a=6RTI|1|X|CFZ|15 B=6RTI|1|X|G|32
  2 Basepair    15   32 CG cWW 
pMakeNodes probe for inserts:  a=6RTI|1|X|CFZ|16 B=6RTI|1|X|A|31
    Insertion on left  6RTI|1|X|CFZ|16
    Insertion on left  6RTI|1|X|UFT|17
    Insertion on right 6RTI|1|X|A|31
    Insertion on right 6RTI|1|X|A|30
pMakeNodesProbeForInsertions:  a 6RTI|1|X|G|18 interacts with 6RTI|1|X|CFZ|28
pMakeNodesProbeForInsertions:  B 6RTI|1|X|UFT|29 interacts with 6RTI|1|X|UFT|22
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6RTI|1|X|UFT|29 interacts with 6RTI|1|X|UFT|22
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6RTI|1|X|G|18 B=6RTI|1|X|UFT|29
pMakeNodes checking on making a cluster a=6RTI|1|X|G|18 B=6RTI|1|X|UFT|29
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 4 to 9 and then 11 to 14
aa is 9 bb is 11
  3 Cluster   6RTI|1|X|G|18:6RTI|1|X|UFT|24 6RTI|1|X|UFT|26:6RTI|1|X|UFT|29
    LR Inter  6RTI|1|X|A|19 6RTI|1|X|UFT|26 tHW 
    LR Inter  6RTI|1|X|G|18 6RTI|1|X|CFZ|28 tWW 
    LR Inter  6RTI|1|X|UFT|24 6RTI|1|X|CFZ|28 tSW 
    LR Inter  6RTI|1|X|UFT|22 6RTI|1|X|UFT|29 cWW 
    LL Inter  6RTI|1|X|G|18 6RTI|1|X|CFZ|23 tSW 
    Left  strand conserved insertion 6RTI|1|X|UFT|21 at position 3
    Right strand conserved insertion 6RTI|1|X|A|27 at position 2
pMakeNodesCluster a=10 B=10 at the end
pMakeNodesCluster a=10 B=10 at the end
pMakeNodes adding hairpin:     a=6RTI|1|X|A|25 B=6RTI|1|X|A|25
    Right strand conserved insertion A  25 at right strand position 1
  4 Hairpin   25:25 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3   Cluster Left  4  5  6  7  8  9 Right 11 12 13 14
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6RTI|1|X|CFZ|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6RTI|1|X|UFT|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6RTI|1|X|A|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6RTI|1|X|UFT|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: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 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: 'CCU'
           RightLetter: 'AAG'
               Comment: ' // Basepair C15 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6RTI|1|X|CFZ|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 2
              NormCons: 0.3876

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6RTI|1|X|UFT|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 10
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A25'}
      JunctionDeletion: []
          InterIndices: [10 10]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6RTI|1|X|A|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

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

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

Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 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 6RTI|1|X|UFT|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Cluster'
              nextnode: 12
             LeftIndex: [4 5 6 7 8 9]
            RightIndex: [11 12 13 14]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAUUCU'
           RightLetter: 'UACU'
               Comment: ' // Cluster node 6RTI|1|X|G|18:6RTI|1|X|UFT|24 and 6RTI|1|X|UFT|26:6RTI|1|X|UFT|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 2
              NormCons: 0.3876

Node 12

ans = 

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

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

Node 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 10
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A25:A25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 10
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A25'}
      JunctionDeletion: []
          InterIndices: [10 10]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  4 Right 14
pMakeMotifModelFromSSF:  11   Cluster Left  4  5  6  7  8  9 Right 11 12 13 14
pMakeMotifModelFromSSF:  12   Initial Left 10 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left 10 Right 10
pNextNodeJunction: Found a hairpin at node 13
pUpdateModelWithSSF: HL_14757.1 allow insertions from initial node 12?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_14757.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5917

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_15118.1, number 40 of 253
pMakeNodes starting loop:     a=3IWN|1|A|C|57 B=3IWN|1|A|G|68
  2 Basepair    57   68 CG cWW 
pMakeNodes adding hairpin:     a=3IWN|1|A|A|58 B=3IWN|1|A|C|67
    Right strand conserved insertion A  58 at right strand position 1
    Right strand conserved insertion U  59 at right strand position 2
    Right strand conserved insertion U  60 at right strand position 3
    Right strand conserved insertion G  61 at right strand position 4
    Right strand conserved insertion A  63 at right strand position 5
    Right strand conserved insertion C  64 at right strand position 6
    Right strand conserved insertion U  65 at right strand position 7
    Right strand conserved insertion C  66 at right strand position 8
    Right strand conserved insertion C  67 at right strand position 9
  3 Hairpin   58:67 AUUGACUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C57 - G68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUGACUCC'
           RightLetter: ''
               Comment: ' // Hairpin node A58:C67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_15118.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5594

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_15574.1, number 41 of 253
pMakeNodes starting loop:     a=4R4V|1|A|G|670 B=4R4V|1|A|C|676
  2 Basepair   670  676 GC cWW 
pMakeNodes adding hairpin:     a=4R4V|1|A|A|671 B=4R4V|1|A|A|675
    Right strand conserved insertion A 671 at right strand position 1
    Right strand conserved insertion A 672 at right strand position 2
    Right strand conserved insertion A 673 at right strand position 3
    Right strand conserved insertion C 674 at right strand position 4
    Right strand conserved insertion A 675 at right strand position 5
  3 Hairpin   671:675 AAACA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G670 - C676 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAACA'
           RightLetter: ''
               Comment: ' // Hairpin node A671:A675'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_15574.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.1260
   -5.8191

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_15802.1, number 42 of 253
pMakeNodes starting loop:     a=3AL0|1|E|A|31 B=3AL0|1|E|U|39
  2 Basepair    31   39 AU cWW 
No need to probe because of interaction between a=3AL0|1|E|C|32 B=3AL0|1|E|A|38
  3 Basepair    32   38 CA cWW 
pMakeNodes adding hairpin:     a=3AL0|1|E|C|34 B=3AL0|1|E|G|36
    Right strand conserved insertion C  34 at right strand position 1
    Right strand conserved insertion U  35 at right strand position 2
    Right strand conserved insertion G  36 at right strand position 3
  4 Hairpin   34:36 CUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C32 - A38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUG'
           RightLetter: ''
               Comment: ' // Hairpin node C34:G36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_15802.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2013

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_16398.2, number 43 of 253
pMakeNodes starting loop:     a=8SYK|1|A|G|57 B=8SYK|1|A|C|69
  2 Basepair    57   69 GC cWW 
No need to probe because of interaction between a=8SYK|1|A|A|58 B=8SYK|1|A|C|68
  3 Basepair    58   68 AC cWW 
pMakeNodes adding hairpin:     a=8SYK|1|A|A|59 B=8SYK|1|A|A|67
    Right strand conserved insertion A  59 at right strand position 1
    Right strand conserved insertion G  60 at right strand position 2
    Right strand conserved insertion A  61 at right strand position 3
    Right strand conserved insertion A  67 at right strand position 4
  4 Hairpin   59:67 AGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G57 - C69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A58 - C68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGAA'
           RightLetter: ''
               Comment: ' // Hairpin node A59:A67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_16398.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.1502
  -12.1502
  -15.0444

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_16991.1, number 44 of 253
pMakeNodes starting loop:     a=8EYU|1|A|U|26 B=8EYU|1|A|A|37
  2 Basepair    26   37 UA cWW 
No need to probe because of interaction between a=8EYU|1|A|G|27 B=8EYU|1|A|G|35
  3 Basepair    27   35 GG cWH 
pMakeNodes probe for inserts:  a=8EYU|1|A|G|29 B=8EYU|1|A|G|33
pMakeNodesProbeForInsertions:  a 8EYU|1|A|G|29 interacts with 8EYU|1|A|G|32
pMakeNodesProbeForInsertions:  B 8EYU|1|A|G|33 interacts with 8EYU|1|A|G|30
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8EYU|1|A|G|33 interacts with 8EYU|1|A|G|30
pMakeNodes probed for insert:  a=8EYU|1|A|G|29 B=8EYU|1|A|G|33
pMakeNodes checking on making a cluster a=8EYU|1|A|G|29 B=8EYU|1|A|G|33
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 4 and then 5 to 6
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=8EYU|1|A|G|29 B=8EYU|1|A|G|33
  4 Hairpin   29:33 GGGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U26 - A37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G27 - G35 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGG'
           RightLetter: ''
               Comment: ' // Hairpin node G29:G33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G29 - G32 cWH '  ' // Hairpin Interaction G30 - G33 cWH '}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_16991.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4750

Timestamp 18-Jul-2025 22:26:34
pMakeSCFGModels: Making JAR3D model for motif group HL_18423.1, number 45 of 253
pMakeNodes starting loop:     a=3HJW|1|D|U|23 B=3HJW|1|D|G|33
  2 Basepair    23   33 UG cWW 
No need to probe because of interaction between a=3HJW|1|D|G|24 B=3HJW|1|D|A|32
  3 Basepair    24   32 GA tSH 
No need to probe because of interaction between a=3HJW|1|D|A|25 B=3HJW|1|D|G|31
  4 Basepair    25   31 AG tHS 
pMakeNodes adding hairpin:     a=3HJW|1|D|A|29 B=3HJW|1|D|A|29
    Right strand conserved insertion A  29 at right strand position 1
  5 Hairpin   29:29 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U23 - G33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G24 - A32 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A25 - G31 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A29:A29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A29'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_18423.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.2929

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_18565.1, number 46 of 253
pMakeNodes starting loop:     a=2ZZN|1|D|A|31 B=2ZZN|1|D|U|39
  2 Basepair    31   39 AU cWW 
No need to probe because of interaction between a=2ZZN|1|D|C|32 B=2ZZN|1|D|A|38
  3 Basepair    32   38 CA cWW 
pMakeNodes probe for inserts:  a=2ZZN|1|D|U|33 B=2ZZN|1|D|A|36
    Insertion on right 2ZZN|1|D|A|36
pMakeNodesProbeForInsertions:  a 2ZZN|1|D|U|33 interacts with 2ZZN|1|D|C|35
pMakeNodesProbeForInsertions:  B 2ZZN|1|D|C|35 interacts with 2ZZN|1|D|U|33
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 2ZZN|1|D|C|35 interacts with 2ZZN|1|D|U|33
pMakeNodes probed for insert:  a=2ZZN|1|D|U|33 B=2ZZN|1|D|C|35
  4 Basepair    33   35 UC cSH 
pMakeNodes adding hairpin:     a=2ZZN|1|D|G|34 B=2ZZN|1|D|G|34
    Right strand conserved insertion G  34 at right strand position 1
  5 Hairpin   34:34 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2ZZN|1|D|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 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: 'AA'
               Comment: ' // Basepair C32 - A38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2ZZN|1|D|A|36'
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 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: 'G'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G34'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

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

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 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: 'C'
               Comment: ' // Basepair U33 - C35 cSH '
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G34:G34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G34'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_18565.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6980
   -5.1692

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_18978.1, number 47 of 253
pMakeNodes starting loop:     a=9FN3|1|B|C|18 B=9FN3|1|B|G|27
  2 Basepair    18   27 CG cWW 
No need to probe because of interaction between a=9FN3|1|B|U|19 B=9FN3|1|B|A|26
  3 Basepair    19   26 UA tSH 
No need to probe because of interaction between a=9FN3|1|B|G|20 B=9FN3|1|B|G|24
  4 Basepair    20   24 GG tHW 
pMakeNodes adding hairpin:     a=9FN3|1|B|U|21 B=9FN3|1|B|C|23
    Right strand conserved insertion U  21 at right strand position 1
    Right strand conserved insertion U  22 at right strand position 2
    Right strand conserved insertion C  23 at right strand position 3
  5 Hairpin   21:23 UUC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C18 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U19 - A26 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G20 - G24 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUC'
           RightLetter: ''
               Comment: ' // Hairpin node U21:C23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  6
pNextNodeJunction: Found a hairpin at node 5
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 3,7 for nucleotide 3 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_18978.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1826

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_19210.3, number 48 of 253
pMakeNodes starting loop:     a=1MMS|1|C|C|1064 B=1MMS|1|C|G|1074
  2 Basepair  1064 1074 CG cWW 
pMakeNodes adding hairpin:     a=1MMS|1|C|U|1065 B=1MMS|1|C|A|1073
    Right strand conserved insertion U1065 at right strand position 1
    Right strand conserved insertion U1066 at right strand position 2
    Right strand conserved insertion A1067 at right strand position 3
    Right strand conserved insertion G1068 at right strand position 4
    Right strand conserved insertion A1069 at right strand position 5
    Right strand conserved insertion G1071 at right strand position 6
    Right strand conserved insertion C1072 at right strand position 7
    Right strand conserved insertion A1073 at right strand position 8
  3 Hairpin   1065:1073 UUAGAGCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1064 - G1074 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAGAGCA'
           RightLetter: ''
               Comment: ' // Hairpin node U1065:A1073'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_19210.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8159
   -4.8159
   -4.8159
   -4.8159
   -6.8219
   -6.8219
   -9.6775

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_20167.2, number 49 of 253
pMakeNodes starting loop:     a=7A0S|1|X|G|1932 B=7A0S|1|X|C|1940
  2 Basepair  1932 1940 GC cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|1933 B=7A0S|1|X|U|1939
    Insertion on left  7A0S|1|X|G|1933
    Insertion on right 7A0S|1|X|U|1939
    Insertion on right 7A0S|1|X|G|1937
pMakeNodesProbeForInsertions:  a 7A0S|1|X|U|1934 interacts with 7A0S|1|X|A|1936
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|1936 interacts with 7A0S|1|X|U|1934
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|1936 interacts with 7A0S|1|X|U|1934
pMakeNodes probed for insert:  a=7A0S|1|X|U|1934 B=7A0S|1|X|A|1936
  3 Basepair  1934 1936 UA tSH 
pMakeNodes adding hairpin:     a=7A0S|1|X|A|1935 B=7A0S|1|X|A|1935
    Right strand conserved insertion A1935 at right strand position 1
  4 Hairpin   1935:1935 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|1933
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|U|1938
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|1937
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'GUC'
               Comment: ' // Basepair G1932 - C1940 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|G|1933'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1935'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 7A0S|1|X|U|1938'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7A0S|1|X|G|1937'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1934 - A1936 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A1935:A1935'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1935'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20167.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5702
   -5.5702
   -5.5702
   -5.5702
   -8.7108
   -8.4749
   -8.4749
   -9.7446
  -12.9830
  -12.0369

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_20535.2, number 50 of 253
pMakeNodes starting loop:     a=5VOE|1|A|G|15 B=5VOE|1|A|CFL|22
  2 Basepair    15   22 GC cWW 
pMakeNodes adding hairpin:     a=5VOE|1|A|A|16 B=5VOE|1|A|UFT|20
    Right strand conserved insertion A  16 at right strand position 1
    Right strand conserved insertion U  17 at right strand position 2
    Right strand conserved insertion A  19 at right strand position 3
    Right strand conserved insertion U  20 at right strand position 4
  3 Hairpin   16:20 AUAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUAU'
           RightLetter: ''
               Comment: ' // Hairpin node A16:U20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20535.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5796
  -11.1457
  -10.4018

Timestamp 18-Jul-2025 22:26:35
pMakeSCFGModels: Making JAR3D model for motif group HL_20743.5, number 51 of 253
pMakeNodes starting loop:     a=5KPY|1|A|G|31 B=5KPY|1|A|C|39
  2 Basepair    31   39 GC cWW 
pMakeNodes probe for inserts:  a=5KPY|1|A|G|32 B=5KPY|1|A|G|38
    Insertion on left  5KPY|1|A|G|32
    Insertion on right 5KPY|1|A|G|38
pMakeNodesProbeForInsertions:  a 5KPY|1|A|A|33 interacts with 5KPY|1|A|G|37
pMakeNodesProbeForInsertions:  B 5KPY|1|A|G|37 interacts with 5KPY|1|A|A|33
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5KPY|1|A|G|37 interacts with 5KPY|1|A|A|33
pMakeNodes probed for insert:  a=5KPY|1|A|A|33 B=5KPY|1|A|G|37
  3 Basepair    33   37 AG cSS 
pMakeNodes adding hairpin:     a=5KPY|1|A|U|34 B=5KPY|1|A|A|35
    Right strand conserved insertion U  34 at right strand position 1
    Right strand conserved insertion A  35 at right strand position 2
  4 Hairpin   34:35 UA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|G|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5KPY|1|A|G|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: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'GC'
               Comment: ' // Basepair G31 - C39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|G|32'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'UA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U34'  ' // Hairpin conserved non-basepairing position A35'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 5KPY|1|A|G|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A33 - G37 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UA'
           RightLetter: ''
               Comment: ' // Hairpin node U34:A35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U34'  ' // Hairpin conserved non-basepairing position A35'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20743.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3669
   -5.3669
   -5.6828
   -5.7675
   -5.3669
   -6.5865
   -6.5865

Timestamp 18-Jul-2025 22:26:36
pMakeSCFGModels: Making JAR3D model for motif group HL_20751.2, number 52 of 253
pMakeNodes starting loop:     a=3D0U|1|A|C|38 B=3D0U|1|A|G|51
  2 Basepair    38   51 CG cWW 
pMakeNodes probe for inserts:  a=3D0U|1|A|A|39 B=3D0U|1|A|U|49
    Insertion on right 3D0U|1|A|U|49
    Insertion on right 3D0U|1|A|A|48
pMakeNodesProbeForInsertions:  a 3D0U|1|A|A|39 interacts with 3D0U|1|A|A|47
pMakeNodesProbeForInsertions:  B 3D0U|1|A|A|47 interacts with 3D0U|1|A|A|39
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3D0U|1|A|A|47 interacts with 3D0U|1|A|A|39
pMakeNodes probed for insert:  a=3D0U|1|A|A|39 B=3D0U|1|A|A|47
  3 Basepair    39   47 AA tHW 
pMakeNodes adding hairpin:     a=3D0U|1|A|G|40 B=3D0U|1|A|G|46
    Right strand conserved insertion G  40 at right strand position 1
    Right strand conserved insertion G  41 at right strand position 2
    Right strand conserved insertion G  42 at right strand position 3
    Right strand conserved insertion G  43 at right strand position 4
    Right strand conserved insertion A  44 at right strand position 5
    Right strand conserved insertion G  45 at right strand position 6
    Right strand conserved insertion G  46 at right strand position 7
  4 Hairpin   40:46 GGGGAGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3D0U|1|A|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3D0U|1|A|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'AUG'
               Comment: ' // Basepair C38 - G51 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3D0U|1|A|U|49'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GGGGAGG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3D0U|1|A|A|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

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

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A39 - A47 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGAGG'
           RightLetter: ''
               Comment: ' // Hairpin node G40:G46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  2 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  9
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20751.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6242
   -8.6242
  -13.2439

Timestamp 18-Jul-2025 22:26:36
pMakeSCFGModels: Making JAR3D model for motif group HL_20781.1, number 53 of 253
pMakeNodes starting loop:     a=5XWP|1|C|C|9 B=5XWP|1|C|G|19
  2 Basepair     9   19 CG cWW 
pMakeNodes adding hairpin:     a=5XWP|1|C|A|10 B=5XWP|1|C|A|18
    Right strand conserved insertion A  10 at right strand position 1
    Right strand conserved insertion A  11 at right strand position 2
    Right strand conserved insertion A  12 at right strand position 3
    Right strand conserved insertion A  13 at right strand position 4
    Right strand conserved insertion A  14 at right strand position 5
    Right strand conserved insertion G  16 at right strand position 6
    Right strand conserved insertion A  17 at right strand position 7
    Right strand conserved insertion A  18 at right strand position 8
  3 Hairpin   10:18 AAAAAGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C9 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAAAAGAA'
           RightLetter: ''
               Comment: ' // Hairpin node A10:A18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20781.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8663

Timestamp 18-Jul-2025 22:26:36
pMakeSCFGModels: Making JAR3D model for motif group HL_20811.4, number 54 of 253
pMakeNodes starting loop:     a=1QF6|1|B|C|13 B=1QF6|1|B|G|22
  2 Basepair    13   22 CG cWW 
No need to probe because of interaction between a=1QF6|1|B|A|14 B=1QF6|1|B|A|21
  3 Basepair    14   21 AA cWS 
pMakeNodes adding hairpin:     a=1QF6|1|B|G|15 B=1QF6|1|B|G|15
    Right strand conserved insertion G  15 at right strand position 1
  4 Hairpin   15:15 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A21 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G15:G15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G15'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_20811.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7674
   -8.8660
   -7.6562
  -14.2679
   -8.8660
   -8.7095
   -8.8660
   -7.5199
  -11.5253
   -8.8660
   -9.9646
   -7.5199
   -8.7548
  -11.2745

Timestamp 18-Jul-2025 22:26:36
pMakeSCFGModels: Making JAR3D model for motif group HL_21372.1, number 55 of 253
pMakeNodes starting loop:     a=1KOG|1|O|U|82 B=1KOG|1|O|G|90
  2 Basepair    82   90 UG cWW 
pMakeNodes adding hairpin:     a=1KOG|1|O|U|83 B=1KOG|1|O|U|87
    Right strand conserved insertion U  83 at right strand position 1
  3 Hairpin   83:87 UGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U82 - G90 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGU'
           RightLetter: ''
               Comment: ' // Hairpin node U83:U87'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G86 - U87 cSH '  ' // Hairpin conserved non-basepairing position U83'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_21372.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9177
   -8.2538

Timestamp 18-Jul-2025 22:26:36
pMakeSCFGModels: Making JAR3D model for motif group HL_21400.1, number 56 of 253
pMakeNodes starting loop:     a=8EYU|1|A|A|16 B=8EYU|1|A|U|38
  2 Basepair    16   38 AU cWW 
pMakeNodes probe for inserts:  a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodesProbeForInsertions:  a 8EYU|1|A|G|17 interacts with 8EYU|1|A|A|34
pMakeNodesProbeForInsertions:  B 8EYU|1|A|A|37 interacts with 8EYU|1|A|U|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8EYU|1|A|A|37 interacts with 8EYU|1|A|U|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodes checking on making a cluster a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 9 and then 10 to 17
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
  3 Hairpin   17:37 GGGGGGGUGGGGGAGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 17
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A16 - U38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGGGGUGGGGGAGA'
           RightLetter: ''
               Comment: ' // Hairpin node G17:A37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×15 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [15×2 double]
    InteractionComment: {1×15 cell}
      JunctionDeletion: []
          InterIndices: [15×2 double]
                  lpar: []
                  rpar: []
              NormCons: 2.8796e-05

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 17
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_21400.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0896

Timestamp 18-Jul-2025 22:26:37
pMakeSCFGModels: Making JAR3D model for motif group HL_22135.1, number 57 of 253
pMakeNodes starting loop:     a=6FQ3|1|B|U|5 B=6FQ3|1|B|A|9
  2 Basepair     5    9 UA cWW 
pMakeNodes adding hairpin:     a=6FQ3|1|B|C|7 B=6FQ3|1|B|A|8
    Right strand conserved insertion C   7 at right strand position 1
    Right strand conserved insertion A   8 at right strand position 2
  3 Hairpin   7:8 CA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U5 - A9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: ''
               Comment: ' // Hairpin node C7:A8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C7'  ' // Hairpin conserved non-basepairing position A8'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_22135.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.2074

Timestamp 18-Jul-2025 22:26:37
pMakeSCFGModels: Making JAR3D model for motif group HL_22584.6, number 58 of 253
pMakeNodes starting loop:     a=8VM9|1|R|G|57 B=8VM9|1|R|C|63
  2 Basepair    57   63 GC cWW 
No need to probe because of interaction between a=8VM9|1|R|A|59 B=8VM9|1|R|A|62
  3 Basepair    59   62 AA tSW 
pMakeNodes adding hairpin:     a=8VM9|1|R|C|61 B=8VM9|1|R|C|61
    Right strand conserved insertion C  61 at right strand position 1
  4 Hairpin   61:61 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G57 - C63 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A59 - A62 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C61:C61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C61'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_22584.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -2.3968
   -7.3961
  -10.6900
   -8.5034

Timestamp 18-Jul-2025 22:26:37
pMakeSCFGModels: Making JAR3D model for motif group HL_22622.1, number 59 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|1451 B=5J7L|1|DA|G|1459
  2 Basepair  1451 1459 CG cWW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|G|1455 B=5J7L|1|DA|U|1458
    Right strand conserved insertion G1455 at right strand position 1
    Right strand conserved insertion G1456 at right strand position 2
    Right strand conserved insertion U1457 at right strand position 3
    Right strand conserved insertion U1458 at right strand position 4
  3 Hairpin   1455:1458 GGUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1451 - G1459 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGUU'
           RightLetter: ''
               Comment: ' // Hairpin node G1455:U1458'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_22622.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0141
   -7.4736

Timestamp 18-Jul-2025 22:26:37
pMakeSCFGModels: Making JAR3D model for motif group HL_23010.1, number 60 of 253
pMakeNodes starting loop:     a=4V7M|1|AY|C|12 B=4V7M|1|AY|G|22
  2 Basepair    12   22 CG cWW 
No need to probe because of interaction between a=4V7M|1|AY|A|13 B=4V7M|1|AY|A|21
  3 Basepair    13   21 AA tSH 
pMakeNodes adding hairpin:     a=4V7M|1|AY|A|14 B=4V7M|1|AY|U|19
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion C  16 at right strand position 3
    Right strand conserved insertion U  19 at right strand position 4
  4 Hairpin   14:19 AGCU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C12 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A13 - A21 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCU'
           RightLetter: ''
               Comment: ' // Hairpin node A14:U19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_23010.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8097

Timestamp 18-Jul-2025 22:26:37
pMakeSCFGModels: Making JAR3D model for motif group HL_23115.1, number 61 of 253
pMakeNodes starting loop:     a=6UFG|1|B|C|13 B=6UFG|1|B|G|23
  2 Basepair    13   23 CG cWW 
pMakeNodes adding hairpin:     a=6UFG|1|B|A|14 B=6UFG|1|B|U|21
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion G  16 at right strand position 3
    Right strand conserved insertion U  20 at right strand position 4
    Right strand conserved insertion U  21 at right strand position 5
  3 Hairpin   14:21 AGGUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGGUU'
           RightLetter: ''
               Comment: ' // Hairpin node A14:U21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_23115.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7180
   -6.7180

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_23509.1, number 62 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|G|2534 B=8P9A|1|AR|C|2545
pMakeNodes checking on making a cluster a=8P9A|1|AR|G|2534 B=8P9A|1|AR|C|2545
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 2 and then 11 to 11
aa is 2 bb is 11
  2 Cluster   8P9A|1|AR|G|2534:8P9A|1|AR|A|2535 8P9A|1|AR|C|2545:8P9A|1|AR|C|2545
    LR Inter  8P9A|1|AR|G|2534 8P9A|1|AR|C|2545 cWW 
    LR Inter  8P9A|1|AR|A|2535 8P9A|1|AR|C|2545 bif 
    LL Inter  8P9A|1|AR|G|2534 8P9A|1|AR|A|2535 cSH 
pMakeNodesCluster a=3 B=10 at the end
pMakeNodesCluster a=3 B=10 at the end
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|2536 B=8P9A|1|AR|U|2544
    Insertion on left  8P9A|1|AR|A|2536
    Insertion on right 8P9A|1|AR|U|2544
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|2537 interacts with 8P9A|1|AR|U|2543
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|2543 interacts with 8P9A|1|AR|U|2537
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|2543 interacts with 8P9A|1|AR|U|2537
  3 Initial   2536 (1 insertion) and 2544 (1 insertion)
pMakeNodes probed for insert:  a=8P9A|1|AR|U|2537 B=8P9A|1|AR|U|2543
  4 Basepair  2537 2543 UU cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|U|2538 B=8P9A|1|AR|U|2542
    Right strand conserved insertion U2538 at right strand position 1
    Right strand conserved insertion A2540 at right strand position 2
    Right strand conserved insertion U2541 at right strand position 3
    Right strand conserved insertion U2542 at right strand position 4
  5 Hairpin   2538:2542 UAUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|2536
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|U|2543
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 0 0 0 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Cluster node 8P9A|1|AR|G|2534:8P9A|1|AR|A|2535 and 8P9A|1|AR|C|2545:8P9A|1|AR|C|2545'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0303
                  lpar: []
                  rpar: []

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Initial node 8P9A|1|AR|A|2536 - 8P9A|1|AR|U|2544 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|2536'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UAUU'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000
                  lpar: []
                  rpar: []

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|U|2543'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U2537 - U2543 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAUU'
           RightLetter: ''
               Comment: ' // Hairpin node U2538:U2542'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  8
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_23509.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4579

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_24792.1, number 63 of 253
pMakeNodes starting loop:     a=6XJQ|1|A|G|26 B=6XJQ|1|A|C|35
pMakeNodes checking on making a cluster a=6XJQ|1|A|G|26 B=6XJQ|1|A|C|35
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 1 and then 4 to 6
aa is 1 bb is 4
  2 Cluster   6XJQ|1|A|G|26:6XJQ|1|A|G|26 6XJQ|1|A|C|29:6XJQ|1|A|C|35
    LR Inter  6XJQ|1|A|G|26 6XJQ|1|A|C|35 cWW 
    RR Inter  6XJQ|1|A|C|29 6XJQ|1|A|C|35 cWS 
    Right strand conserved insertion 6XJQ|1|A|G|30 at position 2
pMakeNodesCluster a=2 B=3 at the end
pMakeNodesCluster a=2 B=3 at the end
pMakeNodes adding hairpin:     a=6XJQ|1|A|C|27 B=6XJQ|1|A|C|28
    Right strand conserved insertion C  27 at right strand position 1
    Right strand conserved insertion C  28 at right strand position 2
  3 Hairpin   27:28 CC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  4  5  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: [4 5 6]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'CGC'
               Comment: ' // Cluster node 6XJQ|1|A|G|26:6XJQ|1|A|G|26 and 6XJQ|1|A|C|29:6XJQ|1|A|C|35'
              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

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: ''
               Comment: ' // Hairpin node C27:C28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C27'  ' // Hairpin conserved non-basepairing position C28'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  4  5  6
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_24792.1 allow insertions from initial node 3?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_24792.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4227

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_25061.1, number 64 of 253
pMakeNodes starting loop:     a=6MWN|1|B|U|624 B=6MWN|1|B|G|632
  2 Basepair   624  632 UG cWW 
pMakeNodes adding hairpin:     a=6MWN|1|B|G|625 B=6MWN|1|B|A|630
    Right strand conserved insertion G 625 at right strand position 1
    Right strand conserved insertion U 626 at right strand position 2
    Right strand conserved insertion A 630 at right strand position 3
  3 Hairpin   625:630 GUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U624 - G632 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUA'
           RightLetter: ''
               Comment: ' // Hairpin node G625:A630'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_25061.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7371
  -10.8535

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_25847.2, number 65 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|G|1910 B=9DFE|1|1A|OMC|1920
  2 Basepair  1910 1920 GC cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|PSU|1911 B=9DFE|1|1A|A|1919
    Insertion on left  9DFE|1|1A|PSU|1911
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|1912 interacts with 9DFE|1|1A|PSU|1917
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|1919 interacts with 9DFE|1|1A|A|1918
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|1919 interacts with 9DFE|1|1A|A|1918
pMakeNodes probed for insert:  a=9DFE|1|1A|A|1912 B=9DFE|1|1A|A|1919
pMakeNodes checking on making a cluster a=9DFE|1|1A|A|1912 B=9DFE|1|1A|A|1919
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 3 and then 7 to 9
aa is 3 bb is 7
  3 Cluster   9DFE|1|1A|A|1912:9DFE|1|1A|A|1912 9DFE|1|1A|PSU|1917:9DFE|1|1A|A|1919
    LR Inter  9DFE|1|1A|A|1912 9DFE|1|1A|PSU|1917 tHW 
    RR Inter  9DFE|1|1A|A|1918 9DFE|1|1A|A|1919 cSH 
pMakeNodesCluster a=4 B=6 at the end
pMakeNodesCluster a=4 B=6 at the end
pMakeNodes adding hairpin:     a=9DFE|1|1A|C|1914 B=9DFE|1|1A|A|1916
    Right strand conserved insertion C1914 at right strand position 1
    Right strand conserved insertion U1915 at right strand position 2
    Right strand conserved insertion A1916 at right strand position 3
  4 Hairpin   1914:1916 CUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  3 Right  7  8  9
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|PSU|1911
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G1910 - C1920 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|PSU|1911'
              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: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: 3
            RightIndex: [7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UAA'
               Comment: ' // Cluster node 9DFE|1|1A|A|1912:9DFE|1|1A|A|1912 and 9DFE|1|1A|PSU|1917:9DFE|1|1A|A|1919'
              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: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUA'
           RightLetter: ''
               Comment: ' // Hairpin node C1914:A1916'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

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   Cluster Left  3 Right  7  8  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: HL_25847.2 allow insertions from initial node 6?
ans =

    0.0161    0.9670    0.0161    0.0008


ans =

    0.7000    0.1000    0.1000    0.1000         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_25847.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3430
   -4.8330
   -4.3430

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_25967.2, number 66 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|G|1719 B=8P9A|1|AR|C|1725
  2 Basepair  1719 1725 GC cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|1720 B=8P9A|1|AR|U|1724
  3 Basepair  1720 1724 UU cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|U|1721 B=8P9A|1|AR|A|1723
    Right strand conserved insertion U1721 at right strand position 1
    Right strand conserved insertion U1722 at right strand position 2
    Right strand conserved insertion A1723 at right strand position 3
  4 Hairpin   1721:1723 UUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1719 - C1725 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U1720 - U1724 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUA'
           RightLetter: ''
               Comment: ' // Hairpin node U1721:A1723'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_25967.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4355
   -4.4355
   -9.3439

Timestamp 18-Jul-2025 22:26:38
pMakeSCFGModels: Making JAR3D model for motif group HL_26631.1, number 67 of 253
pMakeNodes starting loop:     a=3SNP|1|D|C|14 B=3SNP|1|D|G|18
  2 Basepair    14   18 CG cWW 
pMakeNodes adding hairpin:     a=3SNP|1|D|A|15 B=3SNP|1|D|U|17
    Right strand conserved insertion A  15 at right strand position 1
    Right strand conserved insertion G  16 at right strand position 2
    Right strand conserved insertion U  17 at right strand position 3
  3 Hairpin   15:17 AGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGU'
           RightLetter: ''
               Comment: ' // Hairpin node A15:U17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_26631.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.5658
   -2.5658

Timestamp 18-Jul-2025 22:26:39
pMakeSCFGModels: Making JAR3D model for motif group HL_26934.1, number 68 of 253
pMakeNodes starting loop:     a=3IVN|1|A|G|37 B=3IVN|1|A|C|44
  2 Basepair    37   44 GC cWW 
pMakeNodes probe for inserts:  a=3IVN|1|A|U|38 B=3IVN|1|A|A|43
    Insertion on left  3IVN|1|A|U|38
    Insertion on right 3IVN|1|A|A|43
pMakeNodesProbeForInsertions:  a 3IVN|1|A|G|39 interacts with 3IVN|1|A|U|42
pMakeNodesProbeForInsertions:  B 3IVN|1|A|U|42 interacts with 3IVN|1|A|G|39
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3IVN|1|A|U|42 interacts with 3IVN|1|A|G|39
pMakeNodes probed for insert:  a=3IVN|1|A|G|39 B=3IVN|1|A|U|42
  3 Basepair    39   42 GU tSW 
pMakeNodes adding hairpin:     a=3IVN|1|A|U|40 B=3IVN|1|A|C|41
    Right strand conserved insertion U  40 at right strand position 1
    Right strand conserved insertion C  41 at right strand position 2
  4 Hairpin   40:41 UC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IVN|1|A|U|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IVN|1|A|A|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 0 0 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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: 'GU'
           RightLetter: 'AC'
               Comment: ' // Basepair G37 - C44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IVN|1|A|U|38'
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U40'  ' // Hairpin conserved non-basepairing position C41'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 3IVN|1|A|A|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G39 - U42 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UC'
           RightLetter: ''
               Comment: ' // Hairpin node U40:C41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U40'  ' // Hairpin conserved non-basepairing position C41'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_26934.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.7607

Timestamp 18-Jul-2025 22:26:39
pMakeSCFGModels: Making JAR3D model for motif group HL_27483.1, number 69 of 253
pMakeNodes starting loop:     a=8CRE|1|1|G|539 B=8CRE|1|1|C|546
  2 Basepair   539  546 GC cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|C|540 B=8CRE|1|1|C|543
  3 Hairpin   540:543 CC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G539 - C546 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: ''
               Comment: ' // Hairpin node C540:C543'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction C540 - C543 cWW '}
      JunctionDeletion: []
          InterIndices: [2 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_27483.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1054
   -4.1923

Timestamp 18-Jul-2025 22:26:39
pMakeSCFGModels: Making JAR3D model for motif group HL_27670.2, number 70 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|327 B=5J7L|1|DA|C|335
  2 Basepair   327  335 GC cWW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|U|328 B=5J7L|1|DA|C|334
    Right strand conserved insertion G 333 at right strand position 3
    Right strand conserved insertion C 334 at right strand position 4
  3 Hairpin   328:334 UAGC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G327 - C335 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAGC'
           RightLetter: ''
               Comment: ' // Hairpin node U328:C334'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_27670.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.4207
   -8.9315
   -6.5961
   -6.4358
   -6.3068
   -6.3068
   -5.8589
   -7.7495
   -5.8589
   -7.7495
   -5.4314
   -5.4314
   -5.7960

Timestamp 18-Jul-2025 22:26:39
pMakeSCFGModels: Making JAR3D model for motif group HL_28075.1, number 71 of 253
pMakeNodes starting loop:     a=6N5P|1|A|A|14 B=6N5P|1|A|U|22
  2 Basepair    14   22 AU cWW 
No need to probe because of interaction between a=6N5P|1|A|U|15 B=6N5P|1|A|U|21
  3 Basepair    15   21 UU cWW 
pMakeNodes adding hairpin:     a=6N5P|1|A|G|16 B=6N5P|1|A|G|19
    Right strand conserved insertion G  16 at right strand position 1
    Right strand conserved insertion U  17 at right strand position 2
    Right strand conserved insertion G  19 at right strand position 3
  4 Hairpin   16:19 GUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A14 - U22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            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 U15 - U21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUG'
           RightLetter: ''
               Comment: ' // Hairpin node G16:G19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_28075.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4253
   -7.8217
   -9.7881
   -8.0266

Timestamp 18-Jul-2025 22:26:39
pMakeSCFGModels: Making JAR3D model for motif group HL_28252.8, number 72 of 253
pMakeNodes starting loop:     a=4RDX|1|C|G|53 B=4RDX|1|C|C|61
  2 Basepair    53   61 GC cWW 
pMakeNodes probe for inserts:  a=4RDX|1|C|U|54 B=4RDX|1|C|U|60
    Insertion on right 4RDX|1|C|U|60
    Insertion on right 4RDX|1|C|G|59
pMakeNodesProbeForInsertions:  a 4RDX|1|C|U|54 interacts with 4RDX|1|C|A|58
pMakeNodesProbeForInsertions:  B 4RDX|1|C|A|58 interacts with 4RDX|1|C|U|54
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4RDX|1|C|A|58 interacts with 4RDX|1|C|U|54
pMakeNodes probed for insert:  a=4RDX|1|C|U|54 B=4RDX|1|C|A|58
  3 Basepair    54   58 UA tWH 
pMakeNodes adding hairpin:     a=4RDX|1|C|U|55 B=4RDX|1|C|A|57
    Right strand conserved insertion U  55 at right strand position 1
    Right strand conserved insertion C  56 at right strand position 2
    Right strand conserved insertion A  57 at right strand position 3
  4 Hairpin   55:57 UCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4RDX|1|C|U|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4RDX|1|C|G|59
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'GUC'
               Comment: ' // Basepair G53 - C61 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4RDX|1|C|U|60'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UCA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4RDX|1|C|G|59'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            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 U54 - A58 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCA'
           RightLetter: ''
               Comment: ' // Hairpin node U55:A57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_28252.8_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.0609
   -2.6287
   -2.7926
   -2.7926
   -2.7926
   -2.6287
   -3.0609
   -3.0609
   -2.7926
   -3.0609
   -2.7926
   -3.0609
   -2.3605
   -3.0609
   -2.3605
   -3.6399
   -4.0041
   -3.0609
   -2.7926
   -2.6287
   -2.3605
   -2.6287
   -2.7926
   -3.2078
   -3.6399
   -2.7926
   -2.6287
   -3.0609
   -3.0609
   -2.7926
   -2.6287
   -3.0609
   -2.3605
   -2.6287
   -3.2078
   -2.3605
   -2.7926
   -2.3605
   -5.5998
   -3.0609
   -2.7926
   -2.6287
   -5.0207
   -3.2078
   -2.6287
   -6.4116
   -3.6399
   -2.7926
   -2.7926
   -2.7926
   -2.3605
   -5.5998
   -2.3605
   -3.6399
   -5.5998
   -3.0609
   -3.0609
   -3.2078
   -6.4116
   -5.3967
   -2.3605
   -2.6287
   -4.0041
   -2.3605
   -2.3605
   -2.7926
   -4.0041
   -4.0041
   -6.7930
   -3.2078
   -3.0609
   -3.0609
   -2.6287
   -3.2078
   -6.0211
   -2.3605
   -3.0609
   -5.5998
   -3.2078
   -2.7926
   -6.5248
   -6.5248
   -6.5248
   -3.2078
   -2.3605
   -2.6287
   -2.6287
   -3.0609
   -3.2078
   -2.6287
   -5.5998
   -3.2078
   -2.3605
   -2.6287
   -2.3605
   -2.3605
   -2.3605
   -3.6399
   -3.0609
   -3.2078
   -2.7926
   -4.0041
   -2.7926
   -4.0041
   -5.0362
   -3.0609
   -4.0041
   -3.2078
   -6.5248
   -2.3605
  -10.3493
   -3.0609
  -14.7778
   -7.1880
  -11.7103
   -5.5998
   -6.5248
   -4.0041
   -7.4282
  -18.5261
   -2.3605
  -15.1337
  -11.7103
   -6.5248
   -3.0609
   -2.3605
   -5.0362
  -18.1952
  -17.5845
   -3.0609
  -18.1952
   -8.6005
  -17.5845
   -8.9168
   -3.0609
   -2.3605
   -2.7926
   -2.6287
   -3.2078
   -2.3605

Timestamp 18-Jul-2025 22:26:40
pMakeSCFGModels: Making JAR3D model for motif group HL_28791.1, number 73 of 253
pMakeNodes starting loop:     a=2Y9H|1|N|C|11 B=2Y9H|1|N|G|16
  2 Basepair    11   16 CG cWW 
pMakeNodes adding hairpin:     a=2Y9H|1|N|G|12 B=2Y9H|1|N|U|15
    Right strand conserved insertion G  12 at right strand position 1
    Right strand conserved insertion C  13 at right strand position 2
    Right strand conserved insertion G  14 at right strand position 3
    Right strand conserved insertion U  15 at right strand position 4
  3 Hairpin   12:15 GCGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C11 - G16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCGU'
           RightLetter: ''
               Comment: ' // Hairpin node G12:U15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_28791.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.7921

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_29129.3, number 74 of 253
pMakeNodes starting loop:     a=5TPY|1|A|U|28 B=5TPY|1|A|G|38
  2 Basepair    28   38 UG cWW 
No need to probe because of interaction between a=5TPY|1|A|U|29 B=5TPY|1|A|A|36
  3 Basepair    29   36 UA tWH 
pMakeNodes adding hairpin:     a=5TPY|1|A|G|32 B=5TPY|1|A|A|35
    Right strand conserved insertion G  32 at right strand position 1
    Right strand conserved insertion G  33 at right strand position 2
    Right strand conserved insertion G  34 at right strand position 3
    Right strand conserved insertion A  35 at right strand position 4
  4 Hairpin   32:35 GGGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U28 - G38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U29 - A36 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGA'
           RightLetter: ''
               Comment: ' // Hairpin node G32:A35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_29129.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8801
   -6.8801
   -8.4073

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_29762.1, number 75 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|U|1347 B=8P9A|1|AR|G|1357
  2 Basepair  1347 1357 UG cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|U|1348 B=8P9A|1|AR|A|1355
    Right strand conserved insertion U1348 at right strand position 1
    Right strand conserved insertion G1349 at right strand position 2
    Right strand conserved insertion A1350 at right strand position 3
    Right strand conserved insertion U1351 at right strand position 4
    Right strand conserved insertion A1355 at right strand position 5
  3 Hairpin   1348:1355 UGAUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1347 - G1357 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAUA'
           RightLetter: ''
               Comment: ' // Hairpin node U1348:A1355'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_29762.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0440

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_29958.1, number 76 of 253
pMakeNodes starting loop:     a=2NZ4|1|Q|A|31 B=2NZ4|1|Q|U|43
  2 Basepair    31   43 AU cWW 
pMakeNodes adding hairpin:     a=2NZ4|1|Q|G|32 B=2NZ4|1|Q|U|40
    Right strand conserved insertion G  32 at right strand position 1
    Right strand conserved insertion G  33 at right strand position 2
    Right strand conserved insertion G  35 at right strand position 3
    Right strand conserved insertion G  36 at right strand position 4
    Right strand conserved insertion G  37 at right strand position 5
    Right strand conserved insertion G  38 at right strand position 6
    Right strand conserved insertion U  39 at right strand position 7
    Right strand conserved insertion U  40 at right strand position 8
  3 Hairpin   32:40 GGGGGGUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGGGUU'
           RightLetter: ''
               Comment: ' // Hairpin node G32:U40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_29958.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9378

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_29966.1, number 77 of 253
pMakeNodes starting loop:     a=6IV9|1|B|A|-21 B=6IV9|1|B|U|-16
  2 Basepair   -21  -16 AU cWW 
pMakeNodes adding hairpin:     a=6IV9|1|B|A|-20 B=6IV9|1|B|U|-18
    Right strand conserved insertion A -20 at right strand position 1
    Right strand conserved insertion A -19 at right strand position 2
    Right strand conserved insertion U -18 at right strand position 3
  3 Hairpin   -20:-18 AAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 A-21 - U-16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAU'
           RightLetter: ''
               Comment: ' // Hairpin node A-20:U-18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_29966.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4128

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_30068.2, number 78 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|U|38 B=8P9A|1|AR|A|45
  2 Basepair    38   45 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|A|39 B=8P9A|1|AR|U|44
  3 Basepair    39   44 AU tSH 
pMakeNodes adding hairpin:     a=8P9A|1|AR|G|41 B=8P9A|1|AR|C|42
    Right strand conserved insertion G  41 at right strand position 1
    Right strand conserved insertion C  42 at right strand position 2
  4 Hairpin   41:42 GC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U38 - A45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A39 - U44 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GC'
           RightLetter: ''
               Comment: ' // Hairpin node G41:C42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G41'  ' // Hairpin conserved non-basepairing position C42'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_30068.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0518
   -6.0518
   -6.3560
   -6.3560
   -6.3560
   -6.3560
   -6.3560
   -6.2638
   -6.2638
   -6.2638
   -6.2588
   -6.2588
   -6.2638
   -8.9539
   -7.5720

Timestamp 18-Jul-2025 22:26:41
pMakeSCFGModels: Making JAR3D model for motif group HL_30680.3, number 79 of 253
pMakeNodes starting loop:     a=5FJC|1|A|G|23 B=5FJC|1|A|C|29
  2 Basepair    23   29 GC cWW 
pMakeNodes adding hairpin:     a=5FJC|1|A|A|24 B=5FJC|1|A|G|28
    Right strand conserved insertion A  24 at right strand position 1
    Right strand conserved insertion C  25 at right strand position 2
    Right strand conserved insertion U  26 at right strand position 3
    Right strand conserved insertion G  27 at right strand position 4
    Right strand conserved insertion G  28 at right strand position 5
  3 Hairpin   24:28 ACUGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G23 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACUGG'
           RightLetter: ''
               Comment: ' // Hairpin node A24:G28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_30680.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4673
   -6.4673
  -10.0395
   -6.4673
   -6.4673
   -8.0106
  -11.9052
   -9.0552
   -7.6802
   -9.0552
   -7.3437
   -7.6802
   -7.3437
  -14.8388
  -14.4063

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_31581.6, number 80 of 253
pMakeNodes starting loop:     a=4PR6|1|B|C|147 B=4PR6|1|B|G|158
  2 Basepair   147  158 CG cWW 
pMakeNodes adding hairpin:     a=4PR6|1|B|A|148 B=4PR6|1|B|C|157
    Right strand conserved insertion A 148 at right strand position 1
    Right strand conserved insertion U 149 at right strand position 2
    Right strand conserved insertion U 150 at right strand position 3
    Right strand conserved insertion G 151 at right strand position 4
    Right strand conserved insertion A 153 at right strand position 5
    Right strand conserved insertion C 154 at right strand position 6
    Right strand conserved insertion C 157 at right strand position 9
  3 Hairpin   148:157 AUUGACUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C147 - G158 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUGACUCC'
           RightLetter: ''
               Comment: ' // Hairpin node A148:C157'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_31581.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1505
   -7.1505
   -9.2504

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_31585.4, number 81 of 253
pMakeNodes starting loop:     a=4XNR|1|X|G|46 B=4XNR|1|X|C|53
  2 Basepair    46   53 GC cWW 
pMakeNodes adding hairpin:     a=4XNR|1|X|U|47 B=4XNR|1|X|A|52
    Right strand conserved insertion U  47 at right strand position 1
    Right strand conserved insertion U  49 at right strand position 2
    Right strand conserved insertion C  50 at right strand position 3
    Right strand conserved insertion U  51 at right strand position 4
    Right strand conserved insertion A  52 at right strand position 5
  3 Hairpin   47:52 UUCUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G46 - C53 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCUA'
           RightLetter: ''
               Comment: ' // Hairpin node U47:A52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_31585.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4455
   -6.4455
   -6.4455
   -6.4455
   -8.2398
   -6.4455
   -7.0815
   -8.2398
  -11.5371
   -7.9450
  -14.7779
   -9.1882
   -8.9220
   -9.3414
   -8.3030
   -8.9220
   -8.6538
   -9.3513
   -8.1275
   -8.1275

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_32346.4, number 82 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|C|2205 B=9DFE|1|1A|G|2219
  2 Basepair  2205 2219 CG cWW 
pMakeNodes adding hairpin:     a=9DFE|1|1A|A|2208 B=9DFE|1|1A|A|2208
    Right strand conserved insertion A2208 at right strand position 1
  3 Hairpin   2208:2208 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C2205 - G2219 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A2208:A2208'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2208'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_32346.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0390
   -5.6093
   -5.3317
   -4.0119
   -4.9783
   -4.8208
   -4.2348
   -4.4110
   -4.8003

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_32392.1, number 83 of 253
pMakeNodes starting loop:     a=5B2P|1|B|U|82 B=5B2P|1|B|A|86
  2 Basepair    82   86 UA cWW 
pMakeNodes adding hairpin:     a=5B2P|1|B|U|84 B=5B2P|1|B|G|85
    Right strand conserved insertion U  84 at right strand position 1
    Right strand conserved insertion G  85 at right strand position 2
  3 Hairpin   84:85 UG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U82 - A86 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UG'
           RightLetter: ''
               Comment: ' // Hairpin node U84:G85'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U84'  ' // Hairpin conserved non-basepairing position G85'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_32392.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.6707
   -4.3639

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_32735.2, number 84 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|A|2471 B=5J7L|1|DA|U|2479
  2 Basepair  2471 2479 AU cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|2472 B=5J7L|1|DA|A|2478
  3 Basepair  2472 2478 GA tSH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|U|2473 B=5J7L|1|DA|U|2477
    Right strand conserved insertion U2473 at right strand position 1
    Right strand conserved insertion U2474 at right strand position 2
    Right strand conserved insertion C2475 at right strand position 3
    Right strand conserved insertion A2476 at right strand position 4
    Right strand conserved insertion U2477 at right strand position 5
  4 Hairpin   2473:2477 UUCAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2471 - U2479 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2472 - A2478 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCAU'
           RightLetter: ''
               Comment: ' // Hairpin node U2473:U2477'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_32735.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.6330
   -3.6630
   -4.4214
   -5.1272
   -4.3087
   -3.6630
   -6.4343

Timestamp 18-Jul-2025 22:26:42
pMakeSCFGModels: Making JAR3D model for motif group HL_33074.4, number 85 of 253
pMakeNodes starting loop:     a=4C4W|1|H|C|11 B=4C4W|1|H|G|22
  2 Basepair    11   22 CG cWW 
pMakeNodes adding hairpin:     a=4C4W|1|H|A|12 B=4C4W|1|H|C|21
    Right strand conserved insertion A  12 at right strand position 1
    Right strand conserved insertion U  13 at right strand position 2
    Right strand conserved insertion U  14 at right strand position 3
    Right strand conserved insertion G  15 at right strand position 4
    Right strand conserved insertion A  17 at right strand position 5
    Right strand conserved insertion C  18 at right strand position 6
    Right strand conserved insertion C  20 at right strand position 7
    Right strand conserved insertion C  21 at right strand position 8
  3 Hairpin   12:21 AUUGACCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C11 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUGACCC'
           RightLetter: ''
               Comment: ' // Hairpin node A12:C21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_33074.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -6.0889
   -1.8806
   -1.8806
   -6.0889
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806
   -1.8806

Timestamp 18-Jul-2025 22:26:43
pMakeSCFGModels: Making JAR3D model for motif group HL_33983.1, number 86 of 253
pMakeNodes starting loop:     a=8WND|1|T|C|31 B=8WND|1|T|G|39
  2 Basepair    31   39 CG cWW 
pMakeNodes adding hairpin:     a=8WND|1|T|C|32 B=8WND|1|T|A|37
    Right strand conserved insertion C  32 at right strand position 1
    Right strand conserved insertion U  33 at right strand position 2
    Right strand conserved insertion A  35 at right strand position 3
    Right strand conserved insertion U  36 at right strand position 4
    Right strand conserved insertion A  37 at right strand position 5
  3 Hairpin   32:37 CUAUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAUA'
           RightLetter: ''
               Comment: ' // Hairpin node C32:A37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_33983.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5674

Timestamp 18-Jul-2025 22:26:43
pMakeSCFGModels: Making JAR3D model for motif group HL_34617.5, number 87 of 253
pMakeNodes starting loop:     a=5Y85|1|D|C|28 B=5Y85|1|D|G|33
  2 Basepair    28   33 CG cWW 
No need to probe because of interaction between a=5Y85|1|D|U|29 B=5Y85|1|D|G|32
  3 Basepair    29   32 UG tSW 
pMakeNodes adding hairpin:     a=5Y85|1|D|C|31 B=5Y85|1|D|C|31
    Right strand conserved insertion C  31 at right strand position 1
  4 Hairpin   31:31 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C28 - G33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U29 - G32 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C31:C31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C31'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_34617.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -1.9414
   -2.8691
   -1.9414
   -1.9414
   -2.8691
   -1.9414
   -2.9635
   -1.9414
   -1.9414
   -2.8691
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -8.7933
   -1.9414
   -3.3855
   -3.3855
   -3.3855
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -4.3132
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -4.4841
   -1.9414
   -2.9635
   -8.7933
   -3.3855
   -1.9414
   -1.9414
   -1.9414
   -5.9692
   -2.8691
   -1.9414
   -3.3855
   -8.5521
   -1.9414
   -1.9414
   -1.9414
   -1.9414
   -2.8691
   -6.8837
   -9.7629
   -1.9414
  -14.5282
   -1.9414
   -6.7572
   -6.8837

Timestamp 18-Jul-2025 22:26:43
pMakeSCFGModels: Making JAR3D model for motif group HL_34964.1, number 88 of 253
pMakeNodes starting loop:     a=2DU3|1|D|A|912 B=2DU3|1|D|U|922
  2 Basepair   912  922 AU cWW 
No need to probe because of interaction between a=2DU3|1|D|G|913 B=2DU3|1|D|U|921
  3 Basepair   913  921 GU cWW 
pMakeNodes adding hairpin:     a=2DU3|1|D|A|914 B=2DU3|1|D|G|918
    Right strand conserved insertion A 914 at right strand position 1
    Right strand conserved insertion G 915 at right strand position 2
    Right strand conserved insertion G 916 at right strand position 3
  4 Hairpin   914:918 AGGGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A912 - U922 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G913 - U921 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGGGG'
           RightLetter: ''
               Comment: ' // Hairpin node A914:G918'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_34964.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.9853
   -9.5519

Timestamp 18-Jul-2025 22:26:44
pMakeSCFGModels: Making JAR3D model for motif group HL_35354.1, number 89 of 253
pMakeNodes starting loop:     a=6E8S|1|A|A|8 B=6E8S|1|A|U|31
  2 Basepair     8   31 AU cWW 
pMakeNodes probe for inserts:  a=6E8S|1|A|G|9 B=6E8S|1|A|A|30
pMakeNodesProbeForInsertions:  a 6E8S|1|A|G|9 interacts with 6E8S|1|A|G|25
pMakeNodesProbeForInsertions:  B 6E8S|1|A|A|30 interacts with 6E8S|1|A|U|24
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6E8S|1|A|A|30 interacts with 6E8S|1|A|U|24
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6E8S|1|A|G|9 B=6E8S|1|A|A|30
pMakeNodes checking on making a cluster a=6E8S|1|A|G|9 B=6E8S|1|A|A|30
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 11 and then 12 to 20
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=6E8S|1|A|G|9 B=6E8S|1|A|A|30
    Right strand conserved insertion A  12 at right strand position 3
  3 Hairpin   9:30 GGAGGAGGUAUGUGGUAUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 20
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [21×21 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A8 - U31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAGGAGGUAUGUGGUAUA'
           RightLetter: ''
               Comment: ' // Hairpin node G9:A30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
              NormCons: 0.0056

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 20
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_35354.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3000

Timestamp 18-Jul-2025 22:26:44
pMakeSCFGModels: Making JAR3D model for motif group HL_35677.3, number 90 of 253
pMakeNodes starting loop:     a=2XDB|1|G|U|4 B=2XDB|1|G|A|13
  2 Basepair     4   13 UA cWW 
pMakeNodes adding hairpin:     a=2XDB|1|G|G|5 B=2XDB|1|G|U|12
    Right strand conserved insertion G   5 at right strand position 1
    Right strand conserved insertion U   7 at right strand position 2
    Right strand conserved insertion G  10 at right strand position 5
    Right strand conserved insertion C  11 at right strand position 6
    Right strand conserved insertion U  12 at right strand position 7
  3 Hairpin   5:12 GUUUGCU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U4 - A13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUUUGCU'
           RightLetter: ''
               Comment: ' // Hairpin node G5:U12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_35677.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.3767
   -7.3767
   -7.3767
  -11.6458
  -10.0137
  -10.0137
  -12.6952

Timestamp 18-Jul-2025 22:26:44
pMakeSCFGModels: Making JAR3D model for motif group HL_35941.1, number 91 of 253
pMakeNodes starting loop:     a=4O26|1|E|C|186 B=4O26|1|E|G|190
  2 Basepair   186  190 CG cWW 
pMakeNodes adding hairpin:     a=4O26|1|E|C|188 B=4O26|1|E|C|188
    Right strand conserved insertion C 188 at right strand position 1
  3 Hairpin   188:188 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C186 - G190 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C188:C188'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C188'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_35941.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.7846

Timestamp 18-Jul-2025 22:26:44
pMakeSCFGModels: Making JAR3D model for motif group HL_36335.1, number 92 of 253
pMakeNodes starting loop:     a=5W1H|1|B|C|-19 B=5W1H|1|B|G|-10
  2 Basepair   -19  -10 CG cWW 
pMakeNodes probe for inserts:  a=5W1H|1|B|A|-18 B=5W1H|1|B|A|-11
    Insertion on left  5W1H|1|B|A|-18
    Insertion on right 5W1H|1|B|A|-11
pMakeNodesProbeForInsertions:  a 5W1H|1|B|A|-17 interacts with 5W1H|1|B|G|-12
pMakeNodesProbeForInsertions:  B 5W1H|1|B|G|-12 interacts with 5W1H|1|B|A|-17
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5W1H|1|B|G|-12 interacts with 5W1H|1|B|A|-17
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5W1H|1|B|A|-17 B=5W1H|1|B|G|-12
  3 Basepair   -17  -12 AG cSS 
No need to probe because of interaction between a=5W1H|1|B|G|-16 B=5W1H|1|B|A|-13
  4 Basepair   -16  -13 GA cSS 
pMakeNodes adding hairpin:     a=5W1H|1|B|A|-15 B=5W1H|1|B|A|-15
    Right strand conserved insertion A -15 at right strand position 1
  5 Hairpin   -15:-15 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5W1H|1|B|A|-18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5W1H|1|B|G|-12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'AG'
               Comment: ' // Basepair C-19 - G-10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5W1H|1|B|A|-18'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5W1H|1|B|G|-12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A-15'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              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: []
              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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 A-17 - G-12 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            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 G-16 - A-13 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A-15:A-15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A-15'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_36335.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9142
   -7.9142

Timestamp 18-Jul-2025 22:26:44
pMakeSCFGModels: Making JAR3D model for motif group HL_36684.4, number 93 of 253
pMakeNodes starting loop:     a=5IB8|1|1L|G|30 B=5IB8|1|1L|C|40
  2 Basepair    30   40 GC cWW 
pMakeNodes adding hairpin:     a=5IB8|1|1L|A|31 B=5IB8|1|1L|U|39
    Right strand conserved insertion A  31 at right strand position 1
    Right strand conserved insertion C  32 at right strand position 2
    Right strand conserved insertion U  33 at right strand position 3
    Right strand conserved insertion U  34 at right strand position 4
    Right strand conserved insertion U  35 at right strand position 5
    Right strand conserved insertion U  36 at right strand position 6
    Right strand conserved insertion A  37 at right strand position 7
    Right strand conserved insertion A  38 at right strand position 8
    Right strand conserved insertion U  39 at right strand position 9
  3 Hairpin   31:39 ACUUUUAAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G30 - C40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACUUUUAAU'
           RightLetter: ''
               Comment: ' // Hairpin node A31:U39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_36684.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4890
   -7.8135
   -8.4013
  -11.3100
  -10.5479
   -8.7351
   -9.8337

Timestamp 18-Jul-2025 22:26:45
pMakeSCFGModels: Making JAR3D model for motif group HL_37344.1, number 94 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|C|2567 B=8P9A|1|AR|G|2574
  2 Basepair  2567 2574 CG cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|2568 B=8P9A|1|AR|G|2573
  3 Basepair  2568 2573 CG cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|A|2569 B=8P9A|1|AR|U|2570
    Right strand conserved insertion A2569 at right strand position 1
    Right strand conserved insertion U2570 at right strand position 2
  4 Hairpin   2569:2570 AU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2567 - G2574 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2568 - G2573 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AU'
           RightLetter: ''
               Comment: ' // Hairpin node A2569:U2570'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2569'  ' // Hairpin conserved non-basepairing position U2570'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_37344.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1047
   -6.4857

Timestamp 18-Jul-2025 22:26:45
pMakeSCFGModels: Making JAR3D model for motif group HL_37369.2, number 95 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|C|246 B=9DFE|1|1A|G|252
  2 Basepair   246  252 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|G|247 B=9DFE|1|1A|A|251
  3 Basepair   247  251 GA tSH 
pMakeNodes adding hairpin:     a=9DFE|1|1A|G|248 B=9DFE|1|1A|G|250
    Right strand conserved insertion G 248 at right strand position 1
    Right strand conserved insertion C 249 at right strand position 2
    Right strand conserved insertion G 250 at right strand position 3
  4 Hairpin   248:250 GCG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C246 - G252 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G247 - A251 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCG'
           RightLetter: ''
               Comment: ' // Hairpin node G248:G250'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_37369.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.3463
   -3.3463
   -3.3463
   -3.3463
   -3.3463
   -3.3463
   -4.8816
   -7.5497
   -7.5497

Timestamp 18-Jul-2025 22:26:45
pMakeSCFGModels: Making JAR3D model for motif group HL_37824.7, number 96 of 253
pMakeNodes starting loop:     a=5UZ6|1|A|C|15 B=5UZ6|1|A|G|20
  2 Basepair    15   20 CG cWW 
No need to probe because of interaction between a=5UZ6|1|A|G|16 B=5UZ6|1|A|A|19
  3 Basepair    16   19 GA tSH 
pMakeNodes adding hairpin:     a=5UZ6|1|A|A|17 B=5UZ6|1|A|A|18
    Right strand conserved insertion A  17 at right strand position 1
    Right strand conserved insertion A  18 at right strand position 2
  4 Hairpin   17:18 AA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C15 - G20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G16 - A19 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: ''
               Comment: ' // Hairpin node A17:A18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A17'  ' // Hairpin conserved non-basepairing position A18'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_37824.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -3.2985
   -1.7593
   -1.7593
   -2.5448
   -2.5448
   -1.7593
   -1.7593
   -1.7593
   -2.5448
   -3.2985
   -1.7593
   -1.7593
   -2.5448
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -5.5688
   -1.7593
   -2.5448
   -3.4315
   -2.5448
   -1.7593
   -1.7593
   -1.7593
   -1.7593
   -2.5448
   -1.7593
   -1.7593
   -3.2985
   -1.7593
   -2.5448
   -1.7593
   -3.2985
   -1.7593
   -3.2985
   -2.5448
   -1.7593
   -3.2657
   -2.5448
   -3.9191
   -3.2657
   -3.2985
   -3.4315
   -1.7593
   -3.1336
   -3.2985
   -1.7593
   -3.1336
   -1.7593
   -2.5448
   -3.2985
   -3.4898
   -1.7593
   -1.7593
   -2.5448
   -3.4315
   -2.5448
   -1.7593
   -1.7593
   -1.7593
   -6.9878
   -1.7593
   -1.7593
   -1.7593
   -2.5448
   -3.5613
   -3.2657
   -4.6728
   -2.5448
   -1.7593
   -3.1336
   -1.7593
   -3.4315
   -1.7593
   -3.4898
   -3.4315
   -2.5448
   -5.6496
   -3.1336
   -5.6627
   -1.7593
   -3.4315
   -3.1336
   -3.5613
   -3.4315
   -2.5448
   -2.5448
   -2.5448
   -3.5613
   -3.5613
   -3.5613
   -2.5448
   -2.5448
   -1.7593
   -3.2985
   -1.7593
   -1.7593
   -1.7593
   -3.2657
   -3.2985
   -2.5448
   -1.7593
   -1.7593
   -3.1336
   -2.5448
   -5.5688
   -1.7593
   -3.5613
   -2.5448
   -1.7593
   -4.2754
   -3.2657
   -3.9191
   -4.1945
   -4.1945
   -2.5448
   -3.5613
   -2.5448
   -1.7593
   -3.2985
   -6.6351
   -3.1336
   -6.3705
   -3.4898
   -3.1336
   -1.7593
   -3.2985
   -3.5613
   -5.1858
   -2.5448
   -4.8057
   -1.7593
   -1.7593
   -3.2657
   -7.3049
   -1.7593
   -3.4898
   -3.2657
   -1.7593
   -2.5448
   -1.7593
   -3.5613
   -2.5448
   -2.5448
   -1.7593
   -3.2657
   -1.7593
   -4.3468
   -8.2323
   -1.7593
   -3.2657
   -3.4315
   -2.5448
   -8.1834
   -1.7593
   -3.2657
   -2.5448
   -4.8641
   -4.9356
   -1.7593
   -5.1858
   -1.7593
   -4.2754
   -3.9191
   -2.5448
   -3.2657
   -3.2985
   -2.5448
   -3.4315
   -3.5613
   -1.7593
   -3.5613
   -4.1945
   -1.7593
   -3.1336
   -4.8057
   -2.5448
   -5.5688
   -3.2657
   -6.4420
   -3.2657
  -13.8308
   -1.7593
   -3.1336
   -5.6496
  -10.5224
   -5.2335
   -1.7593
   -1.7593
   -1.7593
   -7.1737
   -3.2985
   -3.4898
   -8.1834
   -4.8641
   -1.7593
   -3.1336
   -5.0677
   -8.1834
   -7.1737
   -2.5448
   -1.7593
   -5.2335
   -3.4315
   -2.5448
   -4.8641
   -3.4315
   -1.7593
   -4.8641
   -1.7593
   -3.4315
  -10.7015
   -2.5448
   -4.2754
   -4.3468
   -4.8641
   -4.8641
   -4.9356
   -3.4315
  -10.3783
   -3.2985
   -1.7593
   -2.5448
   -8.6134
   -2.5448
   -4.8641
   -6.7065
   -6.4033
   -3.1336
   -3.2985
   -6.3705
   -4.9045
   -6.3705
   -3.1336
   -4.9356
   -1.7593
   -6.3705
   -1.7593
   -4.8641
   -1.7593
   -4.9045
   -4.9045
   -5.7211
   -1.7593
   -4.8641
   -4.9356
   -1.7593
   -1.7593
   -3.4315
   -1.7593
   -2.5448
   -4.9045
  -11.6837
   -1.7593
   -4.8641
   -6.7630
   -4.9356
   -5.6496
   -5.7211
   -3.1336
   -3.2657
   -3.1336
   -1.7593
   -5.7211
   -5.6496
   -3.5613
   -4.1945
   -7.5623
   -7.6832
   -7.5623
   -1.7593
   -6.3705
   -4.8641
   -2.5448
   -6.4033
   -1.7593
   -8.8373
   -4.8641
   -4.9356
   -7.8008
   -3.5613
   -3.4898
   -3.2985
   -5.0290
   -9.1729
   -7.6337
   -4.2754
   -3.5613
   -1.7593
   -6.6173
   -1.7593
   -1.7593
   -3.1336
   -4.3468
   -9.6679
   -6.5363
  -10.4197
  -10.4197
  -13.9965
   -3.4898
   -1.7593
   -7.5380
   -7.9916
   -6.8580
  -13.0477
   -8.1253
   -8.2662
   -5.2825
   -1.7593
  -11.1062
   -5.9988
   -8.1253
  -13.7371
  -10.6363
  -11.5193
   -4.9801
   -8.4687
   -4.1945
   -4.1945
   -5.9775
   -8.1253
   -1.7593
  -11.5193
   -7.5039
   -8.4687
   -8.7221
   -9.1499
  -11.1596
   -5.5608
  -11.7090
  -10.5607
   -9.0120
   -7.2725
   -7.6710
   -3.2657
   -7.5468
  -11.7090
   -3.5613
   -9.8794

Timestamp 18-Jul-2025 22:26:47
pMakeSCFGModels: Making JAR3D model for motif group HL_38046.1, number 97 of 253
pMakeNodes starting loop:     a=7A0S|1|X|A|2188 B=7A0S|1|X|U|2196
  2 Basepair  2188 2196 AU cWW 
pMakeNodes adding hairpin:     a=7A0S|1|X|A|2189 B=7A0S|1|X|C|2195
    Right strand conserved insertion A2189 at right strand position 1
    Right strand conserved insertion A2190 at right strand position 2
    Right strand conserved insertion U2192 at right strand position 3
    Right strand conserved insertion C2193 at right strand position 4
    Right strand conserved insertion A2194 at right strand position 5
    Right strand conserved insertion C2195 at right strand position 6
  3 Hairpin   2189:2195 AAUCAC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2188 - U2196 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUCAC'
           RightLetter: ''
               Comment: ' // Hairpin node A2189:C2195'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_38046.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5024

Timestamp 18-Jul-2025 22:26:47
pMakeSCFGModels: Making JAR3D model for motif group HL_38168.1, number 98 of 253
pMakeNodes starting loop:     a=8J72|1|C|C|4 B=8J72|1|C|G|8
  2 Basepair     4    8 CG cWW 
pMakeNodes adding hairpin:     a=8J72|1|C|A|7 B=8J72|1|C|A|7
    Right strand conserved insertion A   7 at right strand position 1
  3 Hairpin   7:7 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C4 - G8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A7:A7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A7'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_38168.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.9890
   -7.9710

Timestamp 18-Jul-2025 22:26:47
pMakeSCFGModels: Making JAR3D model for motif group HL_38649.1, number 99 of 253
pMakeNodes starting loop:     a=3HHN|1|E|G|1 B=3HHN|1|E|C|12
  2 Basepair     1   12 GC cWW 
No need to probe because of interaction between a=3HHN|1|E|G|2 B=3HHN|1|E|A|11
  3 Basepair     2   11 GA tSH 
pMakeNodes adding hairpin:     a=3HHN|1|E|C|5 B=3HHN|1|E|U|10
    Right strand conserved insertion C   5 at right strand position 1
    Right strand conserved insertion A   6 at right strand position 2
    Right strand conserved insertion C   7 at right strand position 3
    Right strand conserved insertion U   8 at right strand position 4
    Right strand conserved insertion A   9 at right strand position 5
    Right strand conserved insertion U  10 at right strand position 6
  4 Hairpin   5:10 CACUAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1 - C12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2 - A11 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CACUAU'
           RightLetter: ''
               Comment: ' // Hairpin node C5:U10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  8
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_38649.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1131
  -10.1131
  -14.1174
  -15.2238
  -13.9722

Timestamp 18-Jul-2025 22:26:47
pMakeSCFGModels: Making JAR3D model for motif group HL_38808.1, number 100 of 253
pMakeNodes starting loop:     a=4QEI|1|C|A|31 B=4QEI|1|C|U|39
  2 Basepair    31   39 AU cWW 
pMakeNodes adding hairpin:     a=4QEI|1|C|U|32 B=4QEI|1|C|U|38
  3 Hairpin   32:38 UU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UU'
           RightLetter: ''
               Comment: ' // Hairpin node U32:U38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction U32 - U38 cWW '}
      JunctionDeletion: []
          InterIndices: [2 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_38808.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9167
   -8.9167
  -11.5827
  -12.5733

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_38901.2, number 101 of 253
pMakeNodes starting loop:     a=3AM1|1|B|U|18 B=3AM1|1|B|A|23
  2 Basepair    18   23 UA cWW 
pMakeNodes adding hairpin:     a=3AM1|1|B|U|19 B=3AM1|1|B|U|22
    Right strand conserved insertion U  19 at right strand position 1
  3 Hairpin   19:22 UGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U18 - A23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGU'
           RightLetter: ''
               Comment: ' // Hairpin node U19:U22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G21 - U22 cSH '  ' // Hairpin conserved non-basepairing position U19'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_38901.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0358
   -4.9741
   -4.8846
   -4.8846
   -6.6480
   -6.8509
   -7.3958

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_39243.1, number 102 of 253
pMakeNodes starting loop:     a=3BT7|1|D|G|53 B=3BT7|1|D|C|61
  2 Basepair    53   61 GC cWW 
pMakeNodes adding hairpin:     a=3BT7|1|D|U|55 B=3BT7|1|D|A|58
    Right strand conserved insertion U  55 at right strand position 1
    Right strand conserved insertion C  56 at right strand position 2
    Right strand conserved insertion G  57 at right strand position 3
    Right strand conserved insertion A  58 at right strand position 4
  3 Hairpin   55:58 UCGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G53 - C61 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCGA'
           RightLetter: ''
               Comment: ' // Hairpin node U55:A58'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_39243.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9039
   -7.0068

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_40252.4, number 103 of 253
pMakeNodes starting loop:     a=4JYZ|1|B|C|912 B=4JYZ|1|B|G|923
  2 Basepair   912  923 CG cWW 
No need to probe because of interaction between a=4JYZ|1|B|A|913 B=4JYZ|1|B|A|922
  3 Basepair   913  922 AA tSH 
No need to probe because of interaction between a=4JYZ|1|B|A|914 B=4JYZ|1|B|A|921
  4 Basepair   914  921 AA cWS 
pMakeNodes adding hairpin:     a=4JYZ|1|B|G|915 B=4JYZ|1|B|G|915
    Right strand conserved insertion G 915 at right strand position 1
  5 Hairpin   915:915 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C912 - G923 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 A913 - A922 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A914 - A921 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G915:G915'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G915'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_40252.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2529
  -12.1995
  -13.4101
  -12.1995
  -10.2529

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_41464.2, number 104 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|G|686 B=8P9A|1|AR|C|694
  2 Basepair   686  694 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|U|687 B=8P9A|1|AR|A|693
    Insertion on left  8P9A|1|AR|U|687
    Insertion on right 8P9A|1|AR|A|693
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|688 interacts with 8P9A|1|AR|A|692
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|692 interacts with 8P9A|1|AR|G|688
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|692 interacts with 8P9A|1|AR|G|688
pMakeNodes probed for insert:  a=8P9A|1|AR|G|688 B=8P9A|1|AR|A|692
  3 Basepair   688  692 GA tSH 
pMakeNodes adding hairpin:     a=8P9A|1|AR|A|690 B=8P9A|1|AR|A|690
    Right strand conserved insertion A 690 at right strand position 1
  4 Hairpin   690:690 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|687
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|A|691
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'AC'
               Comment: ' // Basepair G686 - C694 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|687'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'A'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A690'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|A|691'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G688 - A692 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A690:A690'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A690'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_41464.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0258
   -8.0258
  -13.1319
  -12.9710

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_41543.1, number 105 of 253
pMakeNodes starting loop:     a=7MKY|1|A|G|9 B=7MKY|1|A|C|20
  2 Basepair     9   20 GC cWW 
No need to probe because of interaction between a=7MKY|1|A|U|10 B=7MKY|1|A|G|18
  3 Basepair    10   18 UG bif 
pMakeNodes probe for inserts:  a=7MKY|1|A|G|11 B=7MKY|1|A|C|17
    Insertion on left  7MKY|1|A|G|11
    Insertion on right 7MKY|1|A|C|17
    Insertion on right 7MKY|1|A|C|16
pMakeNodesProbeForInsertions:  a 7MKY|1|A|A|13 interacts with 7MKY|1|A|C|15
pMakeNodesProbeForInsertions:  B 7MKY|1|A|C|15 interacts with 7MKY|1|A|A|13
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7MKY|1|A|C|15 interacts with 7MKY|1|A|A|13
pMakeNodes probed for insert:  a=7MKY|1|A|A|13 B=7MKY|1|A|C|15
  4 Basepair    13   15 AC cSH 
pMakeNodes adding hairpin:     a=7MKY|1|A|G|14 B=7MKY|1|A|G|14
    Right strand conserved insertion G  14 at right strand position 1
  5 Hairpin   14:14 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7MKY|1|A|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7MKY|1|A|C|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7MKY|1|A|C|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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G9 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'CCG'
               Comment: ' // Basepair U10 - G18 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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 7MKY|1|A|G|11'
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G14'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 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 7MKY|1|A|C|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7MKY|1|A|C|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A13 - C15 cSH '
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

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

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G14:G14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G14'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  5 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_41543.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0166
   -8.8746

Timestamp 18-Jul-2025 22:26:48
pMakeSCFGModels: Making JAR3D model for motif group HL_41902.1, number 106 of 253
pMakeNodes starting loop:     a=6QN3|1|B|U|32 B=6QN3|1|B|A|43
  2 Basepair    32   43 UA cWW 
No need to probe because of interaction between a=6QN3|1|B|A|33 B=6QN3|1|B|G|42
  3 Basepair    33   42 AG cWW 
pMakeNodes probe for inserts:  a=6QN3|1|B|G|35 B=6QN3|1|B|G|41
    Insertion on right 6QN3|1|B|G|41
    Insertion on right 6QN3|1|B|G|40
pMakeNodesProbeForInsertions:  a 6QN3|1|B|G|35 interacts with 6QN3|1|B|A|37
    Insertion        39 C
    Insertion        38 A
pMakeNodes probed for insert:  a=6QN3|1|B|G|35 B=6QN3|1|B|A|37
  4 Basepair    35   37 GA cWH 
pMakeNodes adding hairpin:     a=6QN3|1|B|G|36 B=6QN3|1|B|G|36
    Right strand conserved insertion G  36 at right strand position 1
  5 Hairpin   36:36 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QN3|1|B|G|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QN3|1|B|C|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QN3|1|B|A|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QN3|1|B|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: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U32 - A43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              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: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'ACGGG'
               Comment: ' // Basepair A33 - G42 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QN3|1|B|G|40'
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G36'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QN3|1|B|C|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             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: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             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 6QN3|1|B|A|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QN3|1|B|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G35 - A37 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G36:G36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G36'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  3 Right  6
pMakeMotifModelFromSSF:  10     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:  11   Initial Left  3 Right  5
pMakeMotifModelFromSSF:  12  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:  13   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_41902.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6206
   -6.6206

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_42046.2, number 107 of 253
pMakeNodes starting loop:     a=5F5H|1|C|C|8 B=5F5H|1|C|G|15
  2 Basepair     8   15 CG cWW 
No need to probe because of interaction between a=5F5H|1|C|G|9 B=5F5H|1|C|A|14
  3 Basepair     9   14 GA tSS 
pMakeNodes adding hairpin:     a=5F5H|1|C|U|10 B=5F5H|1|C|U|13
    Right strand conserved insertion U  10 at right strand position 1
    Right strand conserved insertion U  11 at right strand position 2
    Right strand conserved insertion U  13 at right strand position 3
  4 Hairpin   10:13 UUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C8 - G15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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 G9 - A14 tSS '
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUU'
           RightLetter: ''
               Comment: ' // Hairpin node U10:U13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_42046.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.6378
   -4.6378
   -4.6378
   -4.6378
   -6.2105

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_42998.2, number 108 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|978 B=5J7L|1|DA|C|985
  2 Basepair   978  985 GC cWW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|979 B=5J7L|1|DA|A|984
    Right strand conserved insertion A 979 at right strand position 1
    Right strand conserved insertion A 980 at right strand position 2
    Right strand conserved insertion A 981 at right strand position 3
    Right strand conserved insertion C 982 at right strand position 4
    Right strand conserved insertion A 983 at right strand position 5
    Right strand conserved insertion A 984 at right strand position 6
  3 Hairpin   979:984 AAACAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G978 - C985 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAACAA'
           RightLetter: ''
               Comment: ' // Hairpin node A979:A984'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_42998.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.9827
   -4.4491
   -2.9827
   -2.7314
   -2.7314
   -4.4153
   -4.4153

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_43517.1, number 109 of 253
pMakeNodes starting loop:     a=2OZB|1|C|G|35 B=2OZB|1|C|C|41
  2 Basepair    35   41 GC cWW 
pMakeNodes adding hairpin:     a=2OZB|1|C|U|36 B=2OZB|1|C|A|39
    Right strand conserved insertion U  36 at right strand position 1
    Right strand conserved insertion U  37 at right strand position 2
    Right strand conserved insertion A  39 at right strand position 3
  3 Hairpin   36:39 UUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G35 - C41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUA'
           RightLetter: ''
               Comment: ' // Hairpin node U36:A39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_43517.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0386
   -4.6523

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_45175.1, number 110 of 253
pMakeNodes starting loop:     a=3TUP|1|T|C|13 B=3TUP|1|T|G|22
  2 Basepair    13   22 CG cWW 
No need to probe because of interaction between a=3TUP|1|T|A|14 B=3TUP|1|T|A|21
  3 Basepair    14   21 AA cWS 
pMakeNodes adding hairpin:     a=3TUP|1|T|G|15 B=3TUP|1|T|U|16
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion U  16 at right strand position 2
  4 Hairpin   15:16 GU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A21 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: ''
               Comment: ' // Hairpin node G15:U16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G15'  ' // Hairpin conserved non-basepairing position U16'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_45175.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8600
   -8.8155
   -7.1333
   -8.2319
  -10.7059

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_45785.1, number 111 of 253
pMakeNodes starting loop:     a=8FZA|1|A|G|5 B=8FZA|1|A|C|15
  2 Basepair     5   15 GC cWW 
pMakeNodes probe for inserts:  a=8FZA|1|A|U|6 B=8FZA|1|A|C|14
    Insertion on left  8FZA|1|A|U|6
    Insertion on left  8FZA|1|A|U|7
    Insertion on right 8FZA|1|A|C|14
pMakeNodesProbeForInsertions:  a 8FZA|1|A|C|8 interacts with 8FZA|1|A|C|10
pMakeNodesProbeForInsertions:  B 8FZA|1|A|A|13 interacts with 8FZA|1|A|U|11
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8FZA|1|A|A|13 interacts with 8FZA|1|A|U|11
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodes probed for insert:  a=8FZA|1|A|C|8 B=8FZA|1|A|A|13
pMakeNodes checking on making a cluster a=8FZA|1|A|C|8 B=8FZA|1|A|A|13
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 4 to 6 and then 7 to 8
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=8FZA|1|A|C|8 B=8FZA|1|A|A|13
    Right strand conserved insertion C   9 at right strand position 2
  3 Hairpin   8:13 CCCUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  4 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8FZA|1|A|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8FZA|1|A|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8FZA|1|A|A|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUU'
           RightLetter: 'CC'
               Comment: ' // Basepair G5 - C15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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 8FZA|1|A|U|6'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              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 8FZA|1|A|U|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8FZA|1|A|A|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCUA'
           RightLetter: ''
               Comment: ' // Hairpin node C8:A13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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   Hairpin Left  4 Right  8
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: HL_45785.1 allow insertions from initial node 8?
ans =

     1


ans =

    0.2500    0.2500    0.2500    0.2500


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_45785.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5157
   -6.5157

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_46501.1, number 112 of 253
pMakeNodes starting loop:     a=3DD2|1|B|CFL|11 B=3DD2|1|B|G|16
  2 Basepair    11   16 CG cWW 
No need to probe because of interaction between a=3DD2|1|B|UFT|12 B=3DD2|1|B|A|15
  3 Basepair    12   15 UA cWS 
pMakeNodes adding hairpin:     a=3DD2|1|B|G|13 B=3DD2|1|B|G|13
    Right strand conserved insertion G  13 at right strand position 1
  4 Hairpin   13:13 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C11 - G16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U12 - A15 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G13:G13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G13'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_46501.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0171
   -4.3240

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_47732.1, number 113 of 253
pMakeNodes starting loop:     a=4Z7K|1|C|C|17 B=4Z7K|1|C|G|28
  2 Basepair    17   28 CG cWW 
pMakeNodes adding hairpin:     a=4Z7K|1|C|A|18 B=4Z7K|1|C|A|27
    Right strand conserved insertion A  18 at right strand position 1
    Right strand conserved insertion A  19 at right strand position 2
    Right strand conserved insertion A  21 at right strand position 3
    Right strand conserved insertion C  25 at right strand position 4
    Right strand conserved insertion A  26 at right strand position 5
    Right strand conserved insertion A  27 at right strand position 6
  3 Hairpin   18:27 AAACAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C17 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAACAA'
           RightLetter: ''
               Comment: ' // Hairpin node A18:A27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_47732.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8596
   -6.8596

Timestamp 18-Jul-2025 22:26:49
pMakeSCFGModels: Making JAR3D model for motif group HL_47787.2, number 114 of 253
pMakeNodes starting loop:     a=4V9F|1|9|C|37 B=4V9F|1|9|G|43
  2 Basepair    37   43 CG cWW 
pMakeNodes adding hairpin:     a=4V9F|1|9|A|38 B=4V9F|1|9|C|42
    Right strand conserved insertion A  38 at right strand position 1
    Right strand conserved insertion U  39 at right strand position 2
    Right strand conserved insertion C  41 at right strand position 3
    Right strand conserved insertion C  42 at right strand position 4
  3 Hairpin   38:42 AUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C37 - G43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUCC'
           RightLetter: ''
               Comment: ' // Hairpin node A38:C42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_47787.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8232
   -4.8232
   -3.7245
   -3.7245
   -5.4778
   -3.7245
   -4.3792
   -3.7245
  -10.8023
  -10.4576

Timestamp 18-Jul-2025 22:26:50
pMakeSCFGModels: Making JAR3D model for motif group HL_47854.1, number 115 of 253
pMakeNodes starting loop:     a=4Z0C|1|C|G|4 B=4Z0C|1|C|C|11
  2 Basepair     4   11 GC cWW 
pMakeNodes adding hairpin:     a=4Z0C|1|C|A|5 B=4Z0C|1|C|A|9
    Right strand conserved insertion A   5 at right strand position 1
    Right strand conserved insertion A   7 at right strand position 2
    Right strand conserved insertion G   8 at right strand position 3
    Right strand conserved insertion A   9 at right strand position 4
  3 Hairpin   5:9 AAGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - C11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGA'
           RightLetter: ''
               Comment: ' // Hairpin node A5:A9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_47854.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.9116

Timestamp 18-Jul-2025 22:26:50
pMakeSCFGModels: Making JAR3D model for motif group HL_48417.5, number 116 of 253
pMakeNodes starting loop:     a=6D12|1|C|C|328 B=6D12|1|C|G|334
  2 Basepair   328  334 CG cWW 
pMakeNodes adding hairpin:     a=6D12|1|C|A|329 B=6D12|1|C|U|330
    Right strand conserved insertion A 329 at right strand position 1
    Right strand conserved insertion U 330 at right strand position 2
  3 Hairpin   329:330 AU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C328 - G334 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AU'
           RightLetter: ''
               Comment: ' // Hairpin node A329:U330'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A329'  ' // Hairpin conserved non-basepairing position U330'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_48417.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8613
   -8.1208
   -7.8613
   -9.0248
   -7.0184
   -7.0184
   -8.5240
   -7.3628
   -8.0256
  -14.3895
   -7.3628
   -7.9739
   -8.6942
   -8.8739
  -12.4169
   -8.8739
   -7.9621
   -8.2776
   -7.9339
  -10.6147
  -13.6122
   -7.1705
   -5.9356
   -9.0112
  -10.5841
   -7.9035

Timestamp 18-Jul-2025 22:26:50
pMakeSCFGModels: Making JAR3D model for motif group HL_48778.2, number 117 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|C|1792 B=8P9A|1|AR|G|1796
  2 Basepair  1792 1796 CG cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|U|1795 B=8P9A|1|AR|U|1795
    Right strand conserved insertion U1795 at right strand position 1
  3 Hairpin   1795:1795 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C1792 - G1796 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U1795:U1795'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U1795'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_48778.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4979
   -3.2002
   -5.9571
   -5.2416
   -3.2002
   -3.2002
   -3.2002
   -3.2002
   -6.2004
   -6.3278
   -6.4422
   -4.3863
   -6.2896
   -6.2611
   -3.2002
   -3.2002
   -3.2002
   -3.2668
   -3.2002
   -6.2004
   -5.4299
   -6.4422
   -3.2002
   -5.2527
   -6.1294
   -4.3863
   -3.2002
   -4.2481
   -7.0722
   -5.4849
   -3.3383
   -5.2527
   -4.2481
   -5.5048
   -4.3819
  -10.4510
   -7.0008
   -4.4534
   -3.2668
   -3.2668
   -4.3819
   -6.3993
  -10.3126
   -5.4299
   -5.5980
   -4.3819

Timestamp 18-Jul-2025 22:26:50
pMakeSCFGModels: Making JAR3D model for motif group HL_49922.4, number 118 of 253
pMakeNodes starting loop:     a=6QCW|1|V|U|3 B=6QCW|1|V|A|8
  2 Basepair     3    8 UA cWW 
No need to probe because of interaction between a=6QCW|1|V|A|4 B=6QCW|1|V|A|7
  3 Basepair     4    7 AA cSW 
pMakeNodes adding hairpin:     a=6QCW|1|V|G|5 B=6QCW|1|V|G|5
    Right strand conserved insertion G   5 at right strand position 1
  4 Hairpin   5:5 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U3 - A8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A4 - A7 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G5:G5'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G5'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_49922.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.0597
   -4.0597
   -4.0597
   -4.0597
   -4.0597
   -4.0597
   -7.6476
   -7.6476
   -8.6809
   -8.5792

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_49941.1, number 119 of 253
pMakeNodes starting loop:     a=1FFY|1|T|C|13 B=1FFY|1|T|G|22
  2 Basepair    13   22 CG cWW 
No need to probe because of interaction between a=1FFY|1|T|A|14 B=1FFY|1|T|A|21|||A
  3 Basepair    14  21A AA cWS 
pMakeNodes adding hairpin:     a=1FFY|1|T|G|15 B=1FFY|1|T|U|17
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion G  16 at right strand position 2
    Right strand conserved insertion U  17 at right strand position 3
  4 Hairpin   15:17 GGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A21A cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGU'
           RightLetter: ''
               Comment: ' // Hairpin node G15:U17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_49941.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0731
   -8.0731
   -9.5394
   -9.9368

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_50006.2, number 120 of 253
pMakeNodes starting loop:     a=5HR7|1|D|C|31 B=5HR7|1|D|G|39
  2 Basepair    31   39 CG cWW 
pMakeNodes adding hairpin:     a=5HR7|1|D|C|32 B=5HR7|1|D|C|36
  3 Hairpin   32:36 CC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: ''
               Comment: ' // Hairpin node C32:C36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction C32 - C36 tSW '}
      JunctionDeletion: []
          InterIndices: [2 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50006.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3285
   -8.3285
   -9.0098
   -8.2327
  -12.9544

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_50318.1, number 121 of 253
pMakeNodes starting loop:     a=4WF9|1|X|C|587 B=4WF9|1|X|G|594
  2 Basepair   587  594 CG cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|G|588 B=4WF9|1|X|A|592
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|588 interacts with 4WF9|1|X|U|589
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|592 interacts with 4WF9|1|X|U|589
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|592 interacts with 4WF9|1|X|U|589
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodes probed for insert:  a=4WF9|1|X|G|588 B=4WF9|1|X|A|592
pMakeNodes checking on making a cluster a=4WF9|1|X|G|588 B=4WF9|1|X|A|592
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 3 and then 5 to 5
aa is 3 bb is 5
  3 Cluster   4WF9|1|X|G|588:4WF9|1|X|U|589 4WF9|1|X|A|592:4WF9|1|X|A|592
    LR Inter  4WF9|1|X|U|589 4WF9|1|X|A|592 cWH 
    LL Inter  4WF9|1|X|G|588 4WF9|1|X|U|589 cSH 
pMakeNodesCluster a=4 B=4 at the end
pMakeNodesCluster a=4 B=4 at the end
pMakeNodes adding hairpin:     a=4WF9|1|X|A|591 B=4WF9|1|X|A|591
    Right strand conserved insertion A 591 at right strand position 1
  4 Hairpin   591:591 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C587 - G594 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4WF9|1|X|G|588:4WF9|1|X|U|589 and 4WF9|1|X|A|592:4WF9|1|X|A|592'
              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: 0.3154

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A591:A591'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A591'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: HL_50318.1 allow insertions from initial node 4?
ans =

    0.0454    0.9070    0.0454    0.0023


ans =

    0.1667    0.1667    0.1667    0.5000         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50318.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0162

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_50418.1, number 122 of 253
pMakeNodes starting loop:     a=7JRS|1|A|G|63 B=7JRS|1|A|C|73
  2 Basepair    63   73 GC cWW 
pMakeNodes adding hairpin:     a=7JRS|1|A|A|64 B=7JRS|1|A|A|72
    Right strand conserved insertion A  64 at right strand position 1
    Right strand conserved insertion A  65 at right strand position 2
    Right strand conserved insertion G  66 at right strand position 3
    Right strand conserved insertion C  67 at right strand position 4
    Right strand conserved insertion A  68 at right strand position 5
    Right strand conserved insertion G  69 at right strand position 6
    Right strand conserved insertion G  70 at right strand position 7
    Right strand conserved insertion C  71 at right strand position 8
    Right strand conserved insertion A  72 at right strand position 9
  3 Hairpin   64:72 AAGCAGGCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G63 - C73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGCAGGCA'
           RightLetter: ''
               Comment: ' // Hairpin node A64:A72'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50418.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9410
   -8.9410
  -11.5485

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_50537.6, number 123 of 253
pMakeNodes starting loop:     a=4WJ4|1|B|A|31 B=4WJ4|1|B|U|39
  2 Basepair    31   39 AU cWW 
pMakeNodes adding hairpin:     a=4WJ4|1|B|C|32 B=4WJ4|1|B|A|38
    Right strand conserved insertion C  32 at right strand position 1
    Right strand conserved insertion U  35 at right strand position 2
    Right strand conserved insertion A  38 at right strand position 3
  3 Hairpin   32:38 CUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUA'
           RightLetter: ''
               Comment: ' // Hairpin node C32:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50537.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0931
   -8.0828
  -10.4137
   -9.9237

Timestamp 18-Jul-2025 22:26:51
pMakeSCFGModels: Making JAR3D model for motif group HL_50779.4, number 124 of 253
pMakeNodes starting loop:     a=4LFB|1|A|G|963 B=4LFB|1|A|C|972
  2 Basepair   963  972 GC cWW 
pMakeNodes adding hairpin:     a=4LFB|1|A|A|964 B=4LFB|1|A|C|970
    Right strand conserved insertion A 964 at right strand position 1
    Right strand conserved insertion A 965 at right strand position 2
    Right strand conserved insertion G 966 at right strand position 3
    Right strand conserved insertion C 967 at right strand position 4
    Right strand conserved insertion A 968 at right strand position 5
    Right strand conserved insertion A 969 at right strand position 6
    Right strand conserved insertion C 970 at right strand position 7
  3 Hairpin   964:970 AAGCAAC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G963 - C972 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGCAAC'
           RightLetter: ''
               Comment: ' // Hairpin node A964:C970'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50779.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5842
   -5.5842
   -5.0734
   -5.0734

Timestamp 18-Jul-2025 22:26:52
pMakeSCFGModels: Making JAR3D model for motif group HL_50851.1, number 125 of 253
pMakeNodes starting loop:     a=8UTG|1|B|G|8 B=8UTG|1|B|U|19
pMakeNodes checking on making a cluster a=8UTG|1|B|G|8 B=8UTG|1|B|U|19
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 9
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=8UTG|1|B|G|8 B=8UTG|1|B|U|19
  2 Hairpin   8:19 GGGGGUGGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Hairpin Left  1 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: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [1 1 1 1 1 1 1 1 1]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Hairpin'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGGUGGU'
           RightLetter: ''
               Comment: ' // Hairpin node G8:U19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [1 2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
              NormCons: 0.0700

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Hairpin Left  1 Right  9
pNextNodeJunction: Found a hairpin at node 2
pNextNodeJunction: Found a hairpin at node 2

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50851.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5507

Timestamp 18-Jul-2025 22:26:52
pMakeSCFGModels: Making JAR3D model for motif group HL_50860.2, number 126 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|2304 B=5J7L|1|DA|U|2312
  2 Basepair  2304 2312 GU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|2305 B=5J7L|1|DA|A|2311
    Insertion on left  5J7L|1|DA|U|2305
    Insertion on left  5J7L|1|DA|C|2306
    Insertion on left  5J7L|1|DA|G|2307
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|2308 interacts with 5J7L|1|DA|A|2311
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2311 interacts with 5J7L|1|DA|G|2308
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2311 interacts with 5J7L|1|DA|G|2308
pMakeNodes probed for insert:  a=5J7L|1|DA|G|2308 B=5J7L|1|DA|A|2311
  3 Basepair  2308 2311 GA cWH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|2309 B=5J7L|1|DA|C|2310
    Right strand conserved insertion A2309 at right strand position 1
    Right strand conserved insertion C2310 at right strand position 2
  4 Hairpin   2309:2310 AC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2305
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2306
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2307
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUCG'
           RightLetter: 'U'
               Comment: ' // Basepair G2304 - U2312 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|U|2305'
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'AC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2309'  ' // Hairpin conserved non-basepairing position C2310'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2306'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2307'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2308 - A2311 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

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

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: ''
               Comment: ' // Hairpin node A2309:C2310'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A2309'  ' // Hairpin conserved non-basepairing position C2310'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_50860.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3188
   -6.7443
   -4.6324
   -4.8976
   -4.8976
   -6.5195

Timestamp 18-Jul-2025 22:26:52
pMakeSCFGModels: Making JAR3D model for motif group HL_51447.1, number 127 of 253
pMakeNodes starting loop:     a=8KAJ|1|I|C|86 B=8KAJ|1|I|G|92
  2 Basepair    86   92 CG cWW 
pMakeNodes adding hairpin:     a=8KAJ|1|I|G|87 B=8KAJ|1|I|C|91
    Right strand conserved insertion G  87 at right strand position 1
    Right strand conserved insertion A  88 at right strand position 2
    Right strand conserved insertion G  89 at right strand position 3
    Right strand conserved insertion U  90 at right strand position 4
    Right strand conserved insertion C  91 at right strand position 5
  3 Hairpin   87:91 GAGUC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C86 - G92 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAGUC'
           RightLetter: ''
               Comment: ' // Hairpin node G87:C91'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_51447.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.9961

Timestamp 18-Jul-2025 22:26:52
pMakeSCFGModels: Making JAR3D model for motif group HL_51921.1, number 128 of 253
pMakeNodes starting loop:     a=8CRE|1|4|U|69 B=8CRE|1|4|A|89
  2 Basepair    69   89 UA cWW 
No need to probe because of interaction between a=8CRE|1|4|G|70 B=8CRE|1|4|A|88
  3 Basepair    70   88 GA tSH 
No need to probe because of interaction between a=8CRE|1|4|A|71 B=8CRE|1|4|G|87
pMakeNodes checking on making a cluster a=8CRE|1|4|A|71 B=8CRE|1|4|G|87
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 3 and then 13 to 16
aa is 3 bb is 13
  4 Cluster   8CRE|1|4|A|71:8CRE|1|4|A|71 8CRE|1|4|U|82:8CRE|1|4|G|87
    LR Inter  8CRE|1|4|A|71 8CRE|1|4|U|82 tSS 
    LR Inter  8CRE|1|4|A|71 8CRE|1|4|G|87 tHS 
    Right strand conserved insertion 8CRE|1|4|U|83 at position 2
    Right strand conserved insertion 8CRE|1|4|G|85 at position 3
pMakeNodesCluster a=4 B=12 at the end
pMakeNodesCluster a=4 B=12 at the end
pMakeNodes probe for inserts:  a=8CRE|1|4|A|72 B=8CRE|1|4|A|81
    Insertion on left  8CRE|1|4|A|72
    Insertion on right 8CRE|1|4|A|81
    Insertion on right 8CRE|1|4|A|79
pMakeNodesProbeForInsertions:  a 8CRE|1|4|U|73 interacts with 8CRE|1|4|G|78
pMakeNodesProbeForInsertions:  B 8CRE|1|4|G|78 interacts with 8CRE|1|4|U|73
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8CRE|1|4|G|78 interacts with 8CRE|1|4|U|73
  5 Initial     72 (1 insertion) and   81 (2 insertion)
pMakeNodes probed for insert:  a=8CRE|1|4|U|73 B=8CRE|1|4|G|78
  6 Basepair    73   78 UG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|4|U|74 B=8CRE|1|4|A|77
    Right strand conserved insertion U  74 at right strand position 1
    Right strand conserved insertion G  75 at right strand position 2
    Right strand conserved insertion C  76 at right strand position 3
    Right strand conserved insertion A  77 at right strand position 4
  7 Hairpin   74:77 UGCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 13 14 15 16
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|4|A|72
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|4|U|80
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|4|A|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U69 - A89 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G70 - A88 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: 3
            RightIndex: [13 14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UUGG'
               Comment: ' // Cluster node 8CRE|1|4|A|71:8CRE|1|4|A|71 and 8CRE|1|4|U|82:8CRE|1|4|G|87'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3]
              NormCons: 0.4347

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AA'
               Comment: ' // Initial node 8CRE|1|4|A|72 - 8CRE|1|4|A|81 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 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 8CRE|1|4|A|72'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 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: 'UGCA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 8

ans = 

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

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|4|U|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|4|A|79'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U73 - 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGCA'
           RightLetter: ''
               Comment: ' // Hairpin node U74:A77'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 13 14 15 16
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:   9   Initial Left  5 Right 11
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  9
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_51921.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.2799
  -12.2799

Timestamp 18-Jul-2025 22:26:52
pMakeSCFGModels: Making JAR3D model for motif group HL_52953.3, number 129 of 253
pMakeNodes starting loop:     a=4XWF|1|A|G|24 B=4XWF|1|A|C|29
  2 Basepair    24   29 GC cWW 
pMakeNodes adding hairpin:     a=4XWF|1|A|G|25 B=4XWF|1|A|A|28
    Right strand conserved insertion G  25 at right strand position 1
    Right strand conserved insertion A  26 at right strand position 2
    Right strand conserved insertion A  27 at right strand position 3
    Right strand conserved insertion A  28 at right strand position 4
  3 Hairpin   25:28 GAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G24 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAAA'
           RightLetter: ''
               Comment: ' // Hairpin node G25:A28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_52953.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2010
   -4.2010
   -6.2864
   -5.6255
   -5.7337
   -5.7337
   -4.2010
   -5.1147
   -5.1147

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_53454.2, number 130 of 253
pMakeNodes starting loop:     a=7A0S|1|X|C|2383 B=7A0S|1|X|G|2392
  2 Basepair  2383 2392 CG cWW 
No need to probe because of interaction between a=7A0S|1|X|G|2384 B=7A0S|1|X|A|2391
  3 Basepair  2384 2391 GA tSH 
pMakeNodes adding hairpin:     a=7A0S|1|X|G|2386 B=7A0S|1|X|A|2390
    Right strand conserved insertion G2386 at right strand position 1
    Right strand conserved insertion U2387 at right strand position 2
    Right strand conserved insertion G2388 at right strand position 3
    Right strand conserved insertion G2389 at right strand position 4
    Right strand conserved insertion A2390 at right strand position 5
  4 Hairpin   2386:2390 GUGGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2383 - G2392 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2384 - A2391 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUGGA'
           RightLetter: ''
               Comment: ' // Hairpin node G2386:A2390'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_53454.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1449
   -8.9840
   -8.1449
   -9.5371
  -14.8564
  -14.8564

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_53504.3, number 131 of 253
pMakeNodes starting loop:     a=1NBS|1|B|C|96 B=1NBS|1|B|G|107
  2 Basepair    96  107 CG cWW 
No need to probe because of interaction between a=1NBS|1|B|G|97 B=1NBS|1|B|A|106
  3 Basepair    97  106 GA tSH 
pMakeNodes probe for inserts:  a=1NBS|1|B|A|98 B=1NBS|1|B|A|105
    Insertion on left  1NBS|1|B|A|98
pMakeNodesProbeForInsertions:  a 1NBS|1|B|G|100 interacts with 1NBS|1|B|A|105
pMakeNodesProbeForInsertions:  B 1NBS|1|B|A|105 interacts with 1NBS|1|B|G|100
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1NBS|1|B|A|105 interacts with 1NBS|1|B|G|100
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1NBS|1|B|G|100 B=1NBS|1|B|A|105
pMakeNodes checking on making a cluster a=1NBS|1|B|G|100 B=1NBS|1|B|A|105
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 0
pMakeNodesCluster: Cluster goes from 4 to 6 and then 8 to 8
aa is 6 bb is 8
  4 Cluster   1NBS|1|B|G|100:1NBS|1|B|A|103 1NBS|1|B|A|105:1NBS|1|B|A|105
    LR Inter  1NBS|1|B|G|100 1NBS|1|B|A|105 tHW 
    LL Inter  1NBS|1|B|G|100 1NBS|1|B|A|103 tSW 
    Left  strand conserved insertion 1NBS|1|B|C|102 at position 2
pMakeNodesCluster a=7 B=7 at the end
pMakeNodesCluster a=7 B=7 at the end
pMakeNodes adding hairpin:     a=1NBS|1|B|U|104 B=1NBS|1|B|U|104
    Right strand conserved insertion U 104 at right strand position 1
  5 Hairpin   104:104 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Cluster Left  4  5  6 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  7 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 1NBS|1|B|A|98
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C96 - G107 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'A'
               Comment: ' // Basepair G97 - A106 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NBS|1|B|A|98'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 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: 0.2641

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [4 5 6]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: 'A'
               Comment: ' // Cluster node 1NBS|1|B|G|100:1NBS|1|B|A|103 and 1NBS|1|B|A|105:1NBS|1|B|A|105'
              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: 0.2641

Node 7

ans = 

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

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

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U104:U104'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 7
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U104'}
      JunctionDeletion: []
          InterIndices: [7 7]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6   Cluster Left  4  5  6 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  7 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  7
pNextNodeJunction: Found a hairpin at node 8
pUpdateModelWithSSF: HL_53504.3 allow insertions from initial node 7?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_53504.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9934
   -9.3433

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_53890.2, number 132 of 253
pMakeNodes starting loop:     a=7A0S|1|X|A|202 B=7A0S|1|X|U|207
  2 Basepair   202  207 AU cWW 
pMakeNodes adding hairpin:     a=7A0S|1|X|G|203 B=7A0S|1|X|A|205
    Right strand conserved insertion G 203 at right strand position 1
    Right strand conserved insertion A 204 at right strand position 2
    Right strand conserved insertion A 205 at right strand position 3
  3 Hairpin   203:205 GAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 A202 - U207 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: ''
               Comment: ' // Hairpin node G203:A205'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_53890.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1324
   -6.5001
   -6.1324
   -7.1505
   -7.7383
   -6.6303
   -8.5230
   -8.6097
   -8.5230
   -8.1221
   -8.6041
   -8.8319
   -9.5913
   -8.3117
   -9.5913

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_55195.3, number 133 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|U|826 B=9DFE|1|1A|G|831
  2 Basepair   826  831 UG cWW 
pMakeNodes adding hairpin:     a=9DFE|1|1A|A|829 B=9DFE|1|1A|A|829
    Right strand conserved insertion A 829 at right strand position 1
  3 Hairpin   829:829 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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: 'G'
               Comment: ' // Basepair U826 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A829:A829'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A829'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_55195.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.0127
   -3.0127
   -3.0127
   -3.9000
   -6.7332
   -6.4978

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_55305.1, number 134 of 253
pMakeNodes starting loop:     a=3TS2|1|V|U|5 B=3TS2|1|V|A|16
  2 Basepair     5   16 UA cWW 
pMakeNodes adding hairpin:     a=3TS2|1|V|C|6 B=3TS2|1|V|C|14
    Right strand conserved insertion C   6 at right strand position 1
    Right strand conserved insertion A  13 at right strand position 2
    Right strand conserved insertion C  14 at right strand position 3
  3 Hairpin   6:14 CAC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U5 - A16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAC'
           RightLetter: ''
               Comment: ' // Hairpin node C6:C14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_55305.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4071
   -9.4071

Timestamp 18-Jul-2025 22:26:53
pMakeSCFGModels: Making JAR3D model for motif group HL_55436.1, number 135 of 253
pMakeNodes starting loop:     a=2JLT|1|A|G|5 B=2JLT|1|A|C|14
  2 Basepair     5   14 GC cWW 
No need to probe because of interaction between a=2JLT|1|A|G|6 B=2JLT|1|A|A|13
  3 Basepair     6   13 GA cWW 
pMakeNodes adding hairpin:     a=2JLT|1|A|U|7 B=2JLT|1|A|G|12
    Right strand conserved insertion U   7 at right strand position 1
    Right strand conserved insertion C   8 at right strand position 2
    Right strand conserved insertion C   9 at right strand position 3
    Right strand conserved insertion C  10 at right strand position 4
    Right strand conserved insertion A  11 at right strand position 5
    Right strand conserved insertion G  12 at right strand position 6
  4 Hairpin   7:12 UCCCAG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G5 - C14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G6 - A13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCCCAG'
           RightLetter: ''
               Comment: ' // Hairpin node U7:G12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  8
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_55436.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8565
   -8.0736
   -8.1573
  -10.9256

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_56131.2, number 136 of 253
pMakeNodes starting loop:     a=1F7U|1|B|G|931 B=1F7U|1|B|C|939
  2 Basepair   931  939 GC cWW 
pMakeNodes adding hairpin:     a=1F7U|1|B|C|932 B=1F7U|1|B|A|937
    Right strand conserved insertion C 932 at right strand position 1
    Right strand conserved insertion A 937 at right strand position 2
  3 Hairpin   932:937 CA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G931 - C939 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: ''
               Comment: ' // Hairpin node C932:A937'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C932'  ' // Hairpin conserved non-basepairing position A937'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_56131.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4435
  -10.0394
   -7.2099
   -7.2099
   -8.3177
   -9.2682

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_56334.1, number 137 of 253
pMakeNodes starting loop:     a=4V9F|1|0|U|125 B=4V9F|1|0|A|129
  2 Basepair   125  129 UA cWW 
pMakeNodes adding hairpin:     a=4V9F|1|0|A|128 B=4V9F|1|0|A|128
    Right strand conserved insertion A 128 at right strand position 1
  3 Hairpin   128:128 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 U125 - A129 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A128:A128'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A128'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_56334.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1719
   -8.0374
   -6.0258
   -5.1222
   -5.1222
   -5.1867
   -7.7415
   -8.0374
   -5.4770
   -5.1867
   -5.1867
   -5.4770
   -5.1867
   -5.4770
   -7.7691
   -7.7691

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_56676.1, number 138 of 253
pMakeNodes starting loop:     a=8HNT|1|B|U|103 B=8HNT|1|B|G|108
  2 Basepair   103  108 UG cWW 
No need to probe because of interaction between a=8HNT|1|B|G|104 B=8HNT|1|B|A|107
  3 Basepair   104  107 GA tSW 
pMakeNodes adding hairpin:     a=8HNT|1|B|U|105 B=8HNT|1|B|A|106
    Right strand conserved insertion U 105 at right strand position 1
    Right strand conserved insertion A 106 at right strand position 2
  4 Hairpin   105:106 UA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U103 - G108 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G104 - A107 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UA'
           RightLetter: ''
               Comment: ' // Hairpin node U105:A106'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U105'  ' // Hairpin conserved non-basepairing position A106'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_56676.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2134
   -4.4762

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_57176.2, number 139 of 253
pMakeNodes starting loop:     a=4V9F|1|0|G|1430 B=4V9F|1|0|C|1436
  2 Basepair  1430 1436 GC cWW 
pMakeNodes adding hairpin:     a=4V9F|1|0|U|1432 B=4V9F|1|0|A|1434
    Right strand conserved insertion U1432 at right strand position 1
    Right strand conserved insertion G1433 at right strand position 2
    Right strand conserved insertion A1434 at right strand position 3
  3 Hairpin   1432:1434 UGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1430 - C1436 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGA'
           RightLetter: ''
               Comment: ' // Hairpin node U1432:A1434'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_57176.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6116
   -5.5987
   -5.5987
   -5.5987
   -5.8351
   -7.1008
   -6.2418
   -5.8351
   -6.2418
   -5.9685
   -7.8081
   -5.9685
   -5.9685
   -6.2031

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_57863.1, number 140 of 253
pMakeNodes starting loop:     a=5BJO|1|E|G|9 B=5BJO|1|E|C|18
  2 Basepair     9   18 GC cWW 
pMakeNodes probe for inserts:  a=5BJO|1|E|A|10 B=5BJO|1|E|IU|17
    Insertion on left  5BJO|1|E|A|10
    Insertion on right 5BJO|1|E|IU|17
pMakeNodesProbeForInsertions:  a 5BJO|1|E|G|12 interacts with 5BJO|1|E|G|15
pMakeNodesProbeForInsertions:  B 5BJO|1|E|G|16 interacts with 5BJO|1|E|G|13
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5BJO|1|E|G|16 interacts with 5BJO|1|E|G|13
pMakeNodes probed for insert:  a=5BJO|1|E|G|12 B=5BJO|1|E|G|16
pMakeNodes checking on making a cluster a=5BJO|1|E|G|12 B=5BJO|1|E|G|16
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 4 and then 5 to 6
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=5BJO|1|E|G|12 B=5BJO|1|E|G|16
  3 Hairpin   12:16 GGGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  3 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BJO|1|E|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5BJO|1|E|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'UC'
               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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BJO|1|E|A|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G12 - G15 cWH '  ' // Hairpin Interaction G13 - G16 cWH '}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              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 5BJO|1|E|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGG'
           RightLetter: ''
               Comment: ' // Hairpin node G12:G16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G12 - G15 cWH '  ' // Hairpin Interaction G13 - G16 cWH '}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: HL_57863.1 allow insertions from initial node 6?
ans =

     1


ans =

    0.2500    0.2500    0.2500    0.2500


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_57863.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7114
   -5.0183

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_57875.1, number 141 of 253
pMakeNodes starting loop:     a=2A64|1|A|G|31 B=2A64|1|A|C|36
  2 Basepair    31   36 GC cWW 
pMakeNodes adding hairpin:     a=2A64|1|A|G|32 B=2A64|1|A|U|35
    Right strand conserved insertion G  32 at right strand position 1
    Right strand conserved insertion U  35 at right strand position 2
  3 Hairpin   32:35 GU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G31 - C36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: ''
               Comment: ' // Hairpin node G32:U35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G32'  ' // Hairpin conserved non-basepairing position U35'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_57875.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5231
   -9.6864
   -6.7271
   -6.0902
   -7.1214

Timestamp 18-Jul-2025 22:26:54
pMakeSCFGModels: Making JAR3D model for motif group HL_58224.1, number 142 of 253
pMakeNodes starting loop:     a=5CCB|1|N|C|13 B=5CCB|1|N|G|22
  2 Basepair    13   22 CG cWW 
pMakeNodes adding hairpin:     a=5CCB|1|N|A|14 B=5CCB|1|N|U|20
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion C  17 at right strand position 3
    Right strand conserved insertion G  19 at right strand position 4
    Right strand conserved insertion U  20 at right strand position 5
  3 Hairpin   14:20 AGCGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCGU'
           RightLetter: ''
               Comment: ' // Hairpin node A14:U20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_58224.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6948

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_58539.1, number 143 of 253
pMakeNodes starting loop:     a=3Q3Z|1|V|U|31 B=3Q3Z|1|V|G|46
pMakeNodes checking on making a cluster a=3Q3Z|1|V|U|31 B=3Q3Z|1|V|G|46
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 3 and then 12 to 13
aa is 3 bb is 12
  2 Cluster   3Q3Z|1|V|U|31:3Q3Z|1|V|A|34 3Q3Z|1|V|U|45:3Q3Z|1|V|G|46
    LR Inter  3Q3Z|1|V|A|34 3Q3Z|1|V|U|45 tHW 
    LR Inter  3Q3Z|1|V|U|31 3Q3Z|1|V|G|46 cWW 
    LR Inter  3Q3Z|1|V|A|34 3Q3Z|1|V|G|46 tWS 
    Left  strand conserved insertion 3Q3Z|1|V|A|33 at position 2
pMakeNodesCluster a=4 B=11 at the end
pMakeNodesCluster a=4 B=11 at the end
pMakeNodes adding hairpin:     a=3Q3Z|1|V|U|37 B=3Q3Z|1|V|U|44
    Right strand conserved insertion U  37 at right strand position 1
    Right strand conserved insertion G  38 at right strand position 2
    Right strand conserved insertion G  39 at right strand position 3
    Right strand conserved insertion G  40 at right strand position 4
    Right strand conserved insertion C  41 at right strand position 5
    Right strand conserved insertion A  42 at right strand position 6
    Right strand conserved insertion C  43 at right strand position 7
    Right strand conserved insertion U  44 at right strand position 8
  3 Hairpin   37:44 UGGGCACU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right 12 13
pMakeMotifModelFromSSF:   3   Hairpin Left  4 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 0 0 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: []

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: [12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: 'UG'
               Comment: ' // Cluster node 3Q3Z|1|V|U|31:3Q3Z|1|V|A|34 and 3Q3Z|1|V|U|45:3Q3Z|1|V|G|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.1194

Node 3

ans = 

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

                  type: 'Initial'
              nextnode: 4
             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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGGCACU'
           RightLetter: ''
               Comment: ' // Hairpin node U37:U44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [4 5 6 7 8 9 10 11]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right 12 13
pMakeMotifModelFromSSF:   3   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right 11
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_58539.1 allow insertions from initial node 3?
ans =

         0    0.0454    0.9070    0.0454    0.0023


ans =

    0.3750    0.1250    0.1250    0.3750         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_58539.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4256

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_59330.1, number 144 of 253
pMakeNodes starting loop:     a=2W2H|1|R|U|10 B=2W2H|1|R|G|17
  2 Basepair    10   17 UG cWW 
pMakeNodes adding hairpin:     a=2W2H|1|R|C|12 B=2W2H|1|R|G|16
    Right strand conserved insertion C  12 at right strand position 1
    Right strand conserved insertion U  13 at right strand position 2
    Right strand conserved insertion G  14 at right strand position 3
    Right strand conserved insertion C  15 at right strand position 4
    Right strand conserved insertion G  16 at right strand position 5
  3 Hairpin   12:16 CUGCG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U10 - G17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUGCG'
           RightLetter: ''
               Comment: ' // Hairpin node C12:G16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_59330.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4306

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_59564.1, number 145 of 253
pMakeNodes starting loop:     a=4PLX|1|A|U|47 B=4PLX|1|A|A|66
  2 Basepair    47   66 UA cWW 
pMakeNodes probe for inserts:  a=4PLX|1|A|G|48 B=4PLX|1|A|A|65
    Insertion on left  4PLX|1|A|G|48
    Insertion on left  4PLX|1|A|G|49
pMakeNodesProbeForInsertions:  a 4PLX|1|A|C|50 interacts with 4PLX|1|A|A|65
pMakeNodesProbeForInsertions:  B 4PLX|1|A|A|65 interacts with 4PLX|1|A|C|50
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4PLX|1|A|A|65 interacts with 4PLX|1|A|C|50
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4PLX|1|A|C|50 B=4PLX|1|A|A|65
  3 Basepair    50   65 CA cSS 
No need to probe because of interaction between a=4PLX|1|A|C|51 B=4PLX|1|A|A|64
  4 Basepair    51   64 CA cSS 
pMakeNodes adding hairpin:     a=4PLX|1|A|U|52 B=4PLX|1|A|A|63
    Right strand conserved insertion U  52 at right strand position 1
    Right strand conserved insertion U  53 at right strand position 2
    Right strand conserved insertion U  54 at right strand position 3
    Right strand conserved insertion C  55 at right strand position 4
    Right strand conserved insertion U  56 at right strand position 5
    Right strand conserved insertion U  57 at right strand position 6
    Right strand conserved insertion A  58 at right strand position 7
    Right strand conserved insertion A  59 at right strand position 8
    Right strand conserved insertion A  60 at right strand position 9
    Right strand conserved insertion A  61 at right strand position 10
    Right strand conserved insertion A  62 at right strand position 11
    Right strand conserved insertion A  63 at right strand position 12
  5 Hairpin   52:63 UUUCUUAAAAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right 19
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 18
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right 17
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PLX|1|A|G|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PLX|1|A|G|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

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

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGG'
           RightLetter: 'A'
               Comment: ' // Basepair U47 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PLX|1|A|G|48'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: '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 4PLX|1|A|G|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×12 double]
                     Z: []
           MiddleIndex: [6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [12×2 double]
    InteractionComment: {1×12 cell}
      JunctionDeletion: []
          InterIndices: [12×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 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: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            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: 'A'
               Comment: ' // Basepair C50 - A65 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            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: 'A'
               Comment: ' // Basepair C51 - A64 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

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

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUUCUUAAAAAA'
           RightLetter: ''
               Comment: ' // Hairpin node U52:A63'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×12 double]
                     Z: []
           MiddleIndex: [6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [12×2 double]
    InteractionComment: {1×12 cell}
      JunctionDeletion: []
          InterIndices: [12×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  Basepair Left  4 Right 19
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right 18
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right 17
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_59564.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.5353

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_59735.5, number 146 of 253
pMakeNodes starting loop:     a=4WSM|1|1K|C|49 B=4WSM|1|1K|G|55
  2 Basepair    49   55 CG cWW 
pMakeNodes adding hairpin:     a=4WSM|1|1K|A|50 B=4WSM|1|1K|G|54
    Right strand conserved insertion A  50 at right strand position 1
    Right strand conserved insertion A  51 at right strand position 2
    Right strand conserved insertion U  52 at right strand position 3
    Right strand conserved insertion A  53 at right strand position 4
    Right strand conserved insertion G  54 at right strand position 5
  3 Hairpin   50:54 AAUAG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C49 - G55 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUAG'
           RightLetter: ''
               Comment: ' // Hairpin node A50:G54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_59735.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6748
   -5.3444

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_59843.1, number 147 of 253
pMakeNodes starting loop:     a=9C2K|1|C|U|19 B=9C2K|1|C|A|25
  2 Basepair    19   25 UA cWW 
No need to probe because of interaction between a=9C2K|1|C|C|20 B=9C2K|1|C|G|24
  3 Basepair    20   24 CG tSH 
pMakeNodes adding hairpin:     a=9C2K|1|C|A|21 B=9C2K|1|C|A|22
    Right strand conserved insertion A  21 at right strand position 1
    Right strand conserved insertion A  22 at right strand position 2
  4 Hairpin   21:22 AA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U19 - A25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C20 - G24 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: ''
               Comment: ' // Hairpin node A21:A22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A21'  ' // Hairpin conserved non-basepairing position A22'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_59843.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7238
   -5.7478

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_60266.1, number 148 of 253
pMakeNodes starting loop:     a=6DME|1|A|G|78 B=6DME|1|A|C|88
  2 Basepair    78   88 GC cWW 
No need to probe because of interaction between a=6DME|1|A|G|79 B=6DME|1|A|A|87
  3 Basepair    79   87 GA cWW 
No need to probe because of interaction between a=6DME|1|A|A|80 B=6DME|1|A|A|85
  4 Basepair    80   85 AA tWH 
No need to probe because of interaction between a=6DME|1|A|U|81 B=6DME|1|A|A|84
  5 Basepair    81   84 UA tWH 
pMakeNodes adding hairpin:     a=6DME|1|A|A|83 B=6DME|1|A|A|83
    Right strand conserved insertion A  83 at right strand position 1
  6 Hairpin   83:83 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G78 - C88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G79 - A87 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 A80 - A85 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U81 - A84 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A83:A83'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A83'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  5
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_60266.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2590
   -9.7442

Timestamp 18-Jul-2025 22:26:55
pMakeSCFGModels: Making JAR3D model for motif group HL_60293.1, number 149 of 253
pMakeNodes starting loop:     a=5DEA|1|C|U|8 B=5DEA|1|C|G|29
  2 Basepair     8   29 UG cWW 
pMakeNodes probe for inserts:  a=5DEA|1|C|G|9 B=5DEA|1|C|U|28
pMakeNodesProbeForInsertions:  a 5DEA|1|C|G|9 interacts with 5DEA|1|C|G|26
pMakeNodesProbeForInsertions:  B 5DEA|1|C|U|28 interacts with 5DEA|1|C|A|17
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5DEA|1|C|U|28 interacts with 5DEA|1|C|A|17
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5DEA|1|C|G|9 B=5DEA|1|C|U|28
pMakeNodes checking on making a cluster a=5DEA|1|C|G|9 B=5DEA|1|C|U|28
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 9 and then 10 to 17
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=5DEA|1|C|G|9 B=5DEA|1|C|U|28
    Right strand conserved insertion A  14 at right strand position 4
    Right strand conserved insertion U  23 at right strand position 11
    Right strand conserved insertion U  27 at right strand position 15
  3 Hairpin   9:28 GGGAGGAGGGUGGGUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 17
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U8 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGAGGAGGGUGGGUU'
           RightLetter: ''
               Comment: ' // Hairpin node G9:U28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
              NormCons: 0.0026

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 17
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_60293.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3980
   -8.3980

Timestamp 18-Jul-2025 22:26:56
pMakeSCFGModels: Making JAR3D model for motif group HL_60914.1, number 150 of 253
pMakeNodes starting loop:     a=6CYT|1|N|C|30 B=6CYT|1|N|G|34
  2 Basepair    30   34 CG cWW 
pMakeNodes adding hairpin:     a=6CYT|1|N|U|31 B=6CYT|1|N|U|31
    Right strand conserved insertion U  31 at right strand position 1
  3 Hairpin   31:31 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C30 - G34 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U31:U31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U31'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_60914.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.2509

Timestamp 18-Jul-2025 22:26:56
pMakeSCFGModels: Making JAR3D model for motif group HL_61996.2, number 151 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|2027 B=5J7L|1|DA|C|2036
  2 Basepair  2027 2036 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|2028 B=5J7L|1|DA|G|2035
    Insertion on right 5J7L|1|DA|G|2035
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|U|2028 interacts with 5J7L|1|DA|A|2033
    Insertion      2034 U
pMakeNodes probed for insert:  a=5J7L|1|DA|U|2028 B=5J7L|1|DA|A|2033
  3 Basepair  2028 2033 UA tWH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|G|2029 B=5J7L|1|DA|G|2029
    Right strand conserved insertion G2029 at right strand position 1
  4 Hairpin   2029:2029 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2032
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|2031
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'UGC'
               Comment: ' // Basepair G2027 - C2036 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|G|2032'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            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: 'G'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G2029'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|2031'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2028 - A2033 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G2029:G2029'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G2029'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_61996.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8170
   -5.8170
   -5.8170
   -8.5563
   -7.5516
   -7.3531
   -7.3531
  -11.8382

Timestamp 18-Jul-2025 22:26:56
pMakeSCFGModels: Making JAR3D model for motif group HL_62934.1, number 152 of 253
pMakeNodes starting loop:     a=8K0K|1|J|C|42 B=8K0K|1|J|G|48
  2 Basepair    42   48 CG cWW 
No need to probe because of interaction between a=8K0K|1|J|G|43 B=8K0K|1|J|A|47
  3 Basepair    43   47 GA tSH 
pMakeNodes adding hairpin:     a=8K0K|1|J|A|45 B=8K0K|1|J|U|46
    Right strand conserved insertion A  45 at right strand position 1
    Right strand conserved insertion U  46 at right strand position 2
  4 Hairpin   45:46 AU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C42 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G43 - A47 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AU'
           RightLetter: ''
               Comment: ' // Hairpin node A45:U46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A45'  ' // Hairpin conserved non-basepairing position U46'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_62934.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1497
   -5.4339

Timestamp 18-Jul-2025 22:26:56
pMakeSCFGModels: Making JAR3D model for motif group HL_63355.1, number 153 of 253
pMakeNodes starting loop:     a=7A0S|1|X|G|1074 B=7A0S|1|X|C|1087
  2 Basepair  1074 1087 GC cWW 
No need to probe because of interaction between a=7A0S|1|X|C|1075 B=7A0S|1|X|C|1086
  3 Basepair  1075 1086 CC cWW 
pMakeNodes adding hairpin:     a=7A0S|1|X|U|1076 B=7A0S|1|X|G|1085
    Right strand conserved insertion U1076 at right strand position 1
    Right strand conserved insertion U1077 at right strand position 2
    Right strand conserved insertion A1078 at right strand position 3
    Right strand conserved insertion G1079 at right strand position 4
    Right strand conserved insertion A1080 at right strand position 5
    Right strand conserved insertion G1082 at right strand position 6
    Right strand conserved insertion C1083 at right strand position 7
    Right strand conserved insertion A1084 at right strand position 8
    Right strand conserved insertion G1085 at right strand position 9
  4 Hairpin   1076:1085 UUAGAGCAG
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   Hairpin Left  3 Right 11
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 1 1 1 1 1 1 1 1 1 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 G1074 - C1087 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C1075 - C1086 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAGAGCAG'
           RightLetter: ''
               Comment: ' // Hairpin node U1076:G1085'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9 10 11]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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   Hairpin Left  3 Right 11
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_63355.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7878

Timestamp 18-Jul-2025 22:26:56
pMakeSCFGModels: Making JAR3D model for motif group HL_64292.1, number 154 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|G|486 B=8P9A|1|sR|U|501
  2 Basepair   486  501 GU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|G|488 B=8P9A|1|sR|C|500
    Insertion on right 8P9A|1|sR|C|500
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|488 interacts with 8P9A|1|sR|U|499
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|499 interacts with 8P9A|1|sR|G|488
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|499 interacts with 8P9A|1|sR|G|488
pMakeNodes probed for insert:  a=8P9A|1|sR|G|488 B=8P9A|1|sR|U|499
  3 Basepair   488  499 GU tSH 
pMakeNodes adding hairpin:     a=8P9A|1|sR|C|490 B=8P9A|1|sR|G|498
    Right strand conserved insertion C 490 at right strand position 1
    Right strand conserved insertion C 491 at right strand position 2
    Right strand conserved insertion G 496 at right strand position 3
    Right strand conserved insertion G 497 at right strand position 4
    Right strand conserved insertion G 498 at right strand position 5
  4 Hairpin   490:498 CCGGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|494
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 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: 'CU'
               Comment: ' // Basepair G486 - U501 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|494'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'CCGGG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G488 - U499 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCGGG'
           RightLetter: ''
               Comment: ' // Hairpin node C490:G498'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_64292.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.8767
  -18.6220

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_64690.6, number 155 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|2819 B=5J7L|1|DA|C|2827
  2 Basepair  2819 2827 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2821 B=5J7L|1|DA|A|2826
  3 Basepair  2821 2826 AA cSW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|G|2822 B=5J7L|1|DA|G|2825
    Right strand conserved insertion G2822 at right strand position 1
    Right strand conserved insertion A2823 at right strand position 2
    Right strand conserved insertion C2824 at right strand position 3
    Right strand conserved insertion G2825 at right strand position 4
  4 Hairpin   2822:2825 GACG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2819 - C2827 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2821 - A2826 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GACG'
           RightLetter: ''
               Comment: ' // Hairpin node G2822:G2825'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_64690.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4251
   -7.2136
   -7.5237
   -7.2136
   -7.6094
   -7.0129
   -9.5778
  -13.1726
  -13.4526

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_65313.1, number 156 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|C|762 B=8CRE|1|CM|G|767
  2 Basepair   762  767 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|CM|C|763 B=8CRE|1|CM|U|765
    Right strand conserved insertion C 763 at right strand position 1
    Right strand conserved insertion U 764 at right strand position 2
    Right strand conserved insertion U 765 at right strand position 3
  3 Hairpin   763:765 CUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C762 - G767 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUU'
           RightLetter: ''
               Comment: ' // Hairpin node C763:U765'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_65313.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3904

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_65794.5, number 157 of 253
pMakeNodes starting loop:     a=8CRE|1|1|U|3040 B=8CRE|1|1|A|3045
  2 Basepair  3040 3045 UA cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|G|3041 B=8CRE|1|1|C|3044
    Right strand conserved insertion G3041 at right strand position 1
    Right strand conserved insertion A3042 at right strand position 2
    Right strand conserved insertion U3043 at right strand position 3
    Right strand conserved insertion C3044 at right strand position 4
  3 Hairpin   3041:3044 GAUC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U3040 - A3045 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAUC'
           RightLetter: ''
               Comment: ' // Hairpin node G3041:C3044'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_65794.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1827
   -6.1827
   -6.1478
   -5.5730
   -4.4744
   -6.6195
   -4.4744
   -5.3760
   -9.6310
   -8.5890
   -9.0671
   -8.4038
   -9.3184
   -6.2587

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_66103.1, number 158 of 253
pMakeNodes starting loop:     a=3SIU|1|F|C|40 B=3SIU|1|F|G|46
  2 Basepair    40   46 CG cWW 
pMakeNodes adding hairpin:     a=3SIU|1|F|G|41 B=3SIU|1|F|U|44
    Right strand conserved insertion G  41 at right strand position 1
    Right strand conserved insertion U  44 at right strand position 2
  3 Hairpin   41:44 GU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C40 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: ''
               Comment: ' // Hairpin node G41:U44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G41'  ' // Hairpin conserved non-basepairing position U44'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_66103.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7883
   -6.7883

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_66482.1, number 159 of 253
pMakeNodes starting loop:     a=6D3P|1|A|C|12 B=6D3P|1|A|G|29
  2 Basepair    12   29 CG cWW 
pMakeNodes probe for inserts:  a=6D3P|1|A|C|13 B=6D3P|1|A|A|28
pMakeNodesProbeForInsertions:  a 6D3P|1|A|C|13 interacts with 6D3P|1|A|G|27
pMakeNodesProbeForInsertions:  B 6D3P|1|A|A|28 interacts with 6D3P|1|A|U|21
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6D3P|1|A|A|28 interacts with 6D3P|1|A|U|21
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6D3P|1|A|C|13 B=6D3P|1|A|A|28
pMakeNodes checking on making a cluster a=6D3P|1|A|C|13 B=6D3P|1|A|A|28
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 2 and then 10 to 17
aa is 2 bb is 10
  3 Cluster   6D3P|1|A|C|13:6D3P|1|A|C|13 6D3P|1|A|U|21:6D3P|1|A|A|28
    LR Inter  6D3P|1|A|C|13 6D3P|1|A|G|27 cWW 
    RR Inter  6D3P|1|A|U|22 6D3P|1|A|A|26 tWH 
    RR Inter  6D3P|1|A|U|21 6D3P|1|A|A|28 tWW 
    Right strand conserved insertion 6D3P|1|A|G|23 at position 3
    Right strand conserved insertion 6D3P|1|A|C|24 at position 4
    Right strand conserved insertion 6D3P|1|A|A|25 at position 5
pMakeNodesCluster a=3 B=9 at the end
pMakeNodesCluster a=3 B=9 at the end
pMakeNodes adding hairpin:     a=6D3P|1|A|A|14 B=6D3P|1|A|G|20
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion U  15 at right strand position 2
    Right strand conserved insertion C  16 at right strand position 3
    Right strand conserved insertion C  17 at right strand position 4
    Right strand conserved insertion G  18 at right strand position 5
    Right strand conserved insertion A  19 at right strand position 6
    Right strand conserved insertion G  20 at right strand position 7
  4 Hairpin   14:20 AUCCGAG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right 10 11 12 13 14 15 16 17
pMakeMotifModelFromSSF:   4   Hairpin Left  3 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: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 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 C12 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: 2
            RightIndex: [10 11 12 13 14 15 16 17]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'UUGCAAGA'
               Comment: ' // Cluster node 6D3P|1|A|C|13:6D3P|1|A|C|13 and 6D3P|1|A|U|21:6D3P|1|A|A|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4 5 6 7 8]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [3 4 5]
              NormCons: 1.0000

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUCCGAG'
           RightLetter: ''
               Comment: ' // Hairpin node A14:G20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right 10 11 12 13 14 15 16 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  3 Right  9
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: HL_66482.1 allow insertions from initial node 4?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_66482.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.3758

Timestamp 18-Jul-2025 22:26:57
pMakeSCFGModels: Making JAR3D model for motif group HL_66853.7, number 160 of 253
pMakeNodes starting loop:     a=8UO6|1|B|C|13 B=8UO6|1|B|G|22
  2 Basepair    13   22 CG cWW 
No need to probe because of interaction between a=8UO6|1|B|A|14 B=8UO6|1|B|A|21
  3 Basepair    14   21 AA cWS 
pMakeNodes adding hairpin:     a=8UO6|1|B|G|15 B=8UO6|1|B|U|20
    Right strand conserved insertion G  15 at right strand position 1
  4 Hairpin   15:20 GGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A21 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGU'
           RightLetter: ''
               Comment: ' // Hairpin node G15:U20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G19 - U20 cSH '  ' // Hairpin conserved non-basepairing position G15'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_66853.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3513
   -8.3513
   -8.3513
   -8.3513
   -8.6784
   -8.3513
   -7.3434
   -9.0324
  -11.3030
   -7.3434
   -7.3434

Timestamp 18-Jul-2025 22:26:58
pMakeSCFGModels: Making JAR3D model for motif group HL_67079.1, number 161 of 253
pMakeNodes starting loop:     a=4V7M|1|AY|G|51 B=4V7M|1|AY|C|61
  2 Basepair    51   61 GC cWW 
pMakeNodes probe for inserts:  a=4V7M|1|AY|G|52 B=4V7M|1|AY|C|60
    Insertion on left  4V7M|1|AY|G|52
    Insertion on right 4V7M|1|AY|C|60
    Insertion on right 4V7M|1|AY|U|59
pMakeNodesProbeForInsertions:  a 4V7M|1|AY|U|53 interacts with 4V7M|1|AY|A|57
    Insertion        58 A
pMakeNodes probed for insert:  a=4V7M|1|AY|U|53 B=4V7M|1|AY|A|57
  3 Basepair    53   57 UA tWH 
pMakeNodes adding hairpin:     a=4V7M|1|AY|U|54 B=4V7M|1|AY|U|54
    Right strand conserved insertion U  54 at right strand position 1
  4 Hairpin   54:54 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V7M|1|AY|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V7M|1|AY|A|58
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V7M|1|AY|A|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V7M|1|AY|G|56
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'AUCC'
               Comment: ' // Basepair G51 - C61 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V7M|1|AY|G|52'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U54'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V7M|1|AY|A|58'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 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 4V7M|1|AY|A|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V7M|1|AY|G|56'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

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

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U53 - A57 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

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

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U54:U54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U54'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   9     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:  10   Initial Left  3 Right  5
pMakeMotifModelFromSSF:  11  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:  12   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_67079.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.5500
  -13.8067
  -10.6132
  -10.6132

Timestamp 18-Jul-2025 22:26:58
pMakeSCFGModels: Making JAR3D model for motif group HL_67407.5, number 162 of 253
pMakeNodes starting loop:     a=9BZC|1|A|C|77 B=9BZC|1|A|G|87
  2 Basepair    77   87 CG cWW 
pMakeNodes adding hairpin:     a=9BZC|1|A|G|78 B=9BZC|1|A|G|86
    Right strand conserved insertion G  78 at right strand position 1
    Right strand conserved insertion C  80 at right strand position 2
    Right strand conserved insertion C  81 at right strand position 3
    Right strand conserved insertion G  82 at right strand position 4
    Right strand conserved insertion U  83 at right strand position 5
    Right strand conserved insertion C  84 at right strand position 6
    Right strand conserved insertion U  85 at right strand position 7
    Right strand conserved insertion G  86 at right strand position 8
  3 Hairpin   78:86 GCCGUCUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C77 - G87 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCCGUCUG'
           RightLetter: ''
               Comment: ' // Hairpin node G78:G86'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_67407.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7390
   -8.2185
   -7.1199
   -8.2185
  -12.0415
   -8.6945
   -7.7390
  -10.6716
   -9.2053
   -8.6945

Timestamp 18-Jul-2025 22:26:58
pMakeSCFGModels: Making JAR3D model for motif group HL_67667.2, number 163 of 253
pMakeNodes starting loop:     a=7PMQ|1|F|C|30 B=7PMQ|1|F|G|36
  2 Basepair    30   36 CG cWW 
pMakeNodes adding hairpin:     a=7PMQ|1|F|U|34 B=7PMQ|1|F|C|35
    Right strand conserved insertion U  34 at right strand position 1
    Right strand conserved insertion C  35 at right strand position 2
  3 Hairpin   34:35 UC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C30 - G36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UC'
           RightLetter: ''
               Comment: ' // Hairpin node U34:C35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U34'  ' // Hairpin conserved non-basepairing position C35'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_67667.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3941
   -4.3941
   -4.3941

Timestamp 18-Jul-2025 22:26:58
pMakeSCFGModels: Making JAR3D model for motif group HL_68257.1, number 164 of 253
pMakeNodes starting loop:     a=7A0S|1|X|A|253 B=7A0S|1|X|U|266
  2 Basepair   253  266 AU cWW 
No need to probe because of interaction between a=7A0S|1|X|A|254 B=7A0S|1|X|U|265
  3 Basepair   254  265 AU tSH 
No need to probe because of interaction between a=7A0S|1|X|A|255 B=7A0S|1|X|U|264
  4 Basepair   255  264 AU tHW 
No need to probe because of interaction between a=7A0S|1|X|C|256 B=7A0S|1|X|G|263
  5 Basepair   256  263 CG tHW 
No need to probe because of interaction between a=7A0S|1|X|G|257 B=7A0S|1|X|C|262
  6 Basepair   257  262 GC cSH 
pMakeNodes adding hairpin:     a=7A0S|1|X|C|258 B=7A0S|1|X|C|258
    Right strand conserved insertion C 258 at right strand position 1
  7 Hairpin   258:258 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A253 - U266 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A254 - U265 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A255 - U264 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 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 C256 - G263 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 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 G257 - C262 cSH '
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

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

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C258:C258'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 6
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C258'}
      JunctionDeletion: []
          InterIndices: [6 6]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  6
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_68257.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.4155
   -9.0016

Timestamp 18-Jul-2025 22:26:58
pMakeSCFGModels: Making JAR3D model for motif group HL_68572.1, number 165 of 253
pMakeNodes starting loop:     a=4V9I|1|AY|C|11 B=4V9I|1|AY|G|24
  2 Basepair    11   24 CG cWW 
pMakeNodes adding hairpin:     a=4V9I|1|AY|G|12 B=4V9I|1|AY|A|23
    Right strand conserved insertion G  12 at right strand position 1
    Right strand conserved insertion G  13 at right strand position 2
    Right strand conserved insertion A  14 at right strand position 3
    Right strand conserved insertion G  15 at right strand position 4
    Right strand conserved insertion G  21 at right strand position 5
    Right strand conserved insertion A  22 at right strand position 6
    Right strand conserved insertion A  23 at right strand position 7
  3 Hairpin   12:23 GGAGGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C11 - G24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAGGAA'
           RightLetter: ''
               Comment: ' // Hairpin node G12:A23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_68572.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.1290
  -14.3563
  -14.4066

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_68767.1, number 166 of 253
pMakeNodes starting loop:     a=3ZGZ|1|B|G|12 B=3ZGZ|1|B|C|23
  2 Basepair    12   23 GC cWW 
No need to probe because of interaction between a=3ZGZ|1|B|G|13 B=3ZGZ|1|B|A|22
pMakeNodes checking on making a cluster a=3ZGZ|1|B|G|13 B=3ZGZ|1|B|A|22
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 2 and then 6 to 7
aa is 2 bb is 6
  3 Cluster   3ZGZ|1|B|G|13:3ZGZ|1|B|G|13 3ZGZ|1|B|G|21:3ZGZ|1|B|A|22
    LR Inter  3ZGZ|1|B|G|13 3ZGZ|1|B|G|21 cWS 
    LR Inter  3ZGZ|1|B|G|13 3ZGZ|1|B|A|22 tSH 
pMakeNodesCluster a=3 B=5 at the end
pMakeNodesCluster a=3 B=5 at the end
No need to probe because of interaction between a=3ZGZ|1|B|A|14 B=3ZGZ|1|B|A|20|||A
  4 Basepair    14  20A AA cWS 
pMakeNodes adding hairpin:     a=3ZGZ|1|B|A|15 B=3ZGZ|1|B|A|15
    Right strand conserved insertion A  15 at right strand position 1
  5 Hairpin   15:15 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right  6  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G12 - C23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: 2
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'GA'
               Comment: ' // Cluster node 3ZGZ|1|B|G|13:3ZGZ|1|B|G|13 and 3ZGZ|1|B|G|21:3ZGZ|1|B|A|22'
              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: 0.2541

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A20A 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A15:A15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A15'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right  6  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_68767.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3938
   -8.2952
  -11.0720

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_69139.1, number 167 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|U|1040 B=8CRE|1|CM|G|1049
  2 Basepair  1040 1049 UG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|CM|C|1041 B=8CRE|1|CM|U|1048
    Right strand conserved insertion C1041 at right strand position 1
    Right strand conserved insertion U1043 at right strand position 2
    Right strand conserved insertion U1044 at right strand position 3
    Right strand conserved insertion U1045 at right strand position 4
    Right strand conserved insertion A1046 at right strand position 5
    Right strand conserved insertion U1047 at right strand position 6
    Right strand conserved insertion U1048 at right strand position 7
  3 Hairpin   1041:1048 CUUUAUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1040 - G1049 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUUAUU'
           RightLetter: ''
               Comment: ' // Hairpin node C1041:U1048'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_69139.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0077
  -13.0189

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_69752.2, number 168 of 253
pMakeNodes starting loop:     a=8Y03|1|G|C|11 B=8Y03|1|G|G|17
  2 Basepair    11   17 CG cWW 
pMakeNodes adding hairpin:     a=8Y03|1|G|U|12 B=8Y03|1|G|U|12
    Right strand conserved insertion U  12 at right strand position 1
  3 Hairpin   12:12 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C11 - G17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U12:U12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U12'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_69752.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4912
   -6.4912
   -6.4912
   -6.4912
   -6.1635
   -6.1635
   -5.4738

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_70658.1, number 169 of 253
pMakeNodes starting loop:     a=4LVW|1|A|A|33 B=4LVW|1|A|U|45
  2 Basepair    33   45 AU cWW 
No need to probe because of interaction between a=4LVW|1|A|A|34 B=4LVW|1|A|G|44
  3 Basepair    34   44 AG cWW 
No need to probe because of interaction between a=4LVW|1|A|U|35 B=4LVW|1|A|U|42
  4 Basepair    35   42 UU tWH 
pMakeNodes probe for inserts:  a=4LVW|1|A|G|36 B=4LVW|1|A|G|41
    Insertion on right 4LVW|1|A|G|41
pMakeNodesProbeForInsertions:  a 4LVW|1|A|G|36 interacts with 4LVW|1|A|U|40
pMakeNodesProbeForInsertions:  B 4LVW|1|A|U|40 interacts with 4LVW|1|A|G|36
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LVW|1|A|U|40 interacts with 4LVW|1|A|G|36
pMakeNodes probed for insert:  a=4LVW|1|A|G|36 B=4LVW|1|A|U|40
  5 Basepair    36   40 GU tHW 
pMakeNodes adding hairpin:     a=4LVW|1|A|G|37 B=4LVW|1|A|A|39
    Right strand conserved insertion G  37 at right strand position 1
    Right strand conserved insertion G  38 at right strand position 2
    Right strand conserved insertion A  39 at right strand position 3
  6 Hairpin   37:39 GGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LVW|1|A|G|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

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

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A33 - U45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A34 - G44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'GU'
               Comment: ' // Basepair U35 - U42 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 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 4LVW|1|A|G|41'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

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

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 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: 'GGA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 7

ans = 

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

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 G36 - U40 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

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

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGA'
           RightLetter: ''
               Comment: ' // Hairpin node G37:A39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_70658.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7751
  -11.6769

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_70751.1, number 170 of 253
pMakeNodes starting loop:     a=5WTK|1|B|C|7 B=5WTK|1|B|G|17
  2 Basepair     7   17 CG cWW 
pMakeNodes adding hairpin:     a=5WTK|1|B|A|8 B=5WTK|1|B|A|16
    Right strand conserved insertion A   8 at right strand position 1
    Right strand conserved insertion A   9 at right strand position 2
    Right strand conserved insertion U  10 at right strand position 3
    Right strand conserved insertion A  11 at right strand position 4
    Right strand conserved insertion U  12 at right strand position 5
    Right strand conserved insertion C  13 at right strand position 6
    Right strand conserved insertion G  14 at right strand position 7
    Right strand conserved insertion A  15 at right strand position 8
    Right strand conserved insertion A  16 at right strand position 9
  3 Hairpin   8:16 AAUAUCGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUAUCGAA'
           RightLetter: ''
               Comment: ' // Hairpin node A8:A16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_70751.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7470

Timestamp 18-Jul-2025 22:26:59
pMakeSCFGModels: Making JAR3D model for motif group HL_70782.2, number 171 of 253
pMakeNodes starting loop:     a=8CRE|1|1|C|954 B=8CRE|1|1|G|959
  2 Basepair   954  959 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|C|955 B=8CRE|1|1|C|955
    Right strand conserved insertion C 955 at right strand position 1
  3 Hairpin   955:955 C
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C954 - G959 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: ''
               Comment: ' // Hairpin node C955:C955'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position C955'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_70782.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2380
   -7.2380
   -7.7912
   -6.6747

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_71391.1, number 172 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|G|139 B=9DFE|1|1A|C|142|||A
  2 Basepair   139 142A GC cWW 
No need to probe because of interaction between a=9DFE|1|1A|G|140 B=9DFE|1|1A|A|142
  3 Basepair   140  142 GA cWH 
pMakeNodes adding hairpin:     a=9DFE|1|1A|A|141 B=9DFE|1|1A|A|141
    Right strand conserved insertion A 141 at right strand position 1
  4 Hairpin   141:141 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G139 - C142A cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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: 'A'
               Comment: ' // Basepair G140 - A142 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A141:A141'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A141'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_71391.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7712
   -3.7990

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_72628.1, number 173 of 253
pMakeNodes starting loop:     a=3PDR|1|X|C|99 B=3PDR|1|X|G|107
  2 Basepair    99  107 CG cWW 
No need to probe because of interaction between a=3PDR|1|X|G|100 B=3PDR|1|X|A|106
  3 Basepair   100  106 GA tSH 
pMakeNodes adding hairpin:     a=3PDR|1|X|C|102 B=3PDR|1|X|A|105
    Right strand conserved insertion C 102 at right strand position 1
    Right strand conserved insertion A 103 at right strand position 2
    Right strand conserved insertion U 104 at right strand position 3
    Right strand conserved insertion A 105 at right strand position 4
  4 Hairpin   102:105 CAUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C99 - G107 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G100 - A106 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAUA'
           RightLetter: ''
               Comment: ' // Hairpin node C102:A105'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_72628.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6175

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_73183.1, number 174 of 253
pMakeNodes starting loop:     a=6ZDU|1|C|C|1297 B=6ZDU|1|C|G|1314
  2 Basepair  1297 1314 CG cWW 
No need to probe because of interaction between a=6ZDU|1|C|G|1298 B=6ZDU|1|C|A|1313
  3 Basepair  1298 1313 GA tSH 
No need to probe because of interaction between a=6ZDU|1|C|A|1299 B=6ZDU|1|C|U|1312
pMakeNodes checking on making a cluster a=6ZDU|1|C|A|1299 B=6ZDU|1|C|U|1312
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 3 and then 11 to 12
aa is 3 bb is 11
  4 Cluster   6ZDU|1|C|A|1299:6ZDU|1|C|A|1299 6ZDU|1|C|G|1311:6ZDU|1|C|U|1312
    LR Inter  6ZDU|1|C|A|1299 6ZDU|1|C|U|1312 tHW 
    RR Inter  6ZDU|1|C|G|1311 6ZDU|1|C|U|1312 cSH 
pMakeNodesCluster a=4 B=10 at the end
pMakeNodesCluster a=4 B=10 at the end
pMakeNodes adding hairpin:     a=6ZDU|1|C|A|1303 B=6ZDU|1|C|A|1310
    Right strand conserved insertion A1303 at right strand position 1
    Right strand conserved insertion A1304 at right strand position 2
    Right strand conserved insertion U1305 at right strand position 3
    Right strand conserved insertion U1306 at right strand position 4
    Right strand conserved insertion G1307 at right strand position 5
    Right strand conserved insertion A1309 at right strand position 6
    Right strand conserved insertion A1310 at right strand position 7
  5 Hairpin   1303:1310 AAUUGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 11 12
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1297 - G1314 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1298 - A1313 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

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

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: 3
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Cluster node 6ZDU|1|C|A|1299:6ZDU|1|C|A|1299 and 6ZDU|1|C|G|1311:6ZDU|1|C|U|1312'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 5

ans = 

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

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

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

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUUGAA'
           RightLetter: ''
               Comment: ' // Hairpin node A1303:A1310'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 11 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right 10
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: HL_73183.1 allow insertions from initial node 5?
ans =

    0.0119    0.4756    0.0238    0.4762    0.0119    0.0006


ans =

    0.7500    0.0833    0.0833    0.0833         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_73183.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.4890
  -10.2221

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_73247.1, number 175 of 253
pMakeNodes starting loop:     a=7JJU|1|A|C|14 B=7JJU|1|A|G|30
  2 Basepair    14   30 CG cWW 
pMakeNodes probe for inserts:  a=7JJU|1|A|A|17 B=7JJU|1|A|A|29
    Insertion on left  7JJU|1|A|A|17
    Insertion on left  7JJU|1|A|C|18
    Insertion on left  7JJU|1|A|A|19
    Insertion on left  7JJU|1|A|C|20
    Insertion on left  7JJU|1|A|G|21
    Insertion on left  7JJU|1|A|A|22
pMakeNodesProbeForInsertions:  B 7JJU|1|A|A|29 interacts with 7JJU|1|A|U|25
pMakeNodesProbeForInsertions:  B 7JJU|1|A|A|29 interacts with 7JJU|1|A|U|25
pMakeNodes probed for insert:  a=7JJU|1|A|G|23 B=7JJU|1|A|A|29
pMakeNodes checking on making a cluster a=7JJU|1|A|G|23 B=7JJU|1|A|A|29
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 0
pMakeNodesCluster: Cluster goes from 8 to 10 and then 14 to 14
aa is 10 bb is 14
  3 Cluster   7JJU|1|A|G|23:7JJU|1|A|U|25 7JJU|1|A|A|29:7JJU|1|A|A|29
    LR Inter  7JJU|1|A|U|25 7JJU|1|A|A|29 tWH 
    Left  strand conserved insertion 7JJU|1|A|G|23 at position 1
    Left  strand conserved insertion 7JJU|1|A|U|24 at position 2
pMakeNodesCluster a=11 B=13 at the end
pMakeNodesCluster a=11 B=13 at the end
pMakeNodes adding hairpin:     a=7JJU|1|A|G|26 B=7JJU|1|A|A|28
    Right strand conserved insertion G  26 at right strand position 1
    Right strand conserved insertion C  27 at right strand position 2
    Right strand conserved insertion A  28 at right strand position 3
  4 Hairpin   26:28 GCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3   Cluster Left  8  9 10 Right 14
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|U|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|C|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|A|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JJU|1|A|C|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-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: 'CACACGA'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JJU|1|A|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1 2]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            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 7JJU|1|A|U|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [11 12 13]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 6

ans = 

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

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

Node 7

ans = 

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

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JJU|1|A|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

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

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

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

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JJU|1|A|C|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          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: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

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

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JJU|1|A|A|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

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

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

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

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JJU|1|A|C|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

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

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

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

                  type: 'Cluster'
              nextnode: 16
             LeftIndex: [8 9 10]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7JJU|1|A|G|23:7JJU|1|A|U|25 and 7JJU|1|A|A|29:7JJU|1|A|A|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1 2]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 16

ans = 

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

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

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

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // Hairpin node G26:A28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [11 12 13]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  15   Cluster Left  8  9 10 Right 14
pMakeMotifModelFromSSF:  16   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 13
pNextNodeJunction: Found a hairpin at node 17
pUpdateModelWithSSF: HL_73247.1 allow insertions from initial node 16?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_73247.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5750
   -8.5750
   -8.5392

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_73255.1, number 176 of 253
pMakeNodes starting loop:     a=5AOX|1|C|C|32 B=5AOX|1|C|G|41
  2 Basepair    32   41 CG cWW 
pMakeNodes adding hairpin:     a=5AOX|1|C|A|33 B=5AOX|1|C|C|37
    Right strand conserved insertion A  33 at right strand position 1
    Right strand conserved insertion G  34 at right strand position 2
    Right strand conserved insertion C  35 at right strand position 3
    Right strand conserved insertion C  37 at right strand position 4
  3 Hairpin   33:37 AGCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C32 - G41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

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

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCC'
           RightLetter: ''
               Comment: ' // Hairpin node A33:C37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_73255.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7360
  -10.0102

Timestamp 18-Jul-2025 22:27:00
pMakeSCFGModels: Making JAR3D model for motif group HL_73266.9, number 177 of 253
pMakeNodes starting loop:     a=5SWD|1|B|G|59 B=5SWD|1|B|C|67
  2 Basepair    59   67 GC cWW 
pMakeNodes probe for inserts:  a=5SWD|1|B|C|60 B=5SWD|1|B|A|66
    Insertion on left  5SWD|1|B|C|60
    Insertion on right 5SWD|1|B|A|66
pMakeNodesProbeForInsertions:  a 5SWD|1|B|C|61 interacts with 5SWD|1|B|A|65
pMakeNodesProbeForInsertions:  B 5SWD|1|B|A|65 interacts with 5SWD|1|B|C|61
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5SWD|1|B|A|65 interacts with 5SWD|1|B|C|61
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5SWD|1|B|C|61 B=5SWD|1|B|A|65
  3 Basepair    61   65 CA cSW 
pMakeNodes adding hairpin:     a=5SWD|1|B|U|62 B=5SWD|1|B|A|64
    Right strand conserved insertion A  64 at right strand position 3
  4 Hairpin   62:64 UUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5SWD|1|B|C|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5SWD|1|B|A|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

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

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

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

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: 'AC'
               Comment: ' // Basepair G59 - 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]
              NormCons: []

Node 3

ans = 

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

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5SWD|1|B|C|60'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

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

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'UUA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction U62 - U63 cSH '  ' // Hairpin conserved non-basepairing position A64'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

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

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5SWD|1|B|A|66'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 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: []
              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: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C61 - A65 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUA'
           RightLetter: ''
               Comment: ' // Hairpin node U62:A64'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction U62 - U63 cSH '  ' // Hairpin conserved non-basepairing position A64'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_73266.9_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7945
   -4.7945
   -5.0534
   -4.7945
   -5.0534
   -4.7945
   -4.7945
   -4.7945
   -5.0534
   -5.4461
   -5.4296
   -5.4315
   -5.4154

Timestamp 18-Jul-2025 22:27:01
pMakeSCFGModels: Making JAR3D model for motif group HL_73916.1, number 178 of 253
pMakeNodes starting loop:     a=4WT8|1|DV|A|7 B=4WT8|1|DV|U|46
  2 Basepair     7   46 AU cWW 
pMakeNodes probe for inserts:  a=4WT8|1|DV|U|8 B=4WT8|1|DV|G|45
    Insertion on left  4WT8|1|DV|U|8
    Insertion on left  4WT8|1|DV|A|9
    Insertion on left  4WT8|1|DV|G|10
    Insertion on right 4WT8|1|DV|G|45
    Insertion on right 4WT8|1|DV|A|44
    Insertion on right 4WT8|1|DV|G|43
    Insertion on right 4WT8|1|DV|C|42
    Insertion on right 4WT8|1|DV|C|41
    Insertion on right 4WT8|1|DV|U|40
pMakeNodesProbeForInsertions:  a 4WT8|1|DV|C|11 interacts with 4WT8|1|DV|G|24
pMakeNodesProbeForInsertions:  B 4WT8|1|DV|U|39 interacts with 4WT8|1|DV|G|15
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WT8|1|DV|U|39 interacts with 4WT8|1|DV|G|15
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4WT8|1|DV|C|11 B=4WT8|1|DV|U|39
pMakeNodes checking on making a cluster a=4WT8|1|DV|C|11 B=4WT8|1|DV|U|39
pMakeNodesCluster: amax is 17 bmin is 18, use_amax is 0
pMakeNodesCluster: Cluster goes from 5 to 15 and then 30 to 30
aa is 15 bb is 30
  3 Cluster   4WT8|1|DV|C|11:4WT8|1|DV|G|24 4WT8|1|DV|U|39:4WT8|1|DV|U|39
    LR Inter  4WT8|1|DV|G|15 4WT8|1|DV|U|39 tWS 
    LL Inter  4WT8|1|DV|G|15 4WT8|1|DV|U|20 tSH 
    LL Inter  4WT8|1|DV|C|13 4WT8|1|DV|G|22 cWW 
    LL Inter  4WT8|1|DV|C|11 4WT8|1|DV|G|24 cWW 
    Left  strand conserved insertion 4WT8|1|DV|U|12 at position 2
    Left  strand conserved insertion 4WT8|1|DV|A|14 at position 4
    Left  strand conserved insertion 4WT8|1|DV|G|18 at position 6
    Left  strand conserved insertion 4WT8|1|DV|A|21 at position 8
    Left  strand conserved insertion 4WT8|1|DV|A|23 at position 10
pMakeNodesCluster a=16 B=29 at the end
pMakeNodesCluster a=16 B=29 at the end
pMakeNodes adding hairpin:     a=4WT8|1|DV|C|25 B=4WT8|1|DV|A|38
    Right strand conserved insertion C  25 at right strand position 1
    Right strand conserved insertion A  26 at right strand position 2
    Right strand conserved insertion G  27 at right strand position 3
    Right strand conserved insertion G  28 at right strand position 4
    Right strand conserved insertion G  29 at right strand position 5
    Right strand conserved insertion G  30 at right strand position 6
    Right strand conserved insertion A  31 at right strand position 7
    Right strand conserved insertion U  32 at right strand position 8
    Right strand conserved insertion U  33 at right strand position 9
    Right strand conserved insertion G  34 at right strand position 10
    Right strand conserved insertion A  35 at right strand position 11
    Right strand conserved insertion A  36 at right strand position 12
    Right strand conserved insertion A  37 at right strand position 13
    Right strand conserved insertion A  38 at right strand position 14
  4 Hairpin   25:38 CAGGGGAUUGAAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 37
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 37
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7  8  9 10 11 12 13 14 15 Right 30
pMakeMotifModelFromSSF:   4   Hairpin Left 16 Right 29
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|C|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|C|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|U|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|U|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|A|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WT8|1|DV|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: 37
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [37×37 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 37
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AUAG'
           RightLetter: 'UCCGAGU'
               Comment: ' // Basepair A7 - U46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 36
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|U|8'
              NumLoops: []
                  Edge: []
         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: []
          LeftNotInter: [2 4 6 8 10]
         RightNotInter: [1×0 double]
              NormCons: 0.3470

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|A|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: [16 17 18 19 20 21 22 23 24 25 26 27 28 29]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|G|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 36
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|C|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 35
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 35
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|C|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 34
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 34
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|U|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 5
            RightIndex: 33
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 5
            RightIndex: 33
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|U|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 5
            RightIndex: 32
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 5
            RightIndex: 32
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|A|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 5
            RightIndex: 31
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 5
            RightIndex: 31
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WT8|1|DV|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 5
            RightIndex: 30
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 22
             LeftIndex: [5 6 7 8 9 10 11 12 13 14 15]
            RightIndex: 30
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUCAGGUAGAG'
           RightLetter: 'U'
               Comment: ' // Cluster node 4WT8|1|DV|C|11:4WT8|1|DV|G|24 and 4WT8|1|DV|U|39:4WT8|1|DV|U|39'
              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: []
          LeftNotInter: [2 4 6 8 10]
         RightNotInter: [1×0 double]
              NormCons: 0.3470

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 16
            RightIndex: 29
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             LeftIndex: 16
            RightIndex: 29
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAGGGGAUUGAAAA'
           RightLetter: ''
               Comment: ' // Hairpin node C25:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: [16 17 18 19 20 21 22 23 24 25 26 27 28 29]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 37
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 37
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 36
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 36
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 36
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 36
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 36
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 36
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 36
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 35
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right 35
pMakeMotifModelFromSSF:  12   Initial Left  5 Right 34
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right 34
pMakeMotifModelFromSSF:  14   Initial Left  5 Right 33
pMakeMotifModelFromSSF:  15     Fixed Left  5 Right 33
pMakeMotifModelFromSSF:  16   Initial Left  5 Right 32
pMakeMotifModelFromSSF:  17     Fixed Left  5 Right 32
pMakeMotifModelFromSSF:  18   Initial Left  5 Right 31
pMakeMotifModelFromSSF:  19     Fixed Left  5 Right 31
pMakeMotifModelFromSSF:  20   Initial Left  5 Right 30
pMakeMotifModelFromSSF:  21   Cluster Left  5  6  7  8  9 10 11 12 13 14 15 Right 30
pMakeMotifModelFromSSF:  22   Initial Left 16 Right 29
pMakeMotifModelFromSSF:  23   Hairpin Left 16 Right 29
pNextNodeJunction: Found a hairpin at node 23
pUpdateModelWithSSF: HL_73916.1 allow insertions from initial node 22?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 23

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_73916.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -26.3197

Timestamp 18-Jul-2025 22:27:01
pMakeSCFGModels: Making JAR3D model for motif group HL_74055.2, number 179 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|2745 B=5J7L|1|DA|G|2759
  2 Basepair  2745 2759 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|2746 B=5J7L|1|DA|A|2758
pMakeNodes checking on making a cluster a=5J7L|1|DA|U|2746 B=5J7L|1|DA|A|2758
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 0
pMakeNodesCluster: Cluster goes from 2 to 3 and then 10 to 12
aa is 3 bb is 10
  3 Cluster   5J7L|1|DA|U|2746:5J7L|1|DA|G|2747 5J7L|1|DA|U|2756:5J7L|1|DA|A|2758
    LR Inter  5J7L|1|DA|U|2746 5J7L|1|DA|U|2756 tWH 
    LR Inter  5J7L|1|DA|G|2747 5J7L|1|DA|A|2757 tSH 
    LR Inter  5J7L|1|DA|U|2746 5J7L|1|DA|A|2758 tSH 
    RR Inter  5J7L|1|DA|U|2756 5J7L|1|DA|A|2758 cWH 
pMakeNodesCluster a=4 B=9 at the end
pMakeNodesCluster a=4 B=9 at the end
No need to probe because of interaction between a=5J7L|1|DA|A|2748 B=5J7L|1|DA|U|2754
  4 Basepair  2748 2754 AU tHW 
No need to probe because of interaction between a=5J7L|1|DA|A|2749 B=5J7L|1|DA|A|2753
  5 Basepair  2749 2753 AA tHW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|2750 B=5J7L|1|DA|C|2752
  6 Hairpin   2750:2752 AC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right 10 11 12
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2745 - G2759 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: [10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UG'
           RightLetter: 'UAA'
               Comment: ' // Cluster node 5J7L|1|DA|U|2746:5J7L|1|DA|G|2747 and 5J7L|1|DA|U|2756:5J7L|1|DA|A|2758'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0204

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 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 A2748 - U2754 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2749 - A2753 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]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: ''
               Comment: ' // Hairpin node A2750:C2752'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction A2750 - C2752 tSW '}
      JunctionDeletion: []
          InterIndices: [6 7]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right 10 11 12
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  7
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_74055.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1388
   -6.2905
   -6.1388
   -6.1388
   -7.0750
   -7.0750
   -6.1388

Timestamp 18-Jul-2025 22:27:01
pMakeSCFGModels: Making JAR3D model for motif group HL_74292.1, number 180 of 253
pMakeNodes starting loop:     a=4FRN|1|B|G|90 B=4FRN|1|B|C|99
  2 Basepair    90   99 GC cWW 
pMakeNodes adding hairpin:     a=4FRN|1|B|C|91 B=4FRN|1|B|A|98
    Right strand conserved insertion C  91 at right strand position 1
    Right strand conserved insertion A  92 at right strand position 2
    Right strand conserved insertion A  93 at right strand position 3
    Right strand conserved insertion G  94 at right strand position 4
    Right strand conserved insertion G  95 at right strand position 5
    Right strand conserved insertion A  96 at right strand position 6
    Right strand conserved insertion G  97 at right strand position 7
    Right strand conserved insertion A  98 at right strand position 8
  3 Hairpin   91:98 CAAGGAGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G90 - C99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAAGGAGA'
           RightLetter: ''
               Comment: ' // Hairpin node C91:A98'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_74292.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0758

Timestamp 18-Jul-2025 22:27:01
pMakeSCFGModels: Making JAR3D model for motif group HL_74379.3, number 181 of 253
pMakeNodes starting loop:     a=8JY0|1|B|G|42 B=8JY0|1|B|C|53
  2 Basepair    42   53 GC cWW 
pMakeNodes probe for inserts:  a=8JY0|1|B|C|43 B=8JY0|1|B|C|52
    Insertion on left  8JY0|1|B|C|43
    Insertion on right 8JY0|1|B|C|52
pMakeNodesProbeForInsertions:  a 8JY0|1|B|A|44 interacts with 8JY0|1|B|A|51
pMakeNodesProbeForInsertions:  B 8JY0|1|B|A|51 interacts with 8JY0|1|B|A|44
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8JY0|1|B|A|51 interacts with 8JY0|1|B|A|44
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8JY0|1|B|A|44 B=8JY0|1|B|A|51
  3 Basepair    44   51 AA cSS 
No need to probe because of interaction between a=8JY0|1|B|A|45 B=8JY0|1|B|A|50
  4 Basepair    45   50 AA cSS 
pMakeNodes adding hairpin:     a=8JY0|1|B|G|46 B=8JY0|1|B|G|46
    Right strand conserved insertion G  46 at right strand position 1
  5 Hairpin   46:46 G
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8JY0|1|B|C|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8JY0|1|B|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: 'CC'
               Comment: ' // Basepair G42 - C53 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8JY0|1|B|C|43'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'A'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8JY0|1|B|U|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G46'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            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 A44 - A51 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A45 - A50 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: ''
               Comment: ' // Hairpin node G46:G46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 5
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position G46'}
      JunctionDeletion: []
          InterIndices: [5 5]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_74379.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4399
   -9.4399

Timestamp 18-Jul-2025 22:27:02
pMakeSCFGModels: Making JAR3D model for motif group HL_75293.5, number 182 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|A|885 B=8CRE|1|CM|U|894
  2 Basepair   885  894 AU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|886 B=8CRE|1|CM|U|893
    Insertion on left  8CRE|1|CM|G|886
    Insertion on right 8CRE|1|CM|U|893
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|G|887 interacts with 8CRE|1|CM|A|892
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|A|892 interacts with 8CRE|1|CM|G|887
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|A|892 interacts with 8CRE|1|CM|G|887
pMakeNodes probed for insert:  a=8CRE|1|CM|G|887 B=8CRE|1|CM|A|892
  3 Basepair   887  892 GA tSH 
pMakeNodes adding hairpin:     a=8CRE|1|CM|U|888 B=8CRE|1|CM|A|891
    Right strand conserved insertion U 888 at right strand position 1
    Right strand conserved insertion G 889 at right strand position 2
    Right strand conserved insertion A 890 at right strand position 3
    Right strand conserved insertion A 891 at right strand position 4
  4 Hairpin   888:891 UGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|886
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|U|893
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'UU'
               Comment: ' // Basepair A885 - U894 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|886'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UGAA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 8CRE|1|CM|U|893'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G887 - A892 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAA'
           RightLetter: ''
               Comment: ' // Hairpin node U888:A891'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  7
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_75293.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3134
   -8.6036
   -8.6036
   -8.3134
   -9.9106
   -8.5505
   -9.9106
   -8.5505
  -11.2889
   -9.8823
  -14.7366

Timestamp 18-Jul-2025 22:27:02
pMakeSCFGModels: Making JAR3D model for motif group HL_75660.5, number 183 of 253
pMakeNodes starting loop:     a=8CRE|1|1|C|207 B=8CRE|1|1|G|211
  2 Basepair   207  211 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|A|208 B=8CRE|1|1|A|208
    Right strand conserved insertion A 208 at right strand position 1
  3 Hairpin   208:208 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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 C207 - G211 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A208:A208'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A208'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_75660.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0531
   -4.8164
   -4.9539
   -8.3526
   -4.9539
   -6.0295
   -5.3059
   -6.8003
   -4.5368
   -6.1670
   -7.4459
   -7.9849
   -9.2616
   -8.5946
   -7.0782
   -7.0799
   -5.7230
   -4.9539
   -6.8915

Timestamp 18-Jul-2025 22:27:02
pMakeSCFGModels: Making JAR3D model for motif group HL_76094.1, number 184 of 253
pMakeNodes starting loop:     a=9E7E|1|C|C|20 B=9E7E|1|C|G|24
pMakeNodes checking on making a cluster a=9E7E|1|C|C|20 B=9E7E|1|C|G|24
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 1 and then 4 to 5
aa is 1 bb is 4
  2 Cluster   9E7E|1|C|C|20:9E7E|1|C|C|20 9E7E|1|C|U|23:9E7E|1|C|G|24
    LR Inter  9E7E|1|C|C|20 9E7E|1|C|G|24 cWW 
    RR Inter  9E7E|1|C|U|23 9E7E|1|C|G|24 cWS 
pMakeNodesCluster a=2 B=3 at the end
pMakeNodesCluster a=2 B=3 at the end
pMakeNodes adding hairpin:     a=9E7E|1|C|A|21 B=9E7E|1|C|A|22
    Right strand conserved insertion A  21 at right strand position 1
    Right strand conserved insertion A  22 at right strand position 2
  3 Hairpin   21:22 AA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  4  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: [4 5]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'UG'
               Comment: ' // Cluster node 9E7E|1|C|C|20:9E7E|1|C|C|20 and 9E7E|1|C|U|23:9E7E|1|C|G|24'
              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]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2501

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: ''
               Comment: ' // Hairpin node A21:A22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position A21'  ' // Hairpin conserved non-basepairing position A22'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  4  5
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_76094.1 allow insertions from initial node 3?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_76094.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.8581

Timestamp 18-Jul-2025 22:27:02
pMakeSCFGModels: Making JAR3D model for motif group HL_77082.1, number 185 of 253
pMakeNodes starting loop:     a=9DE7|1|A|C|29 B=9DE7|1|A|G|36
  2 Basepair    29   36 CG cWW 
No need to probe because of interaction between a=9DE7|1|A|C|30 B=9DE7|1|A|A|35
  3 Basepair    30   35 CA bif 
pMakeNodes adding hairpin:     a=9DE7|1|A|G|31 B=9DE7|1|A|A|34
    Right strand conserved insertion G  31 at right strand position 1
    Right strand conserved insertion A  32 at right strand position 2
    Right strand conserved insertion A  33 at right strand position 3
    Right strand conserved insertion A  34 at right strand position 4
  4 Hairpin   31:34 GAAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C29 - G36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C30 - A35 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAAA'
           RightLetter: ''
               Comment: ' // Hairpin node G31:A34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_77082.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5076
   -8.0559
   -9.9778
   -8.6955
  -11.9364
   -7.9409
  -10.4475
  -10.4475

Timestamp 18-Jul-2025 22:27:02
pMakeSCFGModels: Making JAR3D model for motif group HL_77436.5, number 186 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|C|1294 B=8CRE|1|CM|G|1301
  2 Basepair  1294 1301 CG cWW 
No need to probe because of interaction between a=8CRE|1|CM|U|1295 B=8CRE|1|CM|U|1300
  3 Basepair  1295 1300 UU cWW 
pMakeNodes adding hairpin:     a=8CRE|1|CM|U|1296 B=8CRE|1|CM|A|1298
    Right strand conserved insertion U1296 at right strand position 1
    Right strand conserved insertion A1297 at right strand position 2
    Right strand conserved insertion A1298 at right strand position 3
  4 Hairpin   1296:1298 UAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1294 - G1301 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U1295 - U1300 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: ''
               Comment: ' // Hairpin node U1296:A1298'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_77436.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5169
   -6.5169
   -6.5169
   -6.5169
   -6.2451
   -6.2451
  -13.4307
  -13.4307
   -7.2361
   -8.1459
   -8.1459
   -8.4384
   -8.5526
   -8.5526
   -6.6467
   -8.5876
  -11.2021
  -10.3851
  -12.6310
  -11.2283
  -13.7588
   -9.4134
   -8.8106

Timestamp 18-Jul-2025 22:27:03
pMakeSCFGModels: Making JAR3D model for motif group HL_77600.2, number 187 of 253
pMakeNodes starting loop:     a=8CRE|1|1|G|303 B=8CRE|1|1|C|312
  2 Basepair   303  312 GC cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|A|307 B=8CRE|1|1|C|311
    Right strand conserved insertion A 307 at right strand position 1
    Right strand conserved insertion A 308 at right strand position 2
    Right strand conserved insertion U 309 at right strand position 3
    Right strand conserved insertion U 310 at right strand position 4
    Right strand conserved insertion C 311 at right strand position 5
  3 Hairpin   307:311 AAUUC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G303 - C312 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUUC'
           RightLetter: ''
               Comment: ' // Hairpin node A307:C311'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_77600.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4822
  -10.4822
  -11.9173
  -12.5472
   -9.7460
  -11.2817
  -13.3997
   -9.8045
  -12.2322
  -13.4670

Timestamp 18-Jul-2025 22:27:03
pMakeSCFGModels: Making JAR3D model for motif group HL_78197.1, number 188 of 253
pMakeNodes starting loop:     a=6UFG|1|A|G|69 B=6UFG|1|A|C|76
  2 Basepair    69   76 GC cWW 
pMakeNodes adding hairpin:     a=6UFG|1|A|G|70 B=6UFG|1|A|C|75
    Right strand conserved insertion G  70 at right strand position 1
    Right strand conserved insertion U  71 at right strand position 2
    Right strand conserved insertion U  72 at right strand position 3
    Right strand conserved insertion G  73 at right strand position 4
    Right strand conserved insertion G  74 at right strand position 5
    Right strand conserved insertion C  75 at right strand position 6
  3 Hairpin   70:75 GUUGGC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G69 - C76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUUGGC'
           RightLetter: ''
               Comment: ' // Hairpin node G70:C75'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_78197.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7357
   -7.7357
   -9.9411
  -11.1777
  -10.5603

Timestamp 18-Jul-2025 22:27:03
pMakeSCFGModels: Making JAR3D model for motif group HL_78284.1, number 189 of 253
pMakeNodes starting loop:     a=5J7L|1|AA|U|1009 B=5J7L|1|AA|G|1020
  2 Basepair  1009 1020 UG cWW 
pMakeNodes adding hairpin:     a=5J7L|1|AA|U|1010 B=5J7L|1|AA|A|1019
    Right strand conserved insertion U1010 at right strand position 1
    Right strand conserved insertion C1011 at right strand position 2
    Right strand conserved insertion A1012 at right strand position 3
    Right strand conserved insertion G1013 at right strand position 4
    Right strand conserved insertion A1014 at right strand position 5
    Right strand conserved insertion G1015 at right strand position 6
    Right strand conserved insertion G1018 at right strand position 7
    Right strand conserved insertion A1019 at right strand position 8
  3 Hairpin   1010:1019 UCAGAGGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1009 - G1020 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCAGAGGA'
           RightLetter: ''
               Comment: ' // Hairpin node U1010:A1019'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_78284.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7410
  -13.5816

Timestamp 18-Jul-2025 22:27:03
pMakeSCFGModels: Making JAR3D model for motif group HL_78347.4, number 190 of 253
pMakeNodes starting loop:     a=5HR6|1|C|U|12 B=5HR6|1|C|G|22
  2 Basepair    12   22 UG cWW 
No need to probe because of interaction between a=5HR6|1|C|A|13 B=5HR6|1|C|A|21
  3 Basepair    13   21 AA cWS 
pMakeNodes adding hairpin:     a=5HR6|1|C|G|14 B=5HR6|1|C|C|19
  4 Hairpin   14:19 GC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U12 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A13 - A21 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GC'
           RightLetter: ''
               Comment: ' // Hairpin node G14:C19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction G14 - C19 tSW '}
      JunctionDeletion: []
          InterIndices: [3 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_78347.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.8443
  -10.8443
  -10.8443
  -13.3006
  -14.9507
  -11.5688
  -11.5688
   -8.0569
   -9.9924

Timestamp 18-Jul-2025 22:27:03
pMakeSCFGModels: Making JAR3D model for motif group HL_78677.1, number 191 of 253
pMakeNodes starting loop:     a=2CZJ|1|B|U|26 B=2CZJ|1|B|G|29
  2 Basepair    26   29 UG cWW 
pMakeNodes adding hairpin:     a=2CZJ|1|B|U|27 B=2CZJ|1|B|U|27
    Right strand conserved insertion U  27 at right strand position 1
  3 Hairpin   27:27 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 3
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [3×3 double]
         Extensibility: [0 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 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: 'G'
               Comment: ' // Basepair U26 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U27:U27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 2
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U27'}
      JunctionDeletion: []
          InterIndices: [2 2]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  3
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  3
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  2
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_78677.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.8850
   -4.9193

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80008.1, number 192 of 253
pMakeNodes starting loop:     a=2R8S|1|R|C|166 B=2R8S|1|R|G|174
  2 Basepair   166  174 CG cWW 
No need to probe because of interaction between a=2R8S|1|R|U|167 B=2R8S|1|R|A|173
  3 Basepair   167  173 UA tHH 
pMakeNodes adding hairpin:     a=2R8S|1|R|G|169 B=2R8S|1|R|A|172
    Right strand conserved insertion G 169 at right strand position 1
    Right strand conserved insertion C 170 at right strand position 2
  4 Hairpin   169:172 GCAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C166 - G174 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U167 - A173 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCAA'
           RightLetter: ''
               Comment: ' // Hairpin node G169:A172'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80008.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4953

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80241.1, number 193 of 253
pMakeNodes starting loop:     a=8V1I|1|B|U|22 B=8V1I|1|B|A|30
  2 Basepair    22   30 UA cWW 
pMakeNodes adding hairpin:     a=8V1I|1|B|G|23 B=8V1I|1|B|C|29
    Right strand conserved insertion G  23 at right strand position 1
    Right strand conserved insertion G  24 at right strand position 2
    Right strand conserved insertion U  25 at right strand position 3
    Right strand conserved insertion U  26 at right strand position 4
    Right strand conserved insertion U  27 at right strand position 5
    Right strand conserved insertion C  28 at right strand position 6
    Right strand conserved insertion C  29 at right strand position 7
  3 Hairpin   23:29 GGUUUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U22 - A30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGUUUCC'
           RightLetter: ''
               Comment: ' // Hairpin node G23:C29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80241.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8457
   -6.8457

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80362.1, number 194 of 253
pMakeNodes starting loop:     a=1GAX|1|D|C|930 B=1GAX|1|D|G|938
  2 Basepair   930  938 CG cWW 
pMakeNodes adding hairpin:     a=1GAX|1|D|A|934 B=1GAX|1|D|A|936
    Right strand conserved insertion A 934 at right strand position 1
    Right strand conserved insertion C 935 at right strand position 2
    Right strand conserved insertion A 936 at right strand position 3
  3 Hairpin   934:936 ACA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C930 - G938 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACA'
           RightLetter: ''
               Comment: ' // Hairpin node A934:A936'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80362.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0681

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80411.1, number 195 of 253
pMakeNodes starting loop:     a=1H4S|1|T|C|13 B=1H4S|1|T|G|22
  2 Basepair    13   22 CG cWW 
pMakeNodes adding hairpin:     a=1H4S|1|T|A|14 B=1H4S|1|T|U|20
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion C  16 at right strand position 3
    Right strand conserved insertion C  17 at right strand position 4
    Right strand conserved insertion C 17A at right strand position 5
  3 Hairpin   14:20 AGCCCGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCCCGU'
           RightLetter: ''
               Comment: ' // Hairpin node A14:U20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80411.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2707

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80599.2, number 196 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|U|2724 B=8P9A|1|AR|G|2732
  2 Basepair  2724 2732 UG cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|2725 B=8P9A|1|AR|U|2731
  3 Basepair  2725 2731 UU cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|C|2726 B=8P9A|1|AR|G|2730
    Right strand conserved insertion C2726 at right strand position 1
    Right strand conserved insertion A2727 at right strand position 2
    Right strand conserved insertion G2728 at right strand position 3
    Right strand conserved insertion U2729 at right strand position 4
    Right strand conserved insertion G2730 at right strand position 5
  4 Hairpin   2726:2730 CAGUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U2724 - G2732 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U2725 - U2731 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAGUG'
           RightLetter: ''
               Comment: ' // Hairpin node C2726:G2730'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80599.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2987
   -5.2987
   -9.2461

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80709.3, number 197 of 253
pMakeNodes starting loop:     a=4V9F|1|0|C|1808 B=4V9F|1|0|G|1812
  2 Basepair  1808 1812 CG cWW 
pMakeNodes adding hairpin:     a=4V9F|1|0|G|1809 B=4V9F|1|0|A|1811
    Right strand conserved insertion G1809 at right strand position 1
    Right strand conserved insertion C1810 at right strand position 2
    Right strand conserved insertion A1811 at right strand position 3
  3 Hairpin   1809:1811 GCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1808 - G1812 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // Hairpin node G1809:A1811'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80709.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.1784
   -3.1784
   -3.1784
   -3.1784
   -3.5462
   -5.8487
   -3.5462
   -3.5462
   -7.5915
   -6.1252
   -6.1252

Timestamp 18-Jul-2025 22:27:04
pMakeSCFGModels: Making JAR3D model for motif group HL_80922.2, number 198 of 253
pMakeNodes starting loop:     a=4V9F|1|0|G|670 B=4V9F|1|0|C|676
  2 Basepair   670  676 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|A|671 B=4V9F|1|0|U|675
  3 Basepair   671  675 AU tSH 
pMakeNodes adding hairpin:     a=4V9F|1|0|U|673 B=4V9F|1|0|U|673
    Right strand conserved insertion U 673 at right strand position 1
  4 Hairpin   673:673 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G670 - C676 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A671 - U675 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U673:U673'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U673'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_80922.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5586
  -11.3862
   -7.9759

Timestamp 18-Jul-2025 22:27:05
pMakeSCFGModels: Making JAR3D model for motif group HL_81100.2, number 199 of 253
pMakeNodes starting loop:     a=2Y8Y|1|B|C|11 B=2Y8Y|1|B|G|16
pMakeNodes checking on making a cluster a=2Y8Y|1|B|C|11 B=2Y8Y|1|B|G|16
pMakeNodesCluster: amax is 1 bmin is 2, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 1 and then 2 to 2
pMakeNodesCluster: Using a hairpin to finish this stem
pMakeNodes making a hairpin a=2Y8Y|1|B|C|11 B=2Y8Y|1|B|G|16
  2 Hairpin   11:16 CG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  2
pMakeMotifModelFromSSF:   2   Hairpin Left  1 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 2
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [2×2 double]
         Extensibility: [1 1]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CG'
           RightLetter: ''
               Comment: ' // Hairpin node C11:G16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [1 2]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction C11 - G16 cWW '}
      JunctionDeletion: []
          InterIndices: [1 2]
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  2
pMakeMotifModelFromSSF:   2   Hairpin Left  1 Right  2
pNextNodeJunction: Found a hairpin at node 2
pNextNodeJunction: Found a hairpin at node 2

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_81100.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9180
   -5.9180
   -6.1720

Timestamp 18-Jul-2025 22:27:05
pMakeSCFGModels: Making JAR3D model for motif group HL_81205.3, number 200 of 253
pMakeNodes starting loop:     a=4LFB|1|A|C|320 B=4LFB|1|A|G|333
  2 Basepair   320  333 CG cWW 
No need to probe because of interaction between a=4LFB|1|A|A|321 B=4LFB|1|A|G|332
  3 Basepair   321  332 AG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|C|322 B=4LFB|1|A|G|331
    Insertion on right 4LFB|1|A|G|331
    Insertion on right 4LFB|1|A|C|330
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|322 interacts with 4LFB|1|A|A|329
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|329 interacts with 4LFB|1|A|C|322
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|329 interacts with 4LFB|1|A|C|322
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|C|322 B=4LFB|1|A|A|329
  4 Basepair   322  329 CA tWH 
pMakeNodes probe for inserts:  a=4LFB|1|A|U|323 B=4LFB|1|A|C|328
    Insertion on right 4LFB|1|A|C|328
pMakeNodesProbeForInsertions:  a 4LFB|1|A|U|323 interacts with 4LFB|1|A|A|327
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|327 interacts with 4LFB|1|A|U|323
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|327 interacts with 4LFB|1|A|U|323
pMakeNodes probed for insert:  a=4LFB|1|A|U|323 B=4LFB|1|A|A|327
  5 Basepair   323  327 UA tWH 
pMakeNodes adding hairpin:     a=4LFB|1|A|G|324 B=4LFB|1|A|G|326
    Right strand conserved insertion G 324 at right strand position 1
    Right strand conserved insertion A 325 at right strand position 2
    Right strand conserved insertion G 326 at right strand position 3
  6 Hairpin   324:326 GAG
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 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|331
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|330
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|328
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C320 - G333 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'CGG'
               Comment: ' // Basepair A321 - G332 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|331'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GAG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|330'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GAG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 3
            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: 'C'
           RightLetter: 'CA'
               Comment: ' // Basepair C322 - A329 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|328'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U323 - A327 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAG'
           RightLetter: ''
               Comment: ' // Hairpin node G324:G326'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_81205.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7721
   -5.7761

Timestamp 18-Jul-2025 22:27:05
pMakeSCFGModels: Making JAR3D model for motif group HL_81312.1, number 201 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|C|70 B=8P9A|1|sR|G|81
  2 Basepair    70   81 CG cWW 
pMakeNodes adding hairpin:     a=8P9A|1|sR|A|71 B=8P9A|1|sR|A|80
    Right strand conserved insertion A  71 at right strand position 1
    Right strand conserved insertion A  72 at right strand position 2
    Right strand conserved insertion U  73 at right strand position 3
    Right strand conserved insertion U  75 at right strand position 4
    Right strand conserved insertion A  76 at right strand position 5
    Right strand conserved insertion A  78 at right strand position 6
    Right strand conserved insertion C  79 at right strand position 7
    Right strand conserved insertion A  80 at right strand position 8
  3 Hairpin   71:80 AAUUAACA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C70 - G81 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUUAACA'
           RightLetter: ''
               Comment: ' // Hairpin node A71:A80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_81312.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2922
   -6.2922

Timestamp 18-Jul-2025 22:27:05
pMakeSCFGModels: Making JAR3D model for motif group HL_81538.2, number 202 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|G|712 B=5J7L|1|DA|C|719
  2 Basepair   712  719 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|713 B=5J7L|1|DA|A|718
  3 Basepair   713  718 GA tSH 
pMakeNodes adding hairpin:     a=5J7L|1|DA|U|714 B=5J7L|1|DA|C|717
    Right strand conserved insertion U 714 at right strand position 1
    Right strand conserved insertion A 715 at right strand position 2
    Right strand conserved insertion A 716 at right strand position 3
    Right strand conserved insertion C 717 at right strand position 4
  4 Hairpin   714:717 UAAC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G712 - C719 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G713 - A718 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAAC'
           RightLetter: ''
               Comment: ' // Hairpin node U714:C717'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_81538.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7878
   -5.9647
   -5.8281
   -5.8281
   -6.9267
   -5.9647
   -6.4022
   -7.9185
   -7.6655
   -9.5194
   -8.1742
  -10.8398
  -11.6194
  -14.1075
  -10.8398
   -8.5573

Timestamp 18-Jul-2025 22:27:05
pMakeSCFGModels: Making JAR3D model for motif group HL_81545.2, number 203 of 253
pMakeNodes starting loop:     a=4V9F|1|0|G|1498 B=4V9F|1|0|C|1507
  2 Basepair  1498 1507 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|U|1499 B=4V9F|1|0|A|1504
  3 Basepair  1499 1504 UA tWH 
pMakeNodes probe for inserts:  a=4V9F|1|0|U|1500 B=4V9F|1|0|U|1503
    Insertion on right 4V9F|1|0|U|1503
pMakeNodesProbeForInsertions:  a 4V9F|1|0|U|1500 interacts with 4V9F|1|0|A|1502
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|1502 interacts with 4V9F|1|0|U|1500
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|1502 interacts with 4V9F|1|0|U|1500
pMakeNodes probed for insert:  a=4V9F|1|0|U|1500 B=4V9F|1|0|A|1502
  4 Basepair  1500 1502 UA tSH 
pMakeNodes adding hairpin:     a=4V9F|1|0|A|1501 B=4V9F|1|0|A|1501
    Right strand conserved insertion A1501 at right strand position 1
  5 Hairpin   1501:1501 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|U|1503
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1498 - C1507 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'UA'
               Comment: ' // Basepair U1499 - A1504 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|U|1503'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 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: 'A'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1501'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1500 - A1502 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A1501:A1501'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 4
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A1501'}
      JunctionDeletion: []
          InterIndices: [4 4]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  4 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_81545.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2796
   -4.2796
   -5.7459
   -4.8674
   -5.3782
   -4.2796
   -6.6203

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_82710.2, number 204 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|G|123 B=9DFE|1|1A|C|128
  2 Basepair   123  128 GC cWW 
pMakeNodes adding hairpin:     a=9DFE|1|1A|G|124 B=9DFE|1|1A|A|127
    Right strand conserved insertion G 124 at right strand position 1
    Right strand conserved insertion A 126 at right strand position 2
    Right strand conserved insertion A 127 at right strand position 3
  3 Hairpin   124:127 GAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G123 - C128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: ''
               Comment: ' // Hairpin node G124:A127'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_82710.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8438
   -4.3329
   -4.3329
   -6.8748

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_83632.1, number 205 of 253
pMakeNodes starting loop:     a=2AKE|1|B|A|31 B=2AKE|1|B|U|39
  2 Basepair    31   39 AU cWW 
pMakeNodes adding hairpin:     a=2AKE|1|B|C|32 B=2AKE|1|B|A|38
    Right strand conserved insertion C  32 at right strand position 1
    Right strand conserved insertion C  34 at right strand position 2
    Right strand conserved insertion C  35 at right strand position 3
    Right strand conserved insertion A  36 at right strand position 4
    Right strand conserved insertion G  37 at right strand position 5
    Right strand conserved insertion A  38 at right strand position 6
  3 Hairpin   32:38 CCCAGA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCAGA'
           RightLetter: ''
               Comment: ' // Hairpin node C32:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_83632.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5022
   -6.9765
   -5.5779
   -5.5779
   -7.3130
   -5.8374

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_83808.4, number 206 of 253
pMakeNodes starting loop:     a=3NKB|1|B|C|20 B=3NKB|1|B|G|28
  2 Basepair    20   28 CG cWW 
No need to probe because of interaction between a=3NKB|1|B|U|21 B=3NKB|1|B|G|26
  3 Basepair    21   26 UG tWW 
pMakeNodes adding hairpin:     a=3NKB|1|B|C|22 B=3NKB|1|B|C|25
    Right strand conserved insertion C  22 at right strand position 1
    Right strand conserved insertion C  23 at right strand position 2
    Right strand conserved insertion C  25 at right strand position 3
  4 Hairpin   22:25 CCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C20 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U21 - G26 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCC'
           RightLetter: ''
               Comment: ' // Hairpin node C22:C25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_83808.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5686
   -5.9296
   -5.9296

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_84299.4, number 207 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|G|330 B=8P9A|1|sR|C|338
  2 Basepair   330  338 GC cWW 
No need to probe because of interaction between a=8P9A|1|sR|A|331 B=8P9A|1|sR|G|336
  3 Basepair   331  336 AG tWH 
pMakeNodes adding hairpin:     a=8P9A|1|sR|U|332 B=8P9A|1|sR|U|335
    Right strand conserved insertion U 332 at right strand position 1
    Right strand conserved insertion A 333 at right strand position 2
    Right strand conserved insertion G 334 at right strand position 3
    Right strand conserved insertion U 335 at right strand position 4
  4 Hairpin   332:335 UAGU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G330 - C338 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A331 - G336 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAGU'
           RightLetter: ''
               Comment: ' // Hairpin node U332:U335'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_84299.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3081
   -5.3081
   -5.8062
   -6.3940
  -12.9093
   -5.2909
   -5.2909
   -5.4915
   -9.9063

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_84847.1, number 208 of 253
pMakeNodes starting loop:     a=7REX|1|A|G|5 B=7REX|1|A|C|18
  2 Basepair     5   18 GC cWW 
pMakeNodes probe for inserts:  a=7REX|1|A|U|6 B=7REX|1|A|C|17
    Insertion on left  7REX|1|A|U|6
    Insertion on left  7REX|1|A|U|7
    Insertion on right 7REX|1|A|C|17
    Insertion on right 7REX|1|A|U|16
    Insertion on right 7REX|1|A|A|15
    Insertion on right 7REX|1|A|C|14
    Insertion on right 7REX|1|A|C|13
pMakeNodesProbeForInsertions:  a 7REX|1|A|C|8 interacts with 7REX|1|A|A|12
pMakeNodesProbeForInsertions:  B 7REX|1|A|A|12 interacts with 7REX|1|A|C|8
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7REX|1|A|A|12 interacts with 7REX|1|A|C|8
pMakeNodes probed for insert:  a=7REX|1|A|C|8 B=7REX|1|A|A|12
  3 Basepair     8   12 CA tWW 
pMakeNodes adding hairpin:     a=7REX|1|A|G|9 B=7REX|1|A|A|11
    Right strand conserved insertion G   9 at right strand position 1
    Right strand conserved insertion C  10 at right strand position 2
    Right strand conserved insertion A  11 at right strand position 3
  4 Hairpin   9:11 GCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7REX|1|A|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7REX|1|A|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7REX|1|A|C|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7REX|1|A|U|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7REX|1|A|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7REX|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7REX|1|A|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUU'
           RightLetter: 'CCAUCC'
               Comment: ' // Basepair G5 - 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]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7REX|1|A|U|6'
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7REX|1|A|U|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7REX|1|A|C|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 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 7REX|1|A|U|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             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 7REX|1|A|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7REX|1|A|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7REX|1|A|C|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 4
            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: 'A'
               Comment: ' // Basepair C8 - A12 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCA'
           RightLetter: ''
               Comment: ' // Hairpin node G9:A11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  4 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  4 Right  9
pMakeMotifModelFromSSF:  15     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:  16   Initial Left  4 Right  8
pMakeMotifModelFromSSF:  17  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:  18   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_84847.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1397

Timestamp 18-Jul-2025 22:27:06
pMakeSCFGModels: Making JAR3D model for motif group HL_85367.2, number 209 of 253
pMakeNodes starting loop:     a=4WF9|1|X|C|2275 B=4WF9|1|X|G|2283
  2 Basepair  2275 2283 CG cWW 
pMakeNodes adding hairpin:     a=4WF9|1|X|U|2276 B=4WF9|1|X|G|2282
    Right strand conserved insertion U2276 at right strand position 1
    Right strand conserved insertion G2278 at right strand position 2
    Right strand conserved insertion G2279 at right strand position 3
    Right strand conserved insertion G2280 at right strand position 4
    Right strand conserved insertion C2281 at right strand position 5
    Right strand conserved insertion G2282 at right strand position 6
  3 Hairpin   2276:2282 UGGGCG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2275 - G2283 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGGCG'
           RightLetter: ''
               Comment: ' // Hairpin node U2276:G2282'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_85367.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7419
   -4.7419
   -4.7419
   -4.7419
   -4.7419
   -4.7419
   -4.7419
   -9.2524
   -8.4051
  -12.9187
  -12.9187

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_85434.1, number 210 of 253
pMakeNodes starting loop:     a=8VM9|1|R|G|15 B=8VM9|1|R|C|24
  2 Basepair    15   24 GC cWW 
No need to probe because of interaction between a=8VM9|1|R|G|16 B=8VM9|1|R|A|23
  3 Basepair    16   23 GA cWW 
No need to probe because of interaction between a=8VM9|1|R|U|17 B=8VM9|1|R|C|22
  4 Basepair    17   22 UC cSW 
pMakeNodes adding hairpin:     a=8VM9|1|R|A|18 B=8VM9|1|R|C|21
    Right strand conserved insertion A  18 at right strand position 1
    Right strand conserved insertion U  19 at right strand position 2
    Right strand conserved insertion C  20 at right strand position 3
    Right strand conserved insertion C  21 at right strand position 4
  5 Hairpin   18:21 AUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G16 - A23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U17 - C22 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUCC'
           RightLetter: ''
               Comment: ' // Hairpin node A18:C21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  7
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_85434.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5869

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_85461.1, number 211 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|G|701 B=8CRE|1|CM|C|720
pMakeNodes checking on making a cluster a=8CRE|1|CM|G|701 B=8CRE|1|CM|C|720
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 2 and then 15 to 15
aa is 2 bb is 15
  2 Cluster   8CRE|1|CM|G|701:8CRE|1|CM|G|702 8CRE|1|CM|C|720:8CRE|1|CM|C|720
    LR Inter  8CRE|1|CM|G|701 8CRE|1|CM|C|720 cWW 
    LR Inter  8CRE|1|CM|G|702 8CRE|1|CM|C|720 cHW 
pMakeNodesCluster a=3 B=14 at the end
pMakeNodesCluster a=3 B=14 at the end
pMakeNodes adding hairpin:     a=8CRE|1|CM|U|703 B=8CRE|1|CM|A|719
    Right strand conserved insertion U 703 at right strand position 1
    Right strand conserved insertion A 704 at right strand position 2
    Right strand conserved insertion G 705 at right strand position 3
    Right strand conserved insertion C 706 at right strand position 4
    Right strand conserved insertion C 707 at right strand position 5
    Right strand conserved insertion A 708 at right strand position 6
    Right strand conserved insertion U 709 at right strand position 7
    Right strand conserved insertion U 710 at right strand position 8
    Right strand conserved insertion G 714 at right strand position 9
    Right strand conserved insertion G 715 at right strand position 10
    Right strand conserved insertion C 716 at right strand position 11
    Right strand conserved insertion A 719 at right strand position 12
  3 Hairpin   703:719 UAGCCAUUGGCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 15
pMakeMotifModelFromSSF:   3   Hairpin Left  3 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [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: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GG'
           RightLetter: 'C'
               Comment: ' // Cluster node 8CRE|1|CM|G|701:8CRE|1|CM|G|702 and 8CRE|1|CM|C|720:8CRE|1|CM|C|720'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAGCCAUUGGCA'
           RightLetter: ''
               Comment: ' // Hairpin node U703:A719'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×12 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9 10 11 12 13 14]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [12×2 double]
    InteractionComment: {1×12 cell}
      JunctionDeletion: []
          InterIndices: [12×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 15
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right 14
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_85461.1 allow insertions from initial node 3?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_85461.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.9399

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_85993.1, number 212 of 253
pMakeNodes starting loop:     a=1S03|1|B|A|22 B=1S03|1|B|U|29
  2 Basepair    22   29 AU cWW 
pMakeNodes adding hairpin:     a=1S03|1|B|G|23 B=1S03|1|B|A|27
    Right strand conserved insertion G  23 at right strand position 1
    Right strand conserved insertion G  24 at right strand position 2
    Right strand conserved insertion C  25 at right strand position 3
    Right strand conserved insertion A  26 at right strand position 4
    Right strand conserved insertion A  27 at right strand position 5
  3 Hairpin   23:27 GGCAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A22 - U29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGCAA'
           RightLetter: ''
               Comment: ' // Hairpin node G23:A27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_85993.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3471

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_86012.1, number 213 of 253
pMakeNodes starting loop:     a=1ZL3|1|B|G|408 B=1ZL3|1|B|C|416
  2 Basepair   408  416 GC cWW 
pMakeNodes probe for inserts:  a=1ZL3|1|B|U|409 B=1ZL3|1|B|C|415
    Insertion on right 1ZL3|1|B|C|415
    Insertion on right 1ZL3|1|B|U|414
pMakeNodesProbeForInsertions:  a 1ZL3|1|B|U|409 interacts with 1ZL3|1|B|A|413
pMakeNodesProbeForInsertions:  B 1ZL3|1|B|A|413 interacts with 1ZL3|1|B|U|409
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1ZL3|1|B|A|413 interacts with 1ZL3|1|B|U|409
pMakeNodes probed for insert:  a=1ZL3|1|B|U|409 B=1ZL3|1|B|A|413
  3 Basepair   409  413 UA tWH 
pMakeNodes adding hairpin:     a=1ZL3|1|B|C|411 B=1ZL3|1|B|G|412
    Right strand conserved insertion C 411 at right strand position 1
    Right strand conserved insertion G 412 at right strand position 2
  4 Hairpin   411:412 CG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1ZL3|1|B|U|414
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1ZL3|1|B|A|413
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'UCC'
               Comment: ' // Basepair G408 - C416 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1ZL3|1|B|U|414'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            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: 'CG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C411'  ' // Hairpin conserved non-basepairing position G412'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1ZL3|1|B|A|413'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 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: 'A'
               Comment: ' // Basepair U409 - A413 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CG'
           RightLetter: ''
               Comment: ' // Hairpin node C411:G412'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C411'  ' // Hairpin conserved non-basepairing position G412'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  2 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_86012.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.0954
   -3.0954

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_86109.1, number 214 of 253
pMakeNodes starting loop:     a=4MGN|1|A|G|51 B=4MGN|1|A|C|63
  2 Basepair    51   63 GC cWW 
pMakeNodes probe for inserts:  a=4MGN|1|A|G|52 B=4MGN|1|A|A|61
    Insertion on left  4MGN|1|A|G|52
    Insertion on left  4MGN|1|A|G|53
    Insertion on left  4MGN|1|A|C|54
    Insertion on left  4MGN|1|A|G|55
pMakeNodesProbeForInsertions:  B 4MGN|1|A|A|61 interacts with 4MGN|1|A|U|57
pMakeNodesProbeForInsertions:  B 4MGN|1|A|A|61 interacts with 4MGN|1|A|U|57
pMakeNodes probed for insert:  a=4MGN|1|A|G|56 B=4MGN|1|A|A|61
pMakeNodes checking on making a cluster a=4MGN|1|A|G|56 B=4MGN|1|A|A|61
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 0
pMakeNodesCluster: Cluster goes from 6 to 7 and then 11 to 11
aa is 7 bb is 11
  3 Cluster   4MGN|1|A|G|56:4MGN|1|A|U|57 4MGN|1|A|A|61:4MGN|1|A|A|61
    LR Inter  4MGN|1|A|U|57 4MGN|1|A|A|61 tWH 
    Left  strand conserved insertion 4MGN|1|A|G|56 at position 1
pMakeNodesCluster a=8 B=10 at the end
pMakeNodesCluster a=8 B=10 at the end
pMakeNodes adding hairpin:     a=4MGN|1|A|G|58 B=4MGN|1|A|G|60
    Right strand conserved insertion G  58 at right strand position 1
    Right strand conserved insertion G  59 at right strand position 2
    Right strand conserved insertion G  60 at right strand position 3
  4 Hairpin   58:60 GGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  6  7 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|G|53
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|C|54
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|G|55
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-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: 'GGGCG'
           RightLetter: 'C'
               Comment: ' // Basepair G51 - C63 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|G|52'
              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: {' // Cluster Interaction 4MGN|1|A|U|57 - 4MGN|1|A|A|61 tWH '  ' // Left strand conserved insertion 4MGN|1|A|G|56'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 1
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|G|53'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|C|54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|G|55'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 12
             LeftIndex: [6 7]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4MGN|1|A|G|56:4MGN|1|A|U|57 and 4MGN|1|A|A|61:4MGN|1|A|A|61'
              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: {' // Cluster Interaction 4MGN|1|A|U|57 - 4MGN|1|A|A|61 tWH '  ' // Left strand conserved insertion 4MGN|1|A|G|56'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 1
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGG'
           RightLetter: ''
               Comment: ' // Hairpin node G58:G60'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11   Cluster Left  6  7 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right 10
pNextNodeJunction: Found a hairpin at node 13
pUpdateModelWithSSF: HL_86109.1 allow insertions from initial node 12?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_86109.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7310
   -6.7310
   -9.4336

Timestamp 18-Jul-2025 22:27:07
pMakeSCFGModels: Making JAR3D model for motif group HL_86769.4, number 215 of 253
pMakeNodes starting loop:     a=4P5J|1|A|A|69 B=4P5J|1|A|U|76
  2 Basepair    69   76 AU cWW 
pMakeNodes probe for inserts:  a=4P5J|1|A|G|70 B=4P5J|1|A|A|75
    Insertion on left  4P5J|1|A|G|70
pMakeNodesProbeForInsertions:  a 4P5J|1|A|G|71 interacts with 4P5J|1|A|A|75
pMakeNodesProbeForInsertions:  B 4P5J|1|A|A|75 interacts with 4P5J|1|A|G|71
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4P5J|1|A|A|75 interacts with 4P5J|1|A|G|71
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4P5J|1|A|G|71 B=4P5J|1|A|A|75
  3 Basepair    71   75 GA cSS 
pMakeNodes adding hairpin:     a=4P5J|1|A|G|72 B=4P5J|1|A|U|73
  4 Hairpin   72:73 GU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4P5J|1|A|G|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: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Basepair A69 - U76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4P5J|1|A|G|70'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 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: 'GU'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction G72 - U73 cSH '}
      JunctionDeletion: []
          InterIndices: [4 5]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G71 - A75 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: ''
               Comment: ' // Hairpin node G72:U73'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction G72 - U73 cSH '}
      JunctionDeletion: []
          InterIndices: [4 5]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  5
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_86769.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0181
   -8.0181
   -8.1791
   -9.5776
  -15.1995

Timestamp 18-Jul-2025 22:27:08
pMakeSCFGModels: Making JAR3D model for motif group HL_86870.2, number 216 of 253
pMakeNodes starting loop:     a=8CRE|1|1|G|759 B=8CRE|1|1|C|764
  2 Basepair   759  764 GC cWW 
No need to probe because of interaction between a=8CRE|1|1|U|760 B=8CRE|1|1|U|763
  3 Basepair   760  763 UU cWW 
pMakeNodes adding hairpin:     a=8CRE|1|1|U|762 B=8CRE|1|1|U|762
    Right strand conserved insertion U 762 at right strand position 1
  4 Hairpin   762:762 U
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G759 - 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]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U760 - U763 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: ''
               Comment: ' // Hairpin node U762:U762'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position U762'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_86870.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3042
   -5.3042
  -11.3191
   -6.5617

Timestamp 18-Jul-2025 22:27:08
pMakeSCFGModels: Making JAR3D model for motif group HL_86883.1, number 217 of 253
pMakeNodes starting loop:     a=8P9A|1|AT|G|124 B=8P9A|1|AT|C|129
  2 Basepair   124  129 GC cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AT|A|126 B=8P9A|1|AT|U|128
    Right strand conserved insertion A 126 at right strand position 1
    Right strand conserved insertion U 127 at right strand position 2
    Right strand conserved insertion U 128 at right strand position 3
  3 Hairpin   126:128 AUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G124 - C129 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUU'
           RightLetter: ''
               Comment: ' // Hairpin node A126:U128'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_86883.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.4589
   -2.4589

Timestamp 18-Jul-2025 22:27:08
pMakeSCFGModels: Making JAR3D model for motif group HL_87463.1, number 218 of 253
pMakeNodes starting loop:     a=4V9F|1|0|G|390 B=4V9F|1|0|C|399
  2 Basepair   390  399 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|U|391 B=4V9F|1|0|U|398
  3 Basepair   391  398 UU cWW 
pMakeNodes adding hairpin:     a=4V9F|1|0|U|392 B=4V9F|1|0|A|397
    Right strand conserved insertion U 392 at right strand position 1
    Right strand conserved insertion G 393 at right strand position 2
    Right strand conserved insertion G 394 at right strand position 3
    Right strand conserved insertion A 395 at right strand position 4
    Right strand conserved insertion A 397 at right strand position 5
  4 Hairpin   392:397 UGGAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G390 - C399 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U391 - U398 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGAA'
           RightLetter: ''
               Comment: ' // Hairpin node U392:A397'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_87463.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6113

Timestamp 18-Jul-2025 22:27:08
pMakeSCFGModels: Making JAR3D model for motif group HL_87553.1, number 219 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|G|910 B=8P9A|1|AR|C|918
  2 Basepair   910  918 GC cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|911 B=8P9A|1|AR|A|917
  3 Basepair   911  917 CA cWW 
pMakeNodes adding hairpin:     a=8P9A|1|AR|G|912 B=8P9A|1|AR|A|915
    Right strand conserved insertion G 912 at right strand position 1
    Right strand conserved insertion A 914 at right strand position 2
    Right strand conserved insertion A 915 at right strand position 3
  4 Hairpin   912:915 GAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G910 - C918 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       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 C911 - A917 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: ''
               Comment: ' // Hairpin node G912:A915'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  5
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_87553.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3149
   -9.3149
  -10.2739
   -9.2989
   -8.7270
   -9.9856
  -12.5903

Timestamp 18-Jul-2025 22:27:08
pMakeSCFGModels: Making JAR3D model for motif group HL_87954.2, number 220 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|U|779 B=5J7L|1|DA|G|785
  2 Basepair   779  785 UG cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|780 B=5J7L|1|DA|A|783
  3 Basepair   780  783 GA tSW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|A|782 B=5J7L|1|DA|A|782
    Right strand conserved insertion A 782 at right strand position 1
  4 Hairpin   782:782 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 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 U779 - G785 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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: 'A'
               Comment: ' // Basepair G780 - A783 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A782:A782'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 3
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A782'}
      JunctionDeletion: []
          InterIndices: [3 3]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  3
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_87954.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6698
   -6.7684
   -5.6698
   -7.0406
   -7.0078
   -7.6549
   -6.4970

Timestamp 18-Jul-2025 22:27:09
pMakeSCFGModels: Making JAR3D model for motif group HL_88205.2, number 221 of 253
pMakeNodes starting loop:     a=8P9A|1|AR|A|876 B=8P9A|1|AR|U|885
pMakeNodes checking on making a cluster a=8P9A|1|AR|A|876 B=8P9A|1|AR|U|885
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 2 and then 5 to 7
aa is 2 bb is 5
  2 Cluster   8P9A|1|AR|A|876:8P9A|1|AR|C|877 8P9A|1|AR|C|881:8P9A|1|AR|U|885
    LR Inter  8P9A|1|AR|C|877 8P9A|1|AR|A|882 tSW 
    LR Inter  8P9A|1|AR|A|876 8P9A|1|AR|U|885 cWW 
    RR Inter  8P9A|1|AR|C|881 8P9A|1|AR|U|885 cWS 
pMakeNodesCluster a=3 B=4 at the end
pMakeNodesCluster a=3 B=4 at the end
pMakeNodes adding hairpin:     a=8P9A|1|AR|G|878 B=8P9A|1|AR|G|880
    Right strand conserved insertion G 878 at right strand position 1
    Right strand conserved insertion G 880 at right strand position 2
  3 Hairpin   878:880 GG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5  6  7
pMakeMotifModelFromSSF:   3   Hairpin Left  3 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: [5 6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'CAU'
               Comment: ' // Cluster node 8P9A|1|AR|A|876:8P9A|1|AR|C|877 and 8P9A|1|AR|C|881:8P9A|1|AR|U|885'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2543

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GG'
           RightLetter: ''
               Comment: ' // Hairpin node G878:G880'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position G878'  ' // Hairpin conserved non-basepairing position G880'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5  6  7
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  4
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_88205.2 allow insertions from initial node 3?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_88205.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7168
   -5.7168
   -9.5689
   -6.2400
   -8.0176
   -6.0963
   -5.8973

Timestamp 18-Jul-2025 22:27:09
pMakeSCFGModels: Making JAR3D model for motif group HL_88364.2, number 222 of 253
pMakeNodes starting loop:     a=4JF2|1|A|U|28 B=4JF2|1|A|A|43
  2 Basepair    28   43 UA cWW 
No need to probe because of interaction between a=4JF2|1|A|A|29 B=4JF2|1|A|G|42
  3 Basepair    29   42 AG cWW 
pMakeNodes adding hairpin:     a=4JF2|1|A|C|30 B=4JF2|1|A|U|41
    Right strand conserved insertion C  30 at right strand position 1
    Right strand conserved insertion U  31 at right strand position 2
    Right strand conserved insertion U  32 at right strand position 3
    Right strand conserved insertion U  34 at right strand position 4
    Right strand conserved insertion U  35 at right strand position 5
    Right strand conserved insertion U  36 at right strand position 6
    Right strand conserved insertion C  37 at right strand position 7
    Right strand conserved insertion C  38 at right strand position 8
    Right strand conserved insertion U  39 at right strand position 9
    Right strand conserved insertion U  40 at right strand position 10
    Right strand conserved insertion U  41 at right strand position 11
  4 Hairpin   30:41 CUUUUUCCUUU
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   Hairpin Left  3 Right 13
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U28 - A43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A29 - G42 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUUUUCCUUU'
           RightLetter: ''
               Comment: ' // Hairpin node C30:U41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×11 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9 10 11 12 13]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [11×2 double]
    InteractionComment: {1×11 cell}
      JunctionDeletion: []
          InterIndices: [11×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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   Hairpin Left  3 Right 13
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_88364.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2607
  -10.2607
  -11.7850

Timestamp 18-Jul-2025 22:27:09
pMakeSCFGModels: Making JAR3D model for motif group HL_88558.1, number 223 of 253
pMakeNodes starting loop:     a=2A64|1|A|C|97 B=2A64|1|A|G|108
  2 Basepair    97  108 CG cWW 
No need to probe because of interaction between a=2A64|1|A|G|98 B=2A64|1|A|A|107
  3 Basepair    98  107 GA tSH 
pMakeNodes adding hairpin:     a=2A64|1|A|A|99 B=2A64|1|A|A|106
    Right strand conserved insertion A  99 at right strand position 1
    Right strand conserved insertion A 100 at right strand position 2
    Right strand conserved insertion U 101 at right strand position 3
    Right strand conserved insertion C 103 at right strand position 4
    Right strand conserved insertion A 104 at right strand position 5
    Right strand conserved insertion U 105 at right strand position 6
    Right strand conserved insertion A 106 at right strand position 7
  4 Hairpin   99:106 AAUCAUA
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   Hairpin Left  3 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: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C97 - G108 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G98 - A107 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUCAUA'
           RightLetter: ''
               Comment: ' // Hairpin node A99:A106'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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   Hairpin Left  3 Right  9
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_88558.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6616

Timestamp 18-Jul-2025 22:27:09
pMakeSCFGModels: Making JAR3D model for motif group HL_89199.2, number 224 of 253
pMakeNodes starting loop:     a=2QUW|1|B|C|32 B=2QUW|1|B|G|37
  2 Basepair    32   37 CG cWW 
pMakeNodes adding hairpin:     a=2QUW|1|B|G|34 B=2QUW|1|B|U|36
    Right strand conserved insertion G  34 at right strand position 1
    Right strand conserved insertion A  35 at right strand position 2
    Right strand conserved insertion U  36 at right strand position 3
  3 Hairpin   34:36 GAU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C32 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAU'
           RightLetter: ''
               Comment: ' // Hairpin node G34:U36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_89199.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.3710
   -2.3710
   -2.3710
   -2.3710
   -2.3710

Timestamp 18-Jul-2025 22:27:09
pMakeSCFGModels: Making JAR3D model for motif group HL_89346.1, number 225 of 253
pMakeNodes starting loop:     a=8P9A|1|sR|A|1691 B=8P9A|1|sR|U|1710
  2 Basepair  1691 1710 AU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|G|1692 B=8P9A|1|sR|C|1709
    Insertion on left  8P9A|1|sR|G|1692
    Insertion on right 8P9A|1|sR|C|1709
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|1693 interacts with 8P9A|1|sR|U|1708
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1708 interacts with 8P9A|1|sR|A|1693
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1708 interacts with 8P9A|1|sR|A|1693
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|1693 B=8P9A|1|sR|U|1708
pMakeNodes checking on making a cluster a=8P9A|1|sR|A|1693 B=8P9A|1|sR|U|1708
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 3 to 3 and then 14 to 15
aa is 3 bb is 14
  3 Cluster   8P9A|1|sR|A|1693:8P9A|1|sR|A|1693 8P9A|1|sR|A|1707:8P9A|1|sR|U|1708
    LR Inter  8P9A|1|sR|A|1693 8P9A|1|sR|A|1707 cWW 
    LR Inter  8P9A|1|sR|A|1693 8P9A|1|sR|U|1708 cWW 
pMakeNodesCluster a=4 B=13 at the end
pMakeNodesCluster a=4 B=13 at the end
No need to probe because of interaction between a=8P9A|1|sR|A|1694 B=8P9A|1|sR|C|1706
  4 Basepair  1694 1706 AC cWW 
pMakeNodes adding hairpin:     a=8P9A|1|sR|G|1695 B=8P9A|1|sR|C|1705
    Right strand conserved insertion G1695 at right strand position 1
    Right strand conserved insertion G1696 at right strand position 2
    Right strand conserved insertion G1697 at right strand position 3
    Right strand conserved insertion G1698 at right strand position 4
    Right strand conserved insertion G1699 at right strand position 5
    Right strand conserved insertion C1703 at right strand position 6
    Right strand conserved insertion U1704 at right strand position 7
    Right strand conserved insertion C1705 at right strand position 8
  5 Hairpin   1695:1705 GGGGGCUC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3   Cluster Left  3 Right 14 15
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|1692
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|C|1706
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'CU'
               Comment: ' // Basepair A1691 - U1710 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|1692'
              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: 0.2504

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|C|1706'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GGGGGCUC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: 3
            RightIndex: [14 15]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'AU'
               Comment: ' // Cluster node 8P9A|1|sR|A|1693:8P9A|1|sR|A|1693 and 8P9A|1|sR|A|1707:8P9A|1|sR|U|1708'
              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: 0.2504

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: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1694 - C1706 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGGCUC'
           RightLetter: ''
               Comment: ' // Hairpin node G1695:C1705'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [5 6 7 8 9 10 11 12]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

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  3 Right 15
pMakeMotifModelFromSSF:   7   Cluster Left  3 Right 14 15
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right 12
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_89346.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -20.6578
  -17.8309

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_89567.2, number 226 of 253
pMakeNodes starting loop:     a=5J7L|1|DA|C|1612 B=5J7L|1|DA|G|1619
  2 Basepair  1612 1619 CG cWW 
pMakeNodes adding hairpin:     a=5J7L|1|DA|G|1613 B=5J7L|1|DA|C|1617
    Right strand conserved insertion G1613 at right strand position 1
    Right strand conserved insertion C1615 at right strand position 2
    Right strand conserved insertion C1617 at right strand position 3
  3 Hairpin   1613:1617 GCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1612 - G1619 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCC'
           RightLetter: ''
               Comment: ' // Hairpin node G1613:C1617'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  4
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_89567.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9163
   -3.9163
   -3.9163
   -3.9163
   -3.9163
   -5.6087
   -5.6087
   -8.9880

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_89881.5, number 227 of 253
pMakeNodes starting loop:     a=4LFB|1|A|U|12 B=4LFB|1|A|G|22
  2 Basepair    12   22 UG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|U|13 B=4LFB|1|A|G|21
    Insertion on right 4LFB|1|A|G|21
pMakeNodesProbeForInsertions:  a 4LFB|1|A|U|13 interacts with 4LFB|1|A|U|20
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|20 interacts with 4LFB|1|A|U|13
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|20 interacts with 4LFB|1|A|U|13
pMakeNodes probed for insert:  a=4LFB|1|A|U|13 B=4LFB|1|A|U|20
  3 Basepair    13   20 UU tHW 
pMakeNodes adding hairpin:     a=4LFB|1|A|G|15 B=4LFB|1|A|C|19
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion A  16 at right strand position 2
    Right strand conserved insertion U  17 at right strand position 3
    Right strand conserved insertion C  18 at right strand position 4
    Right strand conserved insertion C  19 at right strand position 5
  4 Hairpin   15:19 GAUCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|U|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'GG'
               Comment: ' // Basepair U12 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|U|20'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GAUCC'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U13 - U20 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAUCC'
           RightLetter: ''
               Comment: ' // Hairpin node G15:C19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  3 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_89881.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8200
   -5.6673
   -5.1411
   -5.1411

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_89893.1, number 228 of 253
pMakeNodes starting loop:     a=4RUM|1|A|C|27 B=4RUM|1|A|G|33
  2 Basepair    27   33 CG cWW 
pMakeNodes adding hairpin:     a=4RUM|1|A|A|28 B=4RUM|1|A|C|32
    Right strand conserved insertion A  28 at right strand position 1
    Right strand conserved insertion G  29 at right strand position 2
    Right strand conserved insertion G  31 at right strand position 3
    Right strand conserved insertion C  32 at right strand position 4
  3 Hairpin   28:32 AGGC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C27 - G33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGGC'
           RightLetter: ''
               Comment: ' // Hairpin node A28:C32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_89893.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.6417

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_90620.1, number 229 of 253
pMakeNodes starting loop:     a=6P2H|1|A|A|59 B=6P2H|1|A|U|69
  2 Basepair    59   69 AU cWW 
No need to probe because of interaction between a=6P2H|1|A|A|60 B=6P2H|1|A|A|68
  3 Basepair    60   68 AA cWW 
pMakeNodes probe for inserts:  a=6P2H|1|A|C|61 B=6P2H|1|A|A|67
    Insertion on left  6P2H|1|A|C|61
    Insertion on right 6P2H|1|A|A|67
pMakeNodesProbeForInsertions:  a 6P2H|1|A|C|62 interacts with 6P2H|1|A|A|66
pMakeNodesProbeForInsertions:  B 6P2H|1|A|A|66 interacts with 6P2H|1|A|C|62
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6P2H|1|A|A|66 interacts with 6P2H|1|A|C|62
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6P2H|1|A|C|62 B=6P2H|1|A|A|66
  4 Basepair    62   66 CA cSW 
pMakeNodes adding hairpin:     a=6P2H|1|A|G|63 B=6P2H|1|A|A|65
    Right strand conserved insertion A  65 at right strand position 3
  5 Hairpin   63:65 GUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|C|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6P2H|1|A|A|67
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A59 - U69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 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: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: 'AA'
               Comment: ' // Basepair A60 - A68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|C|61'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 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: 'GUA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G63 - U64 cSH '  ' // Hairpin conserved non-basepairing position A65'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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: 1
        leftLetterDist: [0.2500 0.2500 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|67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 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: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 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: 'A'
               Comment: ' // Basepair C62 - A66 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUA'
           RightLetter: ''
               Comment: ' // Hairpin node G63:A65'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin Interaction G63 - U64 cSH '  ' // Hairpin conserved non-basepairing position A65'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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  4 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_90620.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0475
   -7.0475

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_91503.7, number 230 of 253
pMakeNodes starting loop:     a=9DFE|1|1A|G|382 B=9DFE|1|1A|C|392
  2 Basepair   382  392 GC cWW 
pMakeNodes adding hairpin:     a=9DFE|1|1A|U|383 B=9DFE|1|1A|G|391
    Right strand conserved insertion U 383 at right strand position 1
    Right strand conserved insertion U 384 at right strand position 2
    Right strand conserved insertion C 385 at right strand position 3
    Right strand conserved insertion U 387 at right strand position 4
    Right strand conserved insertion G 388 at right strand position 5
    Right strand conserved insertion A 390 at right strand position 6
    Right strand conserved insertion G 391 at right strand position 7
  3 Hairpin   383:391 UUCUGAG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G382 - C392 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCUGAG'
           RightLetter: ''
               Comment: ' // Hairpin node U383:G391'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  8
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_91503.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9866
   -6.9866
   -8.0651

Timestamp 18-Jul-2025 22:27:10
pMakeSCFGModels: Making JAR3D model for motif group HL_91641.1, number 231 of 253
pMakeNodes starting loop:     a=2QWY|1|C|A|24 B=2QWY|1|C|U|40
  2 Basepair    24   40 AU cWW 
pMakeNodes probe for inserts:  a=2QWY|1|C|G|25 B=2QWY|1|C|G|39
    Insertion on left  2QWY|1|C|G|25
    Insertion on left  2QWY|1|C|U|26
    Insertion on left  2QWY|1|C|C|27
    Insertion on right 2QWY|1|C|G|39
    Insertion on right 2QWY|1|C|U|38
    Insertion on right 2QWY|1|C|A|37
pMakeNodesProbeForInsertions:  a 2QWY|1|C|G|28 interacts with 2QWY|1|C|A|36
pMakeNodesProbeForInsertions:  B 2QWY|1|C|A|36 interacts with 2QWY|1|C|G|28
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 2QWY|1|C|A|36 interacts with 2QWY|1|C|G|28
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=2QWY|1|C|G|28 B=2QWY|1|C|A|36
  3 Basepair    28   36 GA cSS 
pMakeNodes probe for inserts:  a=2QWY|1|C|C|29 B=2QWY|1|C|A|35
    Insertion on right 2QWY|1|C|A|35
pMakeNodesProbeForInsertions:  a 2QWY|1|C|C|29 interacts with 2QWY|1|C|A|33
pMakeNodesProbeForInsertions:  B 2QWY|1|C|A|33 interacts with 2QWY|1|C|C|29
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 2QWY|1|C|A|33 interacts with 2QWY|1|C|C|29
pMakeNodes probed for insert:  a=2QWY|1|C|C|29 B=2QWY|1|C|A|33
  4 Basepair    29   33 CA cSW 
pMakeNodes adding hairpin:     a=2QWY|1|C|G|30 B=2QWY|1|C|G|32
    Right strand conserved insertion G  30 at right strand position 1
    Right strand conserved insertion U  31 at right strand position 2
    Right strand conserved insertion G  32 at right strand position 3
  5 Hairpin   30:32 GUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2QWY|1|C|G|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2QWY|1|C|U|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2QWY|1|C|C|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2QWY|1|C|U|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2QWY|1|C|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2QWY|1|C|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2QWY|1|C|U|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGUC'
           RightLetter: 'AUGU'
               Comment: ' // Basepair A24 - U40 cWW '
              NumLoops: []
                  Edge: 1
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Node 3

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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            LeftLetter: 'GUG'
           RightLetter: ''
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                Delete: []
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              NumLoops: []
                  Edge: 5
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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            LeftLetter: 'GUG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
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                Delete: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2QWY|1|C|U|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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            LeftLetter: ''
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               Comment: ' // Fixed node on right for 2QWY|1|C|A|37'
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                Delete: 1.0000e-03
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                     Z: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2QWY|1|C|A|36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'AA'
               Comment: ' // Basepair G28 - A36 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: [17×1 double]
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             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 2QWY|1|C|U|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             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: []
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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: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C29 - A33 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUG'
           RightLetter: ''
               Comment: ' // Hairpin node G30:G32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
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                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
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                  rpar: []
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pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 14
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  5 Right 13
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:  14   Initial Left  5 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  17   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  18  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  19   Hairpin Left  7 Right  9
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_91641.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.7400

Timestamp 18-Jul-2025 22:27:11
pMakeSCFGModels: Making JAR3D model for motif group HL_91939.2, number 232 of 253
pMakeNodes starting loop:     a=4WF9|1|X|C|2291 B=4WF9|1|X|G|2303
  2 Basepair  2291 2303 CG cWW 
No need to probe because of interaction between a=4WF9|1|X|U|2292 B=4WF9|1|X|A|2301
  3 Basepair  2292 2301 UA tSH 
No need to probe because of interaction between a=4WF9|1|X|A|2293 B=4WF9|1|X|A|2300
  4 Basepair  2293 2300 AA tHH 
No need to probe because of interaction between a=4WF9|1|X|A|2294 B=4WF9|1|X|U|2299
  5 Basepair  2294 2299 AU tWW 
pMakeNodes adding hairpin:     a=4WF9|1|X|A|2296 B=4WF9|1|X|G|2298
    Right strand conserved insertion A2296 at right strand position 1
    Right strand conserved insertion G2297 at right strand position 2
    Right strand conserved insertion G2298 at right strand position 3
  6 Hairpin   2296:2298 AGG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2291 - G2303 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2292 - A2301 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2293 - A2300 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 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 A2294 - U2299 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGG'
           RightLetter: ''
               Comment: ' // Hairpin node A2296:G2298'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_91939.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0697
   -9.9568
   -8.0697
   -8.5479
   -8.4601
   -8.4601
   -9.8525
  -15.8402

Timestamp 18-Jul-2025 22:27:11
pMakeSCFGModels: Making JAR3D model for motif group HL_92488.1, number 233 of 253
pMakeNodes starting loop:     a=4UYK|1|R|G|43 B=4UYK|1|R|C|58
  2 Basepair    43   58 GC cWW 
No need to probe because of interaction between a=4UYK|1|R|A|44 B=4UYK|1|R|G|57
  3 Basepair    44   57 AG cWW 
pMakeNodes probe for inserts:  a=4UYK|1|R|A|45 B=4UYK|1|R|A|55
    Insertion on left  4UYK|1|R|A|45
    Insertion on left  4UYK|1|R|A|46
    Insertion on left  4UYK|1|R|C|48
    Insertion on left  4UYK|1|R|G|49
pMakeNodesProbeForInsertions:  B 4UYK|1|R|A|55 interacts with 4UYK|1|R|C|51
pMakeNodesProbeForInsertions:  B 4UYK|1|R|A|55 interacts with 4UYK|1|R|C|51
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4UYK|1|R|C|50 B=4UYK|1|R|A|55
pMakeNodes checking on making a cluster a=4UYK|1|R|C|50 B=4UYK|1|R|A|55
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 7 to 8 and then 11 to 11
aa is 8 bb is 11
  4 Cluster   4UYK|1|R|C|50:4UYK|1|R|C|51 4UYK|1|R|A|55:4UYK|1|R|A|55
    LR Inter  4UYK|1|R|C|51 4UYK|1|R|A|55 cSS 
    Left  strand conserved insertion 4UYK|1|R|C|50 at position 1
pMakeNodesCluster a=9 B=10 at the end
pMakeNodesCluster a=9 B=10 at the end
pMakeNodes adding hairpin:     a=4UYK|1|R|G|52 B=4UYK|1|R|A|53
  5 Hairpin   52:53 GA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  7  8 Right 11
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4UYK|1|R|A|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4UYK|1|R|A|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4UYK|1|R|C|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4UYK|1|R|C|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G43 - C58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            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: 'AAACG'
           RightLetter: 'G'
               Comment: ' // Basepair A44 - G57 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          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: 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 4UYK|1|R|A|45'
              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: {' // Cluster Interaction 4UYK|1|R|C|51 - 4UYK|1|R|A|55 cSS '  ' // Left strand conserved insertion 4UYK|1|R|C|50'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 1
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 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 4UYK|1|R|A|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction G52 - A53 cSS '}
      JunctionDeletion: []
          InterIndices: [9 10]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 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 4UYK|1|R|C|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4UYK|1|R|C|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 13
             LeftIndex: [7 8]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: 'A'
               Comment: ' // Cluster node 4UYK|1|R|C|50:4UYK|1|R|C|51 and 4UYK|1|R|A|55:4UYK|1|R|A|55'
              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: {' // Cluster Interaction 4UYK|1|R|C|51 - 4UYK|1|R|A|55 cSS '  ' // Left strand conserved insertion 4UYK|1|R|C|50'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 1
         RightNotInter: [1×0 double]
              NormCons: 1.0000

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 Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: ''
               Comment: ' // Hairpin node G52:A53'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: [9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 2]
    InteractionComment: {' // Hairpin Interaction G52 - A53 cSS '}
      JunctionDeletion: []
          InterIndices: [9 10]
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  12   Cluster Left  7  8 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right 10
pNextNodeJunction: Found a hairpin at node 14
pUpdateModelWithSSF: HL_92488.1 allow insertions from initial node 13?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.0454    0.9070    0.0454    0.0023


ans =

    0.1667    0.1667    0.1667    0.5000         0

pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_92488.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.2192

Timestamp 18-Jul-2025 22:27:11
pMakeSCFGModels: Making JAR3D model for motif group HL_93135.1, number 234 of 253
pMakeNodes starting loop:     a=7A0S|1|X|C|1466 B=7A0S|1|X|G|1476
  2 Basepair  1466 1476 CG cWW 
pMakeNodes adding hairpin:     a=7A0S|1|X|U|1467 B=7A0S|1|X|A|1474
    Right strand conserved insertion U1467 at right strand position 1
    Right strand conserved insertion G1470 at right strand position 2
    Right strand conserved insertion G1471 at right strand position 3
    Right strand conserved insertion C1472 at right strand position 4
    Right strand conserved insertion U1473 at right strand position 5
    Right strand conserved insertion A1474 at right strand position 6
  3 Hairpin   1467:1474 UGGCUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1466 - G1476 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGCUA'
           RightLetter: ''
               Comment: ' // Hairpin node U1467:A1474'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93135.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5290

Timestamp 18-Jul-2025 22:27:11
pMakeSCFGModels: Making JAR3D model for motif group HL_93324.4, number 235 of 253
pMakeNodes starting loop:     a=4FRN|1|B|U|44 B=4FRN|1|B|A|51
  2 Basepair    44   51 UA cWW 
pMakeNodes adding hairpin:     a=4FRN|1|B|U|45 B=4FRN|1|B|G|50
    Right strand conserved insertion U  45 at right strand position 1
    Right strand conserved insertion A  46 at right strand position 2
    Right strand conserved insertion C  47 at right strand position 3
    Right strand conserved insertion U  48 at right strand position 4
    Right strand conserved insertion U  49 at right strand position 5
    Right strand conserved insertion G  50 at right strand position 6
  3 Hairpin   45:50 UACUUG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U44 - A51 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UACUUG'
           RightLetter: ''
               Comment: ' // Hairpin node U45:G50'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93324.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.6554
   -9.7351
  -10.5330
   -8.6365
   -7.3880
  -11.2146
   -8.3938
   -8.3865
   -9.7111
   -8.3938
   -9.2144
   -9.7111
   -8.5193
   -8.3349
  -12.1819
  -12.0079
  -13.4487
  -11.0340
  -12.0079
  -13.4487
  -12.5171
  -13.9595
  -12.3763
  -14.6954

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_93383.1, number 236 of 253
pMakeNodes starting loop:     a=5K7D|1|A|G|33 B=5K7D|1|A|C|41
pMakeNodes checking on making a cluster a=5K7D|1|A|G|33 B=5K7D|1|A|C|41
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 1 and then 7 to 9
aa is 1 bb is 7
  2 Cluster   5K7D|1|A|G|33:5K7D|1|A|G|33 5K7D|1|A|A|39:5K7D|1|A|C|41
    LR Inter  5K7D|1|A|G|33 5K7D|1|A|A|39 wat 
    LR Inter  5K7D|1|A|G|33 5K7D|1|A|G|40 tHS 
    LR Inter  5K7D|1|A|G|33 5K7D|1|A|C|41 cWW 
    RR Inter  5K7D|1|A|G|40 5K7D|1|A|C|41 cSH 
pMakeNodesCluster a=2 B=6 at the end
pMakeNodesCluster a=2 B=6 at the end
pMakeNodes adding hairpin:     a=5K7D|1|A|C|34 B=5K7D|1|A|A|38
    Right strand conserved insertion C  34 at right strand position 1
    Right strand conserved insertion C  35 at right strand position 2
    Right strand conserved insertion C  36 at right strand position 3
    Right strand conserved insertion U  37 at right strand position 4
    Right strand conserved insertion A  38 at right strand position 5
  3 Hairpin   34:38 CCCUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  7  8  9
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: [7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'AGC'
               Comment: ' // Cluster node 5K7D|1|A|G|33:5K7D|1|A|G|33 and 5K7D|1|A|A|39:5K7D|1|A|C|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0063

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCUA'
           RightLetter: ''
               Comment: ' // Hairpin node C34:A38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  7  8  9
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  2 Right  6
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: HL_93383.1 allow insertions from initial node 3?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93383.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4763
   -3.4763

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_93438.2, number 237 of 253
pMakeNodes starting loop:     a=7A0S|1|X|C|58 B=7A0S|1|X|G|67
  2 Basepair    58   67 CG cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|59 B=7A0S|1|X|U|66
    Insertion on left  7A0S|1|X|G|59
    Insertion on left  7A0S|1|X|A|60
    Insertion on left  7A0S|1|X|U|61
    Insertion on right 7A0S|1|X|U|66
    Insertion on right 7A0S|1|X|C|65
pMakeNodesProbeForInsertions:  a 7A0S|1|X|U|62 interacts with 7A0S|1|X|C|64
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|64 interacts with 7A0S|1|X|U|62
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|64 interacts with 7A0S|1|X|U|62
pMakeNodes probed for insert:  a=7A0S|1|X|U|62 B=7A0S|1|X|C|64
  3 Basepair    62   64 UC cSH 
pMakeNodes adding hairpin:     a=7A0S|1|X|A|63 B=7A0S|1|X|A|63
    Right strand conserved insertion A  63 at right strand position 1
  4 Hairpin   63:63 A
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|59
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|U|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|U|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAU'
           RightLetter: 'CUG'
               Comment: ' // Basepair C58 - G67 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|G|59'
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 6
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A63'}
      JunctionDeletion: []
          InterIndices: [6 6]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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 7A0S|1|X|A|60'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|U|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 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|66'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 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: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 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 7A0S|1|X|C|65'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U62 - C64 cSH '
              NumLoops: []
                  Edge: 9
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: ''
               Comment: ' // Hairpin node A63:A63'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4 double]
                     Z: []
           MiddleIndex: 6
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin conserved non-basepairing position A63'}
      JunctionDeletion: []
          InterIndices: [6 6]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  5 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  6 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93438.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9856
   -7.7548
   -9.8228
   -7.2885
   -8.2947
   -8.2947

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_93535.1, number 238 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|C|567 B=8CRE|1|CM|G|572
  2 Basepair   567  572 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|CM|A|568 B=8CRE|1|CM|C|571
    Right strand conserved insertion A 568 at right strand position 1
    Right strand conserved insertion G 569 at right strand position 2
    Right strand conserved insertion C 570 at right strand position 3
    Right strand conserved insertion C 571 at right strand position 4
  3 Hairpin   568:571 AGCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C567 - G572 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCC'
           RightLetter: ''
               Comment: ' // Hairpin node A568:C571'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93535.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2617
   -6.2617
   -7.6421
   -7.5157
   -6.0995
   -7.8154

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_93616.2, number 239 of 253
pMakeNodes starting loop:     a=5E81|1|2K|C|13 B=5E81|1|2K|G|23
  2 Basepair    13   23 CG cWW 
No need to probe because of interaction between a=5E81|1|2K|A|14 B=5E81|1|2K|A|22
  3 Basepair    14   22 AA cWS 
pMakeNodes adding hairpin:     a=5E81|1|2K|G|15 B=5E81|1|2K|C|18
    Right strand conserved insertion G  15 at right strand position 1
    Right strand conserved insertion C  16 at right strand position 2
    Right strand conserved insertion C  17 at right strand position 3
    Right strand conserved insertion C  18 at right strand position 4
  4 Hairpin   15:18 GCCC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A14 - A22 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCCC'
           RightLetter: ''
               Comment: ' // Hairpin node G15:C18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_93616.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.3493
   -5.8830
   -5.8830
   -5.8830
   -5.8830
   -5.8830
  -14.9897
   -5.8830

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_94376.1, number 240 of 253
pMakeNodes starting loop:     a=1ZCI|1|A|G|7 B=1ZCI|1|A|C|17
  2 Basepair     7   17 GC cWW 
pMakeNodes adding hairpin:     a=1ZCI|1|A|A|8 B=1ZCI|1|A|A|16
    Right strand conserved insertion A   8 at right strand position 1
    Right strand conserved insertion A   9 at right strand position 2
    Right strand conserved insertion G  10 at right strand position 3
    Right strand conserved insertion U  11 at right strand position 4
    Right strand conserved insertion G  12 at right strand position 5
    Right strand conserved insertion C  13 at right strand position 6
    Right strand conserved insertion A  14 at right strand position 7
    Right strand conserved insertion C  15 at right strand position 8
    Right strand conserved insertion A  16 at right strand position 9
  3 Hairpin   8:16 AAGUGCACA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGUGCACA'
           RightLetter: ''
               Comment: ' // Hairpin node A8:A16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9 10]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right 10
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_94376.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7719
   -7.7719
  -12.9427

Timestamp 18-Jul-2025 22:27:12
pMakeSCFGModels: Making JAR3D model for motif group HL_94980.1, number 241 of 253
pMakeNodes starting loop:     a=8CRE|1|CM|C|274 B=8CRE|1|CM|G|277
  2 Basepair   274  277 CG cWW 
pMakeNodes adding hairpin:     a=8CRE|1|CM|U|275 B=8CRE|1|CM|U|276
    Right strand conserved insertion U 275 at right strand position 1
    Right strand conserved insertion U 276 at right strand position 2
  3 Hairpin   275:276 UU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C274 - G277 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UU'
           RightLetter: ''
               Comment: ' // Hairpin node U275:U276'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U275'  ' // Hairpin conserved non-basepairing position U276'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_94980.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.9167

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_97733.1, number 242 of 253
pMakeNodes starting loop:     a=5NWQ|1|A|C|20 B=5NWQ|1|A|G|29
  2 Basepair    20   29 CG cWW 
pMakeNodes adding hairpin:     a=5NWQ|1|A|C|21 B=5NWQ|1|A|A|27
    Right strand conserved insertion C  21 at right strand position 1
    Right strand conserved insertion C  22 at right strand position 2
    Right strand conserved insertion G  23 at right strand position 3
    Right strand conserved insertion A  27 at right strand position 6
  3 Hairpin   21:27 CCGGUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C20 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCGGUA'
           RightLetter: ''
               Comment: ' // Hairpin node C21:A27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  7
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_97733.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0884

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_97756.2, number 243 of 253
pMakeNodes starting loop:     a=4V9F|1|9|U|33 B=4V9F|1|9|A|47
pMakeNodes checking on making a cluster a=4V9F|1|9|U|33 B=4V9F|1|9|A|47
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 0
pMakeNodesCluster: Cluster goes from 1 to 4 and then 14 to 14
aa is 4 bb is 14
  2 Cluster   4V9F|1|9|U|33:4V9F|1|9|C|36 4V9F|1|9|A|47:4V9F|1|9|A|47
    LR Inter  4V9F|1|9|U|33 4V9F|1|9|A|47 cWW 
    LR Inter  4V9F|1|9|C|36 4V9F|1|9|A|47 cWS 
    Left  strand conserved insertion 4V9F|1|9|A|34 at position 2
    Left  strand conserved insertion 4V9F|1|9|C|35 at position 3
pMakeNodesCluster a=5 B=13 at the end
pMakeNodesCluster a=5 B=13 at the end
pMakeNodes probe for inserts:  a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodesProbeForInsertions:  a 4V9F|1|9|C|37 interacts with 4V9F|1|9|G|43
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|46 interacts with 4V9F|1|9|G|43
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|46 interacts with 4V9F|1|9|G|43
  3 Initial     37 (0 insertion) and   46 (0 insertion)
pMakeNodes probed for insert:  a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodes checking on making a cluster a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 0
pMakeNodesCluster: Cluster goes from 5 to 7 and then 10 to 13
aa is 7 bb is 10
  4 Cluster   4V9F|1|9|C|37:4V9F|1|9|U|39 4V9F|1|9|G|43:4V9F|1|9|C|46
    LR Inter  4V9F|1|9|C|37 4V9F|1|9|G|43 cWW 
    LR Inter  4V9F|1|9|U|39 4V9F|1|9|A|44 tSH 
    LR Inter  4V9F|1|9|A|38 4V9F|1|9|A|45 cSW 
    RR Inter  4V9F|1|9|G|43 4V9F|1|9|C|46 tSW 
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
pMakeNodes adding hairpin:     a=4V9F|1|9|C|41 B=4V9F|1|9|C|42
    Right strand conserved insertion C  41 at right strand position 1
    Right strand conserved insertion C  42 at right strand position 2
  5 Hairpin   41:42 CC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5   Hairpin Left  8 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: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 0 0 0 0 1 1 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UACC'
           RightLetter: 'A'
               Comment: ' // Cluster node 4V9F|1|9|U|33:4V9F|1|9|C|36 and 4V9F|1|9|A|47:4V9F|1|9|A|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2458

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 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 4V9F|1|9|C|37 - 4V9F|1|9|C|46 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [5 6 7]
            RightIndex: [10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAU'
           RightLetter: 'GAAC'
               Comment: ' // Cluster node 4V9F|1|9|C|37:4V9F|1|9|U|39 and 4V9F|1|9|G|43:4V9F|1|9|C|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2526

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: ''
               Comment: ' // Hairpin node C41:C42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position C41'  ' // Hairpin conserved non-basepairing position C42'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  9
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: HL_97756.2 allow insertions from initial node 5?
ans =

    0.0082    0.9832    0.0082    0.0004


ans =

    0.0625    0.1875    0.5625    0.1875         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_97756.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7251
   -6.2143
   -4.7790
   -5.1157
   -4.7790
   -4.7790

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_97917.2, number 244 of 253
pMakeNodes starting loop:     a=3OIN|1|C|C|4 B=3OIN|1|C|G|11
  2 Basepair     4   11 CG cWW 
pMakeNodes adding hairpin:     a=3OIN|1|C|U|5 B=3OIN|1|C|C|10
    Right strand conserved insertion U   5 at right strand position 1
    Right strand conserved insertion A   8 at right strand position 2
    Right strand conserved insertion A   9 at right strand position 3
    Right strand conserved insertion C  10 at right strand position 4
  3 Hairpin   5:10 UAAC
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C4 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAAC'
           RightLetter: ''
               Comment: ' // Hairpin node U5:C10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_97917.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5302
   -9.5810
   -8.3964

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_97983.1, number 245 of 253
pMakeNodes starting loop:     a=3TRZ|1|X|A|5 B=3TRZ|1|X|U|13
  2 Basepair     5   13 AU cWW 
pMakeNodes adding hairpin:     a=3TRZ|1|X|U|11 B=3TRZ|1|X|U|12
    Right strand conserved insertion U  11 at right strand position 1
    Right strand conserved insertion U  12 at right strand position 2
  3 Hairpin   11:12 UU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A5 - U13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UU'
           RightLetter: ''
               Comment: ' // Hairpin node U11:U12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: [2 3]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {' // Hairpin conserved non-basepairing position U11'  ' // Hairpin conserved non-basepairing position U12'}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  3
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_97983.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1869

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_98252.1, number 246 of 253
pMakeNodes starting loop:     a=5K36|1|L|A|2 B=5K36|1|L|U|12
  2 Basepair     2   12 AU cWW 
No need to probe because of interaction between a=5K36|1|L|U|4 B=5K36|1|L|U|11
  3 Basepair     4   11 UU tWW 
pMakeNodes adding hairpin:     a=5K36|1|L|A|5 B=5K36|1|L|A|9
    Right strand conserved insertion A   5 at right strand position 1
    Right strand conserved insertion U   6 at right strand position 2
    Right strand conserved insertion U   7 at right strand position 3
    Right strand conserved insertion A   9 at right strand position 4
  4 Hairpin   5:9 AUUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2 - 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]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U4 - U11 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUA'
           RightLetter: ''
               Comment: ' // Hairpin node A5:A9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_98252.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2938

Timestamp 18-Jul-2025 22:27:13
pMakeSCFGModels: Making JAR3D model for motif group HL_98864.1, number 247 of 253
pMakeNodes starting loop:     a=4OJI|1|A|G|23 B=4OJI|1|A|C|32
  2 Basepair    23   32 GC cWW 
pMakeNodes probe for inserts:  a=4OJI|1|A|U|24 B=4OJI|1|A|C|31
    Insertion on right 4OJI|1|A|C|31
    Insertion on right 4OJI|1|A|G|30
pMakeNodesProbeForInsertions:  a 4OJI|1|A|U|24 interacts with 4OJI|1|A|A|29
pMakeNodesProbeForInsertions:  B 4OJI|1|A|A|29 interacts with 4OJI|1|A|U|24
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4OJI|1|A|A|29 interacts with 4OJI|1|A|U|24
pMakeNodes probed for insert:  a=4OJI|1|A|U|24 B=4OJI|1|A|A|29
  3 Basepair    24   29 UA tWH 
pMakeNodes adding hairpin:     a=4OJI|1|A|C|25 B=4OJI|1|A|A|28
    Right strand conserved insertion C  25 at right strand position 1
    Right strand conserved insertion C  26 at right strand position 2
    Right strand conserved insertion C  27 at right strand position 3
    Right strand conserved insertion A  28 at right strand position 4
  4 Hairpin   25:28 CCCA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4OJI|1|A|C|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4OJI|1|A|G|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'GCC'
               Comment: ' // Basepair G23 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 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|C|31'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'CCCA'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4OJI|1|A|G|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U24 - 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]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCA'
           RightLetter: ''
               Comment: ' // Hairpin node C25:A28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_98864.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.6293
   -5.1401
   -4.6293
   -8.5293

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_98870.1, number 248 of 253
pMakeNodes starting loop:     a=6DU4|1|B|C|7 B=6DU4|1|B|G|23
  2 Basepair     7   23 CG cWW 
No need to probe because of interaction between a=6DU4|1|B|G|8 B=6DU4|1|B|A|22
  3 Basepair     8   22 GA tSH 
pMakeNodes probe for inserts:  a=6DU4|1|B|U|9 B=6DU4|1|B|A|21
    Insertion on right 6DU4|1|B|A|21
    Insertion on right 6DU4|1|B|G|20
pMakeNodesProbeForInsertions:  a 6DU4|1|B|U|9 interacts with 6DU4|1|B|A|19
pMakeNodesProbeForInsertions:  B 6DU4|1|B|A|19 interacts with 6DU4|1|B|U|9
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6DU4|1|B|A|19 interacts with 6DU4|1|B|U|9
pMakeNodes probed for insert:  a=6DU4|1|B|U|9 B=6DU4|1|B|A|19
  4 Basepair     9   19 UA tWW 
pMakeNodes adding hairpin:     a=6DU4|1|B|A|15 B=6DU4|1|B|G|18
    Right strand conserved insertion A  15 at right strand position 1
    Right strand conserved insertion C  16 at right strand position 2
    Right strand conserved insertion G  18 at right strand position 3
  5 Hairpin   15:18 ACG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DU4|1|B|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6DU4|1|B|U|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'GAA'
               Comment: ' // Basepair G8 - A22 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6DU4|1|B|A|15'
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 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: 'ACG'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6DU4|1|B|U|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 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: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U9 - A19 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACG'
           RightLetter: ''
               Comment: ' // Hairpin node A15:G18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

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     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  4 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_98870.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.4219
   -9.2985

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_99040.1, number 249 of 253
pMakeNodes starting loop:     a=8S95|1|C|U|92 B=8S95|1|C|G|97
  2 Basepair    92   97 UG cWW 
pMakeNodes adding hairpin:     a=8S95|1|C|U|93 B=8S95|1|C|G|96
    Right strand conserved insertion U  93 at right strand position 1
    Right strand conserved insertion G  94 at right strand position 2
    Right strand conserved insertion C  95 at right strand position 3
    Right strand conserved insertion G  96 at right strand position 4
  3 Hairpin   93:96 UGCG
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U92 - G97 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGCG'
           RightLetter: ''
               Comment: ' // Hairpin node U93:G96'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_99040.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.2183

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_99324.1, number 250 of 253
pMakeNodes starting loop:     a=6XKO|1|A|C|4 B=6XKO|1|A|G|20
  2 Basepair     4   20 CG cWW 
No need to probe because of interaction between a=6XKO|1|A|A|5 B=6XKO|1|A|G|19
  3 Basepair     5   19 AG cWW 
pMakeNodes adding hairpin:     a=6XKO|1|A|A|6 B=6XKO|1|A|A|18
    Right strand conserved insertion A   6 at right strand position 1
    Right strand conserved insertion C   7 at right strand position 2
    Right strand conserved insertion U   8 at right strand position 3
    Right strand conserved insertion U   9 at right strand position 4
    Right strand conserved insertion A  10 at right strand position 5
    Right strand conserved insertion G  11 at right strand position 6
    Right strand conserved insertion G  12 at right strand position 7
    Right strand conserved insertion A  13 at right strand position 8
    Right strand conserved insertion U  14 at right strand position 9
    Right strand conserved insertion U  15 at right strand position 10
    Right strand conserved insertion U  16 at right strand position 11
    Right strand conserved insertion U  17 at right strand position 12
    Right strand conserved insertion A  18 at right strand position 13
  4 Hairpin   6:18 ACUUAGGAUUUUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right 15
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C4 - G20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A5 - 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]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACUUAGGAUUUUA'
           RightLetter: ''
               Comment: ' // Hairpin node A6:A18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: [3 4 5 6 7 8 9 10 11 12 13 14 15]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right 15
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_99324.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.8649
  -13.9415

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_99748.1, number 251 of 253
pMakeNodes starting loop:     a=4P5J|1|A|C|7 B=4P5J|1|A|G|14
  2 Basepair     7   14 CG cWW 
pMakeNodes adding hairpin:     a=4P5J|1|A|C|8 B=4P5J|1|A|U|12
    Right strand conserved insertion C   8 at right strand position 1
    Right strand conserved insertion U  12 at right strand position 4
  3 Hairpin   8:12 CGUU
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGUU'
           RightLetter: ''
               Comment: ' // Hairpin node C8:U12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: [2 3 4 5]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  5
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_99748.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7021

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_99769.3, number 252 of 253
pMakeNodes starting loop:     a=5E6M|1|C|G|12 B=5E6M|1|C|C|23
  2 Basepair    12   23 GC cWW 
No need to probe because of interaction between a=5E6M|1|C|U|13 B=5E6M|1|C|U|22
  3 Basepair    13   22 UU cWW 
pMakeNodes adding hairpin:     a=5E6M|1|C|A|14 B=5E6M|1|C|A|21
    Right strand conserved insertion A  14 at right strand position 1
    Right strand conserved insertion G  15 at right strand position 2
    Right strand conserved insertion U  16 at right strand position 3
    Right strand conserved insertion A  21 at right strand position 4
  4 Hairpin   14:21 AGUA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G12 - C23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U13 - U22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGUA'
           RightLetter: ''
               Comment: ' // Hairpin node A14:A21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: [3 4 5 6]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  6
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_99769.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7695
   -8.7695
  -11.6250
  -14.9996
  -14.1570
  -12.9200

Timestamp 18-Jul-2025 22:27:14
pMakeSCFGModels: Making JAR3D model for motif group HL_99867.1, number 253 of 253
pMakeNodes starting loop:     a=387D|1|A|G|4 B=387D|1|A|C|13
  2 Basepair     4   13 GC cWW 
pMakeNodes adding hairpin:     a=387D|1|A|A|5 B=387D|1|A|A|12
    Right strand conserved insertion A   5 at right strand position 1
    Right strand conserved insertion A   6 at right strand position 2
    Right strand conserved insertion G   7 at right strand position 3
    Right strand conserved insertion U   8 at right strand position 4
    Right strand conserved insertion G   9 at right strand position 5
    Right strand conserved insertion C  10 at right strand position 6
    Right strand conserved insertion A  11 at right strand position 7
    Right strand conserved insertion A  12 at right strand position 8
  3 Hairpin   5:12 AAGUGCAA
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 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: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - C13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGUGCAA'
           RightLetter: ''
               Comment: ' // Hairpin node A5:A12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: [2 3 4 5 6 7 8 9]
                     P: [17×1 double]
                  PIns: 1
               subtype: 'XXXX'
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
              NormCons: 1.0000

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Hairpin Left  2 Right  9
pNextNodeJunction: Found a hairpin at node 3
pNextNodeJunction: Found a hairpin at node 3

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\lib\HL_99867.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5334
   -9.4348
   -9.5838
   -9.0983
   -8.5875

There are 253 motif groups, of which 155 are structured
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     4
     5
     6
     7
     8
     9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    40
    41

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

    26     1

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1067 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1107 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1091 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1143 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1053 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1074 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1064 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1068 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1052 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 962 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 999 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1002 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1040 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1097 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1103 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1016 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1030 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1003 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 975 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 1035 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     4
     5
     6
     7
     8
     9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    40
    41

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

    26     1

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 574 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 523 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 592 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 577 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 531 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 528 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 592 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 558 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 534 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 543 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 604 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 534 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 539 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 539 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 542 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 548 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 502 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 562 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 498 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: Generating 1300 sequences required 530 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     4
     5
     6
     7
     8
     9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    40
    41

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

    26     1

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     4     4     4     4     4     4     4     4     4     4

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.4050
    0.3427
    0.0945
    0.0789
    0.0063
    0.0726

    0.2039
    0.1141
    0.3525
    0.3295

    0.4935    0.1236    0.1827    0.2001
    0.3272    0.1847    0.2599    0.2282
    0.4093    0.1557    0.1994    0.2357
    0.2300    0.2245    0.2241    0.3214

pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Read random sequence variant file HL_RandomMotifSequences_1.fasta
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:27:25
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7671 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9856 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4553 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2603 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1710 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.1116 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:28:29
Parsing 1300 sequences from file HL_RandomMotifSequences_1.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5564 minutes
Parsed against  100 models so far, total time estimate   0.4866 minutes
Parsed against  150 models so far, total time estimate   0.4794 minutes
Parsed against  200 models so far, total time estimate   0.4457 minutes
Parsed against  250 models so far, total time estimate   0.4260 minutes
Read random sequence variant file HL_RandomMotifSequences_2.fasta
max_rotation=0 r=0 n=1 a=CUAG FASTA(n).Sequence=CUAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:28:55
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7963 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   1.0256 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4945 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2963 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1945 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.1253 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:30:01
Parsing 1300 sequences from file HL_RandomMotifSequences_2.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5119 minutes
Parsed against  100 models so far, total time estimate   0.4494 minutes
Parsed against  150 models so far, total time estimate   0.4448 minutes
Parsed against  200 models so far, total time estimate   0.4139 minutes
Parsed against  250 models so far, total time estimate   0.3949 minutes
Read random sequence variant file HL_RandomMotifSequences_3.fasta
max_rotation=0 r=0 n=1 a=UCGA FASTA(n).Sequence=UCGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:30:24
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7627 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9808 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4402 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2486 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1523 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0868 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:31:28
Parsing 1300 sequences from file HL_RandomMotifSequences_3.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5101 minutes
Parsed against  100 models so far, total time estimate   0.4484 minutes
Parsed against  150 models so far, total time estimate   0.4436 minutes
Parsed against  200 models so far, total time estimate   0.4119 minutes
Parsed against  250 models so far, total time estimate   0.3927 minutes
Read random sequence variant file HL_RandomMotifSequences_4.fasta
max_rotation=0 r=0 n=1 a=CCAG FASTA(n).Sequence=CCAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:31:51
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7580 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9819 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4380 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2486 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1581 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0933 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:32:55
Parsing 1300 sequences from file HL_RandomMotifSequences_4.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5150 minutes
Parsed against  100 models so far, total time estimate   0.4557 minutes
Parsed against  150 models so far, total time estimate   0.4503 minutes
Parsed against  200 models so far, total time estimate   0.4173 minutes
Parsed against  250 models so far, total time estimate   0.3990 minutes
Read random sequence variant file HL_RandomMotifSequences_5.fasta
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:33:19
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7692 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9708 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4183 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2308 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1363 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0720 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:34:21
Parsing 1300 sequences from file HL_RandomMotifSequences_5.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5123 minutes
Parsed against  100 models so far, total time estimate   0.4504 minutes
Parsed against  150 models so far, total time estimate   0.4470 minutes
Parsed against  200 models so far, total time estimate   0.4150 minutes
Parsed against  250 models so far, total time estimate   0.3959 minutes
Read random sequence variant file HL_RandomMotifSequences_6.fasta
max_rotation=0 r=0 n=1 a=UGGA FASTA(n).Sequence=UGGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:34:45
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7457 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9637 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4110 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2229 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1283 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0690 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:35:47
Parsing 1300 sequences from file HL_RandomMotifSequences_6.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5110 minutes
Parsed against  100 models so far, total time estimate   0.4489 minutes
Parsed against  150 models so far, total time estimate   0.4455 minutes
Parsed against  200 models so far, total time estimate   0.4132 minutes
Parsed against  250 models so far, total time estimate   0.3944 minutes
Read random sequence variant file HL_RandomMotifSequences_7.fasta
max_rotation=0 r=0 n=1 a=UGGA FASTA(n).Sequence=UGGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:36:11
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7497 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9680 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4137 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2261 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1409 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0830 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:37:14
Parsing 1300 sequences from file HL_RandomMotifSequences_7.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5189 minutes
Parsed against  100 models so far, total time estimate   0.4551 minutes
Parsed against  150 models so far, total time estimate   0.4509 minutes
Parsed against  200 models so far, total time estimate   0.4180 minutes
Parsed against  250 models so far, total time estimate   0.3984 minutes
Read random sequence variant file HL_RandomMotifSequences_8.fasta
max_rotation=0 r=0 n=1 a=UGAG FASTA(n).Sequence=UGAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:37:38
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7444 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9597 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4097 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2383 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1428 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0757 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:38:41
Parsing 1300 sequences from file HL_RandomMotifSequences_8.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5145 minutes
Parsed against  100 models so far, total time estimate   0.4530 minutes
Parsed against  150 models so far, total time estimate   0.4521 minutes
Parsed against  200 models so far, total time estimate   0.4219 minutes
Parsed against  250 models so far, total time estimate   0.4011 minutes
Read random sequence variant file HL_RandomMotifSequences_9.fasta
max_rotation=0 r=0 n=1 a=GUCC FASTA(n).Sequence=GUCC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:39:05
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7283 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9540 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.3931 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2182 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1327 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0707 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:40:07
Parsing 1300 sequences from file HL_RandomMotifSequences_9.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5439 minutes
Parsed against  100 models so far, total time estimate   0.4849 minutes
Parsed against  150 models so far, total time estimate   0.4800 minutes
Parsed against  200 models so far, total time estimate   0.4467 minutes
Parsed against  250 models so far, total time estimate   0.4273 minutes
Read random sequence variant file HL_RandomMotifSequences_10.fasta
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:40:33
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7700 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9769 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4212 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2279 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1302 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0684 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:41:35
Parsing 1300 sequences from file HL_RandomMotifSequences_10.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5087 minutes
Parsed against  100 models so far, total time estimate   0.4491 minutes
Parsed against  150 models so far, total time estimate   0.4445 minutes
Parsed against  200 models so far, total time estimate   0.4190 minutes
Parsed against  250 models so far, total time estimate   0.3998 minutes
Read random sequence variant file HL_RandomMotifSequences_11.fasta
max_rotation=0 r=0 n=1 a=CUUG FASTA(n).Sequence=CUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:41:59
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7219 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9395 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.3800 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2025 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1118 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0469 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:43:00
Parsing 1300 sequences from file HL_RandomMotifSequences_11.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5089 minutes
Parsed against  100 models so far, total time estimate   0.4499 minutes
Parsed against  150 models so far, total time estimate   0.4461 minutes
Parsed against  200 models so far, total time estimate   0.4134 minutes
Parsed against  250 models so far, total time estimate   0.3940 minutes
Read random sequence variant file HL_RandomMotifSequences_12.fasta
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:43:23
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   0.7395 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   0.9657 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   1.4093 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.2198 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   1.1266 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   1.0661 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:44:25
Parsing 1300 sequences from file HL_RandomMotifSequences_12.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   0.5092 minutes
Parsed against  100 models so far, total time estimate   0.5309 minutes
Parsed against  150 models so far, total time estimate   0.7121 minutes
Parsed against  200 models so far, total time estimate   0.7202 minutes
Parsed against  250 models so far, total time estimate   0.7246 minutes
Read random sequence variant file HL_RandomMotifSequences_13.fasta
max_rotation=0 r=0 n=1 a=CUUG FASTA(n).Sequence=CUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:45:09
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.5313 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.2667 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   5.0682 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   4.3845 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   4.0515 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.6797 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:48:43
Parsing 1300 sequences from file HL_RandomMotifSequences_13.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2652 minutes
Parsed against  100 models so far, total time estimate   1.1032 minutes
Parsed against  150 models so far, total time estimate   1.0966 minutes
Parsed against  200 models so far, total time estimate   1.0087 minutes
Parsed against  250 models so far, total time estimate   0.9519 minutes
Read random sequence variant file HL_RandomMotifSequences_14.fasta
max_rotation=0 r=0 n=1 a=AGAU FASTA(n).Sequence=AGAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:49:40
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.3434 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.0616 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   4.6146 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   4.0091 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   3.7070 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.4864 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:53:03
Parsing 1300 sequences from file HL_RandomMotifSequences_14.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2049 minutes
Parsed against  100 models so far, total time estimate   1.0666 minutes
Parsed against  150 models so far, total time estimate   1.0637 minutes
Parsed against  200 models so far, total time estimate   0.9817 minutes
Parsed against  250 models so far, total time estimate   0.9327 minutes
Read random sequence variant file HL_RandomMotifSequences_15.fasta
max_rotation=0 r=0 n=1 a=GUGC FASTA(n).Sequence=GUGC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:53:59
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.3531 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.0400 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   4.5897 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   3.9780 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   3.6656 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.4440 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:57:19
Parsing 1300 sequences from file HL_RandomMotifSequences_15.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.1908 minutes
Parsed against  100 models so far, total time estimate   1.0623 minutes
Parsed against  150 models so far, total time estimate   1.0604 minutes
Parsed against  200 models so far, total time estimate   0.9771 minutes
Parsed against  250 models so far, total time estimate   0.9282 minutes
Read random sequence variant file HL_RandomMotifSequences_16.fasta
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:58:15
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.3511 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   2.4555 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   2.4103 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   1.9930 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   2.0366 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   2.1120 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:00:20
Parsing 1300 sequences from file HL_RandomMotifSequences_16.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2119 minutes
Parsed against  100 models so far, total time estimate   1.0803 minutes
Parsed against  150 models so far, total time estimate   1.0776 minutes
Parsed against  200 models so far, total time estimate   0.9921 minutes
Parsed against  250 models so far, total time estimate   0.9416 minutes
Read random sequence variant file HL_RandomMotifSequences_17.fasta
max_rotation=0 r=0 n=1 a=GUAC FASTA(n).Sequence=GUAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:01:17
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.4239 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.1552 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   4.7499 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   4.1144 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   3.7982 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.5750 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:04:44
Parsing 1300 sequences from file HL_RandomMotifSequences_17.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2205 minutes
Parsed against  100 models so far, total time estimate   1.0969 minutes
Parsed against  150 models so far, total time estimate   1.1026 minutes
Parsed against  200 models so far, total time estimate   1.0122 minutes
Parsed against  250 models so far, total time estimate   0.9571 minutes
Read random sequence variant file HL_RandomMotifSequences_18.fasta
max_rotation=0 r=0 n=1 a=CCGG FASTA(n).Sequence=CCGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:05:42
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.4584 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   2.1685 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   3.3153 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   3.0423 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   2.9143 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   2.8290 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:08:27
Parsing 1300 sequences from file HL_RandomMotifSequences_18.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2091 minutes
Parsed against  100 models so far, total time estimate   1.0780 minutes
Parsed against  150 models so far, total time estimate   1.0732 minutes
Parsed against  200 models so far, total time estimate   0.9866 minutes
Parsed against  250 models so far, total time estimate   0.9377 minutes
Read random sequence variant file HL_RandomMotifSequences_19.fasta
max_rotation=0 r=0 n=1 a=CGGG FASTA(n).Sequence=CGGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:09:24
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.3558 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.0830 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   4.6520 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   4.0368 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   3.7212 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.5067 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:12:48
Parsing 1300 sequences from file HL_RandomMotifSequences_19.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2436 minutes
Parsed against  100 models so far, total time estimate   1.1155 minutes
Parsed against  150 models so far, total time estimate   1.1174 minutes
Parsed against  200 models so far, total time estimate   1.0315 minutes
Parsed against  250 models so far, total time estimate   0.9825 minutes
Read random sequence variant file HL_RandomMotifSequences_20.fasta
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:13:47
Finding core edit distance of 1300 sequences against  253 models over    1 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate   2.4244 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate   3.1181 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate   4.6410 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate   4.0107 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate   3.6948 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate   3.4765 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:17:09
Parsing 1300 sequences from file HL_RandomMotifSequences_20.fasta against 253 models over 1 rotations
Parsed against   50 models so far, total time estimate   1.2292 minutes
Parsed against  100 models so far, total time estimate   1.0909 minutes
Parsed against  150 models so far, total time estimate   1.0825 minutes
Parsed against  200 models so far, total time estimate   0.9952 minutes
Parsed against  250 models so far, total time estimate   0.9440 minutes
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_1.mat
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:08
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_2.mat
max_rotation=0 r=0 n=1 a=CUAG FASTA(n).Sequence=CUAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:08
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_3.mat
max_rotation=0 r=0 n=1 a=UCGA FASTA(n).Sequence=UCGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_4.mat
max_rotation=0 r=0 n=1 a=CCAG FASTA(n).Sequence=CCAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_5.mat
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_6.mat
max_rotation=0 r=0 n=1 a=UGGA FASTA(n).Sequence=UGGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_7.mat
max_rotation=0 r=0 n=1 a=UGGA FASTA(n).Sequence=UGGA
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_8.mat
max_rotation=0 r=0 n=1 a=UGAG FASTA(n).Sequence=UGAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:09
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_9.mat
max_rotation=0 r=0 n=1 a=GUCC FASTA(n).Sequence=GUCC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_10.mat
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_11.mat
max_rotation=0 r=0 n=1 a=CUUG FASTA(n).Sequence=CUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_12.mat
max_rotation=0 r=0 n=1 a=CAAG FASTA(n).Sequence=CAAG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_13.mat
max_rotation=0 r=0 n=1 a=CUUG FASTA(n).Sequence=CUUG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_14.mat
max_rotation=0 r=0 n=1 a=AGAU FASTA(n).Sequence=AGAU
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_15.mat
max_rotation=0 r=0 n=1 a=GUGC FASTA(n).Sequence=GUGC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_16.mat
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:11
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_17.mat
max_rotation=0 r=0 n=1 a=GUAC FASTA(n).Sequence=GUAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:11
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_18.mat
max_rotation=0 r=0 n=1 a=CCGG FASTA(n).Sequence=CCGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:11
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_19.mat
max_rotation=0 r=0 n=1 a=CGGG FASTA(n).Sequence=CGGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:11
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\HL\3.98\diagnostic\HL_RandomMotifSequences_20.mat
max_rotation=0 r=0 n=1 a=GGAC FASTA(n).Sequence=GGAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:18:11
Evaluating how sequences fit models
Saved group data

GroupData = 

  1×253 <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\HL\3.98\HL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\HL\3.98\HL_GroupData.mat
