
ans = 

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

               MotifID: 'J3_00584.1'
             Signature: {'cWW-F-F-tWH-cWW-tSS-F-tHS-F-cWW'}
                 NumNT: 14
          NumBasepairs: 7
            Structured: 1
             NumStacks: 12
                NumBPh: 2
                 NumBR: 2
          NumInstances: 1
              Truncate: [2×1 double]
              NumFixed: 38
              OwnScore: -7.7248
           OwnSequence: {'GGUAAG*CGAGG*CAC'}
          DeficitCoeff: 1
         CoreEditCoeff: 3
       SequenceLengths: 13
    MeanSequenceLength: 13
       DeficitEditData: [2966×2 double]

1 sequences from 3D structures
Using 2966 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.6226 because the cutoff seemed overly generous
Group   1, J3_00584.1  has acceptance rules AlignmentScore >= -27.7248, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.7248
TP   100.00%, TN    97.67%, min    97.67%,   1 3D sequences,     0 alignment sequences, 2966 random sequences,   69 random matches, 14 NTs, cWW-F-F-tWH-cWW-tSS-F-tHS-F-cWW
Sensitivity 100.00%, Specificity  97.67%, Minimum  97.67% using method 8
Number of false positives with core edit > 0 is 69
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_02067.1'
                     Signature: {'cWW-tSS-F-F-F-cWW-cWW-F-F'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -9.5427
                   OwnSequence: {'GUAUC*GAAG*CAAU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [8230×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 8230 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group   2, J3_02067.1  has acceptance rules AlignmentScore >= -29.5427, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.0598
TP   100.00%, TN    95.99%, min    95.99%,   1 3D sequences,     0 alignment sequences, 8230 random sequences,  330 random matches, 13 NTs, cWW-tSS-F-F-F-cWW-cWW-F-F
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 330
1 * Deficit + 3 * Core Edit <= 17.5170
Motif index 1


ans = 

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

                       MotifID: 'J3_04858.1'
                     Signature: {'cWW-F-cWW-F-F-F-F-F-cWW'}
                         NumNT: 12
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 2
                         NumBR: 0
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: [-7.8890 -8.5821]
                   OwnSequence: {'UCGACC*GAAA*UA'  'UCGAUC*GGAAU*AA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 12]
            MeanSequenceLength: 11.5000
               DeficitEditData: [10881×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 10881 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group   3, J3_04858.1  has acceptance rules AlignmentScore >= -27.8890, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  26.1859
TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences, 10881 random sequences,  435 random matches, 12 NTs, cWW-F-cWW-F-F-F-F-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 435
1 * Deficit + 3 * Core Edit <= 18.2969
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_05170.1'
                     Signature: {'cWW-F-tSH-tWH-cSH-cWW-tWS-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 1
                         NumBR: 3
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: -9.6924
                   OwnSequence: {'GGGUUGUA*UG*CAAAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [999×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 999 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group   4, J3_05170.1  has acceptance rules AlignmentScore >= -29.6924, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.3148
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  999 random sequences,   40 random matches, 13 NTs, cWW-F-tSH-tWH-cSH-cWW-tWS-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 40
1 * Deficit + 3 * Core Edit <= 19.6225
Motif index 1


ans = 

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

                       MotifID: 'J3_06335.1'
                     Signature: {'cWW-F-F-tSH-cSS-tWH-F-cWW-cWW-F'}
                         NumNT: 14
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 4
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -7.8508
                   OwnSequence: {'CAAAC*GUGUCAG*CAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [1761×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 1761 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.6620 because the cutoff seemed overly generous
Group   5, J3_06335.1  has acceptance rules AlignmentScore >= -27.8508, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.7101
TP   100.00%, TN    98.01%, min    98.01%,   1 3D sequences,     0 alignment sequences, 1761 random sequences,   35 random matches, 14 NTs, cWW-F-F-tSH-cSS-tWH-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  98.01%, Minimum  98.01% using method 8
Number of false positives with core edit > 0 is 35
1 * Deficit + 3 * Core Edit <= 20.8593
Motif index 1


ans = 

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

                       MotifID: 'J3_06579.1'
                     Signature: {'cWW-F-tHS-F-tHS-F-cWW-cWW'}
                         NumNT: 13
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 3
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -8.0717
                   OwnSequence: {'GGUAUG*CAAG*UGGC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 13
            MeanSequenceLength: 13
               DeficitEditData: [3764×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 3764 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.8840 because the cutoff seemed overly generous
Group   6, J3_06579.1  has acceptance rules AlignmentScore >= -28.0717, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.0717
TP   100.00%, TN    96.94%, min    96.94%,   1 3D sequences,     0 alignment sequences, 3764 random sequences,  115 random matches, 13 NTs, cWW-F-tHS-F-tHS-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.94%, Minimum  96.94% using method 8
Number of false positives with core edit > 0 is 115
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_08394.2'
                     Signature: {'cWW-F-F-F-tHW-F-F-F-tSS-F-cWW-cWW-F-F-F'}
                         NumNT: 20
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 15
                        NumBPh: 4
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 70
                      OwnScore: [-7.8299 -8.3407 -7.8299]
                   OwnSequence: {'CGUCAG*CGCAACC*GACGACG'  'CGUCAG*CGCAACC*GAUGACG'  'CGUCAG*CGCAACC*GACGACG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [19 19 19]
            MeanSequenceLength: 19
               DeficitEditData: [33×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 33 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  26.7888 because the cutoff seemed overly generous
Decreased cutoff to  25.0000 so that it is possible to reject matches
Group   7, J3_08394.2  has acceptance rules AlignmentScore >= -27.8299, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.8299
TP   100.00%, TN   100.00%, min   100.00%,   3 3D sequences,     0 alignment sequences,   33 random sequences,    0 random matches, 20 NTs, cWW-F-F-F-tHW-F-F-F-tSS-F-cWW-cWW-F-F-F
Sensitivity 100.00%, Specificity 100.00%, Minimum 100.00% using method 12
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_08465.1'
                     Signature: {'cWW-cWW-F-F-tHW-F-F-tHH-cWW-cWW'}
                         NumNT: 16
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 2
                         NumBR: 4
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -8.1363
                   OwnSequence: {'GAGACAG*UUG*CUAACC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [370×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 370 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.8253 because the cutoff seemed overly generous
Group   8, J3_08465.1  has acceptance rules AlignmentScore >= -28.1363, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.9671
TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,  370 random sequences,    7 random matches, 16 NTs, cWW-cWW-F-F-tHW-F-F-tHH-cWW-cWW
Sensitivity 100.00%, Specificity  98.11%, Minimum  98.11% using method 8
Number of false positives with core edit > 0 is 7
1 * Deficit + 3 * Core Edit <= 21.8308
Motif index 1


ans = 

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

                       MotifID: 'J3_11279.1'
                     Signature: {'cWW-tSH-tHW-cSH-tHH-cSS-tWW-F-F-cWW-cWW-F'}
                         NumNT: 19
                  NumBasepairs: 12
                    Structured: 1
                     NumStacks: 19
                        NumBPh: 3
                         NumBR: 2
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 54
                      OwnScore: [-10.1511 -10.5670]
                   OwnSequence: {'UGAUUACG*CCAG*CUAGUAA'  'UGAAUACG*CAAG*CUAGUAA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [18 18]
            MeanSequenceLength: 18
               DeficitEditData: [41×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 41 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  23.2424 because the cutoff seemed overly generous
Group   9, J3_11279.1  has acceptance rules AlignmentScore >= -30.1511, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.8409
TP   100.00%, TN    97.56%, min    97.56%,   2 3D sequences,     0 alignment sequences,   41 random sequences,    1 random matches, 19 NTs, cWW-tSH-tHW-cSH-tHH-cSS-tWW-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  97.56%, Minimum  97.56% using method 8
Number of false positives with core edit > 0 is 1
1 * Deficit + 3 * Core Edit <= 22.6898
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_11934.2'
                     Signature: {'cWW-F-cWW-F-F-tWW-F-cWW-F'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 2
                         NumBR: 0
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: [-6.6474 -6.6474 -7.6875 -6.6474]
                   OwnSequence: {'CGCCGAUGG*CAG*UG'  'CGCCGAUGG*CAG*UG'  'UACCGGUGG*CGG*UA'  'CGCCGAUGG*CAG*UG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [1616×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 1616 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.7055 because the cutoff seemed overly generous
Group  10, J3_11934.2  has acceptance rules AlignmentScore >= -26.6474, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  26.7886
TP   100.00%, TN    98.02%, min    98.02%,   4 3D sequences,     0 alignment sequences, 1616 random sequences,   32 random matches, 13 NTs, cWW-F-cWW-F-F-tWW-F-cWW-F
Sensitivity 100.00%, Specificity  98.02%, Minimum  98.02% using method 8
Number of false positives with core edit > 0 is 32
1 * Deficit + 3 * Core Edit <= 20.1412
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_13944.1'
                     Signature: {'cWW-F-F-tSS-F-F-cWW-cWW'}
                         NumNT: 13
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: [-11.2143 -9.9178]
                   OwnSequence: {'CCCAUAG*CGC*GUCAG'  'GCCGUAG*CGC*GGAAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [14 14]
            MeanSequenceLength: 14
               DeficitEditData: [2303×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 2303 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.1773 because the cutoff seemed overly generous
Group  11, J3_13944.1  has acceptance rules AlignmentScore >= -29.9178, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.9178
TP   100.00%, TN    97.74%, min    97.74%,   2 3D sequences,     0 alignment sequences, 2303 random sequences,   52 random matches, 13 NTs, cWW-F-F-tSS-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  97.74%, Minimum  97.74% using method 8
Number of false positives with core edit > 0 is 52
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_15893.1'
                     Signature: {'cWW-tSH-cSS-tHS-F-cWW-cWW-cWW'}
                         NumNT: 14
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 1
                         NumBR: 3
                  NumInstances: 5
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: [-8.8207 -7.7837 -7.9764 -7.7837 -7.8331]
                   OwnSequence: {'UUAAUC*GUAG*CGCA'  'UGAAUC*GUAG*CGAA'  'CGAAUC*GUAC*GGAG'  'UGAAUC*GUAG*CGAA'  'CGAAUC*GUAG*CGAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [3817×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

5 sequences from 3D structures
Using 3817 random sequences, 0 from an alignment, and 5 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  12, J3_15893.1  has acceptance rules AlignmentScore >= -27.7837, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.2278
TP   100.00%, TN    95.99%, min    95.99%,   5 3D sequences,     0 alignment sequences, 3817 random sequences,  153 random matches, 14 NTs, cWW-tSH-cSS-tHS-F-cWW-cWW-cWW
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 153
1 * Deficit + 3 * Core Edit <= 19.4442
Motif index 1
Motif index 2
Motif index 3
Motif index 4
Motif index 5


ans = 

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

                       MotifID: 'J3_18709.1'
                     Signature: {'cWW-F-tWW-cSH-cWW-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 34
                      OwnScore: -8.6198
                   OwnSequence: {'UUACG*CAAAG*CUA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [6006×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 6006 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  13, J3_18709.1  has acceptance rules AlignmentScore >= -28.6198, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.8501
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 6006 random sequences,  240 random matches, 12 NTs, cWW-F-tWW-cSH-cWW-cWW-F
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 240
1 * Deficit + 3 * Core Edit <= 19.2303
Motif index 1


ans = 

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

                       MotifID: 'J3_19256.1'
                     Signature: {'cWW-F-F-F-cWW-F-F-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: [-7.3909 -7.3909]
                   OwnSequence: {'GAAACCC*GC*GAC'  'GAAACCC*GC*GAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 11]
            MeanSequenceLength: 11
               DeficitEditData: [6256×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 6256 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  14, J3_19256.1  has acceptance rules AlignmentScore >= -27.3909, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.8094
TP   100.00%, TN    95.96%, min    95.96%,   2 3D sequences,     0 alignment sequences, 6256 random sequences,  253 random matches, 12 NTs, cWW-F-F-F-cWW-F-F-cWW-F
Sensitivity 100.00%, Specificity  95.96%, Minimum  95.96% using method 6
Number of false positives with core edit > 0 is 253
1 * Deficit + 3 * Core Edit <= 17.4185
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_19286.1'
                     Signature: {'cWW-F-F-tSH-F-cWW-F-F-F-cWW-F'}
                         NumNT: 15
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: -10.4085
                   OwnSequence: {'CUGAUGAU*AUUG*CACG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [1422×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 1422 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.9870 because the cutoff seemed overly generous
Group  15, J3_19286.1  has acceptance rules AlignmentScore >= -30.4085, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.4085
TP   100.00%, TN    97.96%, min    97.96%,   1 3D sequences,     0 alignment sequences, 1422 random sequences,   29 random matches, 15 NTs, cWW-F-F-tSH-F-cWW-F-F-F-cWW-F
Sensitivity 100.00%, Specificity  97.96%, Minimum  97.96% using method 8
Number of false positives with core edit > 0 is 29
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_19431.1'
                     Signature: {'cWW-F-cWW-tSS-F-cWW'}
                         NumNT: 9
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 4
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -5.4173
                   OwnSequence: {'CCAUAU*AG*UG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 9
            MeanSequenceLength: 9
               DeficitEditData: [5796×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 5796 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  16, J3_19431.1  has acceptance rules AlignmentScore >= -25.4173, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  19.8910
TP   100.00%, TN    95.96%, min    95.96%,   1 3D sequences,     0 alignment sequences, 5793 random sequences,  234 random matches,  9 NTs, cWW-F-cWW-tSS-F-cWW
Sensitivity 100.00%, Specificity  95.96%, Minimum  95.96% using method 6
Number of false positives with core edit > 0 is 234
1 * Deficit + 3 * Core Edit <= 14.4737
Motif index 1


ans = 

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

                       MotifID: 'J3_20650.1'
                     Signature: {'cWW-F-F-F-F-cSS-cWW-cWW-F'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 4
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -7.5675
                   OwnSequence: {'CGAGG*CUG*CACUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [8479×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 8479 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.5529 because the cutoff seemed overly generous
Group  17, J3_20650.1  has acceptance rules AlignmentScore >= -27.5675, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.5675
TP   100.00%, TN    96.69%, min    96.69%,   1 3D sequences,     0 alignment sequences, 8479 random sequences,  281 random matches, 13 NTs, cWW-F-F-F-F-cSS-cWW-cWW-F
Sensitivity 100.00%, Specificity  96.69%, Minimum  96.69% using method 8
Number of false positives with core edit > 0 is 281
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_22198.1'
                     Signature: {'cWW-cSH-F-cWW-cSS-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -10.4869
                   OwnSequence: {'AGCC*GAG*CUAAU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 11
            MeanSequenceLength: 11
               DeficitEditData: [11862×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 11862 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  18, J3_22198.1  has acceptance rules AlignmentScore >= -30.4869, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  25.7488
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 11861 random sequences,  474 random matches, 12 NTs, cWW-cSH-F-cWW-cSS-cWW-F
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 474
1 * Deficit + 3 * Core Edit <= 15.2619
Motif index 1


ans = 

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

                       MotifID: 'J3_25217.1'
                     Signature: {'cWW-F-cWW-F-cWW-F-F'}
                         NumNT: 9
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 4
                        NumBPh: 0
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -6.1782
                   OwnSequence: {'CG*UUCG*CGUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 9
            MeanSequenceLength: 9
               DeficitEditData: [10224×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 10224 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  19, J3_25217.1  has acceptance rules AlignmentScore >= -26.1782, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  21.6622
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 10224 random sequences,  409 random matches,  9 NTs, cWW-F-cWW-F-cWW-F-F
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 409
1 * Deficit + 3 * Core Edit <= 15.4840
Motif index 1


ans = 

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

                       MotifID: 'J3_25670.1'
                     Signature: {'cWW-F-F-F-cWW-F-F-cWW'}
                         NumNT: 11
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -8.1632
                   OwnSequence: {'GUAACU*AG*CAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 10
            MeanSequenceLength: 10
               DeficitEditData: [11778×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 11778 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  20, J3_25670.1  has acceptance rules AlignmentScore >= -28.1632, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.0446
TP   100.00%, TN    95.81%, min    95.81%,   1 3D sequences,     0 alignment sequences, 11778 random sequences,  493 random matches, 11 NTs, cWW-F-F-F-cWW-F-F-cWW
Sensitivity 100.00%, Specificity  95.81%, Minimum  95.81% using method 6
Number of false positives with core edit > 0 is 493
1 * Deficit + 3 * Core Edit <= 15.8813
Motif index 1


ans = 

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

                       MotifID: 'J3_28621.2'
                     Signature: {'cWW-tWW-tHS-tSH-cWW-tSS-F-cSS-cWW'}
                         NumNT: 13
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 3
                         NumBR: 1
                  NumInstances: 6
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: [-7.4176 -7.0605 -7.0605 -7.0605 -7.7258 -7.0605]
                   OwnSequence: {1×6 cell}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [12 12 12 12 12 12]
            MeanSequenceLength: 12
               DeficitEditData: [2409×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

6 sequences from 3D structures
Using 2409 random sequences, 0 from an alignment, and 6 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  21, J3_28621.2  has acceptance rules AlignmentScore >= -27.0605, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  23.2676
TP   100.00%, TN    96.01%, min    96.01%,   6 3D sequences,     0 alignment sequences, 2409 random sequences,   96 random matches, 13 NTs, cWW-tWW-tHS-tSH-cWW-tSS-F-cSS-cWW
Sensitivity 100.00%, Specificity  96.01%, Minimum  96.01% using method 6
Number of false positives with core edit > 0 is 96
1 * Deficit + 3 * Core Edit <= 16.2071
Motif index 1
Motif index 2
Motif index 3
Motif index 4
Motif index 5
Motif index 6


ans = 

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

                       MotifID: 'J3_30104.1'
                     Signature: {'cWW-F-F-cWW-cWW'}
                         NumNT: 8
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 6
                        NumBPh: 2
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 32
                      OwnScore: -4.5147
                   OwnSequence: {'CUG*CC*GAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 7
            MeanSequenceLength: 7
               DeficitEditData: [5597×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 5597 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Increased cutoff to   9.5000 so that at least a few sequences with core edit distance 1 can meet the cutoff
Group  22, J3_30104.1  has acceptance rules AlignmentScore >= -24.5147, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  14.0147
TP   100.00%, TN    95.85%, min    95.85%,   1 3D sequences,     0 alignment sequences, 5568 random sequences,  231 random matches,  8 NTs, cWW-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  95.85%, Minimum  95.85% using method 11
Number of false positives with core edit > 0 is 231
1 * Deficit + 3 * Core Edit <= 9.5000
Motif index 1


ans = 

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

                       MotifID: 'J3_32030.1'
                     Signature: {'cWW-tWH-F-F-cWW-tHS-F-F-cWW-F'}
                         NumNT: 15
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -7.8308
                   OwnSequence: {'CUGCAAG*CCCAG*CGG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [832×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 832 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.9797 because the cutoff seemed overly generous
Group  23, J3_32030.1  has acceptance rules AlignmentScore >= -27.8308, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.2727
TP   100.00%, TN    97.96%, min    97.96%,   1 3D sequences,     0 alignment sequences,  832 random sequences,   17 random matches, 15 NTs, cWW-tWH-F-F-cWW-tHS-F-F-cWW-F
Sensitivity 100.00%, Specificity  97.96%, Minimum  97.96% using method 8
Number of false positives with core edit > 0 is 17
1 * Deficit + 3 * Core Edit <= 21.4419
Motif index 1


ans = 

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

                       MotifID: 'J3_32601.2'
                     Signature: {'cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW'}
                         NumNT: 12
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: [-7.6711 -8.8847 -7.6711 -7.6711]
                   OwnSequence: {'AUUAAAG*CAUC*GUU'  'UUUAAAG*CAUC*GUA'  'AUUAAAG*CAUC*GUU'  'AUUAAAG*CAUC*GUU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [1910×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 1910 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  24, J3_32601.2  has acceptance rules AlignmentScore >= -27.6711, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  26.4024
TP   100.00%, TN    96.02%, min    96.02%,   4 3D sequences,     0 alignment sequences, 1910 random sequences,   76 random matches, 12 NTs, cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW
Sensitivity 100.00%, Specificity  96.02%, Minimum  96.02% using method 6
Number of false positives with core edit > 0 is 76
1 * Deficit + 3 * Core Edit <= 18.7312
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_32852.2'
                     Signature: {'cWW-tSH-tHW-F-F-cWW-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 1
                         NumBR: 2
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: [-7.4398 -8.9173 -10.9312 -8.0737]
                   OwnSequence: {'CGUAAG*CGA*UAAG'  'CGUAAG*CGG*UCAG'  'CGAUUG*CAA*UAAG'  'CGGAAG*CAG*CAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [12 12 12 12]
            MeanSequenceLength: 12
               DeficitEditData: [6466×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 6466 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  25, J3_32852.2  has acceptance rules AlignmentScore >= -27.4398, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  25.8340
TP   100.00%, TN    95.99%, min    95.99%,   4 3D sequences,     0 alignment sequences, 6466 random sequences,  259 random matches, 12 NTs, cWW-tSH-tHW-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 259
1 * Deficit + 3 * Core Edit <= 18.3943
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_32857.1'
                     Signature: {'cWW-F-F-F-F-F-cWW-F-cWW-F-F-F-F'}
                         NumNT: 15
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 60
                      OwnScore: -11.2450
                   OwnSequence: {'GAAC*GGUGCC*GGAGCC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [2075×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2075 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.1745 because the cutoff seemed overly generous
Group  26, J3_32857.1  has acceptance rules AlignmentScore >= -31.2450, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  31.2450
TP   100.00%, TN    97.49%, min    97.49%,   1 3D sequences,     0 alignment sequences, 2075 random sequences,   52 random matches, 15 NTs, cWW-F-F-F-F-F-cWW-F-cWW-F-F-F-F
Sensitivity 100.00%, Specificity  97.49%, Minimum  97.49% using method 8
Number of false positives with core edit > 0 is 52
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_33851.1'
                     Signature: {'cWW-tSH-F-F-tHS-cWW-cWW-F-F'}
                         NumNT: 14
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 1
                         NumBR: 3
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: -9.9609
                   OwnSequence: {'CGUAG*UCGAAU*AUAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [2592×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2592 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.2782 because the cutoff seemed overly generous
Group  27, J3_33851.1  has acceptance rules AlignmentScore >= -29.9609, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.9959
TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences, 2592 random sequences,   52 random matches, 14 NTs, cWW-tSH-F-F-tHS-cWW-cWW-F-F
Sensitivity 100.00%, Specificity  97.99%, Minimum  97.99% using method 8
Number of false positives with core edit > 0 is 52
1 * Deficit + 3 * Core Edit <= 20.0350
Motif index 1


ans = 

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

                       MotifID: 'J3_35321.1'
                     Signature: {'cWW-cSS-F-F-F-F-cWW-F-cWW'}
                         NumNT: 12
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 50
                      OwnScore: -9.3308
                   OwnSequence: {'CAUUUGA*UU*AGAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 13
            MeanSequenceLength: 13
               DeficitEditData: [2949×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2949 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  28, J3_35321.1  has acceptance rules AlignmentScore >= -29.3308, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.3516
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 2949 random sequences,  118 random matches, 12 NTs, cWW-cSS-F-F-F-F-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 118
1 * Deficit + 3 * Core Edit <= 19.0208
Motif index 1


ans = 

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

                       MotifID: 'J3_36387.1'
                     Signature: {'cWW-F-F-F-tWW-tHW-tHW-cWW-F-F-cWW'}
                         NumNT: 16
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: -7.0468
                   OwnSequence: {'CUAAG*CCGAAUCC*GUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [424×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 424 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.8643 because the cutoff seemed overly generous
Group  29, J3_36387.1  has acceptance rules AlignmentScore >= -27.0468, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.0432
TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,  424 random sequences,    8 random matches, 16 NTs, cWW-F-F-F-tWW-tHW-tHW-cWW-F-F-cWW
Sensitivity 100.00%, Specificity  98.11%, Minimum  98.11% using method 8
Number of false positives with core edit > 0 is 8
1 * Deficit + 3 * Core Edit <= 20.9964
Motif index 1


ans = 

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

                       MotifID: 'J3_36499.1'
                     Signature: {'cWW-tSS-tSH-tHW-tHS-cWW-cWW-F'}
                         NumNT: 13
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 1
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: -7.2279
                   OwnSequence: {'CUAG*CGAAG*CGUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [3661×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 3661 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  30, J3_36499.1  has acceptance rules AlignmentScore >= -27.2279, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  25.7453
TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences, 3661 random sequences,  146 random matches, 13 NTs, cWW-tSS-tSH-tHW-tHS-cWW-cWW-F
Sensitivity 100.00%, Specificity  96.01%, Minimum  96.01% using method 6
Number of false positives with core edit > 0 is 146
1 * Deficit + 3 * Core Edit <= 18.5174
Motif index 1


ans = 

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

                       MotifID: 'J3_37047.2'
                     Signature: {'cWW-cSS-cSH-F-tWH-F-cWW-cSH-F-cWW-F'}
                         NumNT: 15
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 3
                         NumBR: 3
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 50
                      OwnScore: [-8.5525 -9.3390 -15.4820 -8.5525]
                   OwnSequence: {'CCCAGUUC*GCCG*CAAUG'  'CGUAGUCC*GUCG*CAAUG'  'CGUGCUGG*CGAG*CACUG'  'CCCAGUUC*GCCG*CAAUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [16 16 16 16]
            MeanSequenceLength: 16
               DeficitEditData: [266×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 266 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  24.6903 because the cutoff seemed overly generous
Group  31, J3_37047.2  has acceptance rules AlignmentScore >= -28.5525, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.7779
TP   100.00%, TN    98.12%, min    98.12%,   4 3D sequences,     0 alignment sequences,  266 random sequences,    5 random matches, 15 NTs, cWW-cSS-cSH-F-tWH-F-cWW-cSH-F-cWW-F
Sensitivity 100.00%, Specificity  98.12%, Minimum  98.12% using method 8
Number of false positives with core edit > 0 is 5
1 * Deficit + 3 * Core Edit <= 22.2254
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_37410.1'
                     Signature: {'cWW-F-F-tSH-tHW-F-F-F-cWW-F-cWW-F-F'}
                         NumNT: 18
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 15
                        NumBPh: 2
                         NumBR: 3
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: -9.8837
                   OwnSequence: {'AAGACAUU*AUUG*CUUAUU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 17
            MeanSequenceLength: 17
               DeficitEditData: [136×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 136 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  23.7723 because the cutoff seemed overly generous
Group  32, J3_37410.1  has acceptance rules AlignmentScore >= -29.8837, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.5587
TP   100.00%, TN    97.79%, min    97.79%,   1 3D sequences,     0 alignment sequences,  136 random sequences,    3 random matches, 18 NTs, cWW-F-F-tSH-tHW-F-F-F-cWW-F-cWW-F-F
Sensitivity 100.00%, Specificity  97.79%, Minimum  97.79% using method 8
Number of false positives with core edit > 0 is 3
1 * Deficit + 3 * Core Edit <= 22.6750
Motif index 1


ans = 

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

                       MotifID: 'J3_38151.1'
                     Signature: {'cWW-F-F-F-cWW-cWW-F'}
                         NumNT: 10
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 6
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -7.0266
                   OwnSequence: {'AAG*CAA*UGCU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 9
            MeanSequenceLength: 9
               DeficitEditData: [10563×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 10563 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  33, J3_38151.1  has acceptance rules AlignmentScore >= -27.0266, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  16.7785
TP   100.00%, TN    95.92%, min    95.92%,   1 3D sequences,     0 alignment sequences, 10559 random sequences,  431 random matches, 10 NTs, cWW-F-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  95.92%, Minimum  95.92% using method 6
Number of false positives with core edit > 0 is 431
1 * Deficit + 3 * Core Edit <= 9.7519
Motif index 1


ans = 

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

                       MotifID: 'J3_38446.1'
                     Signature: {'cWW-F-cWW-F-F-F-F-F-F-cWS-F-cWW-F'}
                         NumNT: 17
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 3
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 62
                      OwnScore: -10.6326
                   OwnSequence: {'GAGGACUGCG*CAAGGA*UC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 17
            MeanSequenceLength: 17
               DeficitEditData: [79×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 79 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.6237 because the cutoff seemed overly generous
Group  34, J3_38446.1  has acceptance rules AlignmentScore >= -30.6326, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.9635
TP   100.00%, TN    97.47%, min    97.47%,   1 3D sequences,     0 alignment sequences,   79 random sequences,    2 random matches, 17 NTs, cWW-F-cWW-F-F-F-F-F-F-cWS-F-cWW-F
Sensitivity 100.00%, Specificity  97.47%, Minimum  97.47% using method 8
Number of false positives with core edit > 0 is 2
1 * Deficit + 3 * Core Edit <= 20.3310
Motif index 1


ans = 

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

                       MotifID: 'J3_38616.1'
                     Signature: {'cWW-F-cWW-F-cWW-F-cWW-F-tWW-F-cWW'}
                         NumNT: 17
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 50
                      OwnScore: -11.1986
                   OwnSequence: {'UAACUACUG*CAUUU*AUCA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 17
            MeanSequenceLength: 17
               DeficitEditData: [149×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 149 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.3074 because the cutoff seemed overly generous
Group  35, J3_38616.1  has acceptance rules AlignmentScore >= -31.1986, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.7236
TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,  149 random sequences,    3 random matches, 17 NTs, cWW-F-cWW-F-cWW-F-cWW-F-tWW-F-cWW
Sensitivity 100.00%, Specificity  97.99%, Minimum  97.99% using method 8
Number of false positives with core edit > 0 is 3
1 * Deficit + 3 * Core Edit <= 21.5250
Motif index 1


ans = 

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

                       MotifID: 'J3_39238.2'
                     Signature: {'cWW-tWH-cWW-tSW-F-F-cWW'}
                         NumNT: 11
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 6
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: [-8.4540 -8.3588 -8.6953 -9.2061 -9.3479 -8.7905]
                   OwnSequence: {1×6 cell}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13 13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [4564×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

6 sequences from 3D structures
Using 4564 random sequences, 0 from an alignment, and 6 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.4383 because the cutoff seemed overly generous
Group  36, J3_39238.2  has acceptance rules AlignmentScore >= -28.3588, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.3588
TP   100.00%, TN    96.71%, min    96.71%,   6 3D sequences,     0 alignment sequences, 4563 random sequences,  150 random matches, 11 NTs, cWW-tWH-cWW-tSW-F-F-cWW
Sensitivity 100.00%, Specificity  96.71%, Minimum  96.71% using method 8
Number of false positives with core edit > 0 is 150
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2
Motif index 3
Motif index 4
Motif index 5
Motif index 6


ans = 

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

                       MotifID: 'J3_41097.1'
                     Signature: {'cWW-cWW-F-cWW-cWW'}
                         NumNT: 9
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 30
                      OwnScore: [-5.9049 -5.9049]
                   OwnSequence: {'GUG*CUUUG*UC'  'GUG*CUUUG*UC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [9 9]
            MeanSequenceLength: 9
               DeficitEditData: [7655×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 7655 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  37, J3_41097.1  has acceptance rules AlignmentScore >= -25.9049, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  22.3419
TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences, 7651 random sequences,  306 random matches,  9 NTs, cWW-cWW-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 306
1 * Deficit + 3 * Core Edit <= 16.4371
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_42157.1'
                     Signature: {'cWW-tSH-tWW-tHW-F-F-cWW-cWW'}
                         NumNT: 12
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: [-9.3238 -9.4977 -8.5731]
                   OwnSequence: {'CCCAAAC*GUG*CAAG'  'UGAUAAC*GUC*GAAA'  'CGAGAAC*GUG*UAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [8266×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 8266 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  38, J3_42157.1  has acceptance rules AlignmentScore >= -28.5731, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.8555
TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences, 8265 random sequences,  331 random matches, 12 NTs, cWW-tSH-tWW-tHW-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 331
1 * Deficit + 3 * Core Edit <= 19.2823
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_44724.2'
                     Signature: {'cWW-tSH-F-cWW-tHS-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 3
                         NumBR: 2
                  NumInstances: 5
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: [-6.7443 -6.7443 -6.7443 -13.0857 -6.7443]
                   OwnSequence: {'CGAAC*GAUG*CAG'  'CGAAC*GAUG*CAG'  'CGAAC*GAUG*CAG'  'UGUUAG*CGUG*CAA'  'CGAAC*GAUG*CAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 11 11 12 11]
            MeanSequenceLength: 11.2000
               DeficitEditData: [9172×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

5 sequences from 3D structures
Using 9172 random sequences, 0 from an alignment, and 5 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  39, J3_44724.2  has acceptance rules AlignmentScore >= -26.7443, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.0584
TP   100.00%, TN    96.00%, min    96.00%,   5 3D sequences,     0 alignment sequences, 9171 random sequences,  367 random matches, 12 NTs, cWW-tSH-F-cWW-tHS-cWW-F
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 367
1 * Deficit + 3 * Core Edit <= 17.3141
Motif index 1
Motif index 2
Motif index 3
Motif index 4
Motif index 5


ans = 

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

                       MotifID: 'J3_45941.1'
                     Signature: {'cWW-cWS-cSH-tWH-F-F-F-F-cWW-cWW-F'}
                         NumNT: 13
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 50
                      OwnScore: -9.8072
                   OwnSequence: {'ACGCC*GAA*UGUUGU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 13
            MeanSequenceLength: 13
               DeficitEditData: [2107×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2107 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.2037 because the cutoff seemed overly generous
Group  40, J3_45941.1  has acceptance rules AlignmentScore >= -29.8072, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.8072
TP   100.00%, TN    96.11%, min    96.11%,   1 3D sequences,     0 alignment sequences, 2107 random sequences,   82 random matches, 13 NTs, cWW-cWS-cSH-tWH-F-F-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  96.11%, Minimum  96.11% using method 8
Number of false positives with core edit > 0 is 82
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_47248.1'
                     Signature: {'cWW-F-F-F-F-F-tHH-F-cWW-cWW-F-F-F'}
                         NumNT: 17
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 62
                      OwnScore: -12.0999
                   OwnSequence: {'CGAGAC*GCAAUA*UCUUAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 17
            MeanSequenceLength: 17
               DeficitEditData: [371×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 371 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.6746 because the cutoff seemed overly generous
Group  41, J3_47248.1  has acceptance rules AlignmentScore >= -32.0999, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.4177
TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,  371 random sequences,    7 random matches, 17 NTs, cWW-F-F-F-F-F-tHH-F-cWW-cWW-F-F-F
Sensitivity 100.00%, Specificity  98.11%, Minimum  98.11% using method 8
Number of false positives with core edit > 0 is 7
1 * Deficit + 3 * Core Edit <= 20.3179
Motif index 1


ans = 

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

                       MotifID: 'J3_47376.1'
                     Signature: {'cWW-F-F-cWS-cWW-F-cWW'}
                         NumNT: 10
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 4
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -7.7245
                   OwnSequence: {'GU*ACC*GUCACC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 10
            MeanSequenceLength: 10
               DeficitEditData: [11932×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 11932 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  42, J3_47376.1  has acceptance rules AlignmentScore >= -27.7245, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.2816
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 11932 random sequences,  477 random matches, 10 NTs, cWW-F-F-cWS-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 477
1 * Deficit + 3 * Core Edit <= 16.5571
Motif index 1


ans = 

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

                       MotifID: 'J3_47707.1'
                     Signature: {'cWW-F-F-F-F-F-cWW-F-cWW-F-F-cSH-cSH-cWW-F'}
                         NumNT: 20
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 14
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 68
                      OwnScore: -14.3222
                   OwnSequence: {'ACGUUACUAACG*UGC*GAUUU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 19
            MeanSequenceLength: 19
               DeficitEditData: [4×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 4 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  43, J3_47707.1  has acceptance rules AlignmentScore >= -34.3222, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  39.3222
TP   100.00%, TN   100.00%, min   100.00%,   1 3D sequences,     0 alignment sequences,    4 random sequences,    0 random matches, 20 NTs, cWW-F-F-F-F-F-cWW-F-cWW-F-F-cSH-cSH-cWW-F
Sensitivity 100.00%, Specificity 100.00%, Minimum 100.00% using method 1
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_48314.1'
                     Signature: {'cWW-cWW-F-cWW-F-cWW-F'}
                         NumNT: 11
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 6
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: -7.7472
                   OwnSequence: {'AGAUG*CUG*CAU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 10
            MeanSequenceLength: 10
               DeficitEditData: [12981×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 12981 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  44, J3_48314.1  has acceptance rules AlignmentScore >= -27.7472, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  23.0698
TP   100.00%, TN    95.99%, min    95.99%,   1 3D sequences,     0 alignment sequences, 12981 random sequences,  520 random matches, 11 NTs, cWW-cWW-F-cWW-F-cWW-F
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 520
1 * Deficit + 3 * Core Edit <= 15.3226
Motif index 1


ans = 

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

                       MotifID: 'J3_51910.1'
                     Signature: {'cWW-F-cWW-tWS-F-F-cWW-cWW'}
                         NumNT: 12
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: -8.7685
                   OwnSequence: {'GAAC*GG*CACAAGC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [6928×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 6928 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  45, J3_51910.1  has acceptance rules AlignmentScore >= -28.7685, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.2744
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 6928 random sequences,  277 random matches, 12 NTs, cWW-F-cWW-tWS-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 277
1 * Deficit + 3 * Core Edit <= 18.5059
Motif index 1


ans = 

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

                       MotifID: 'J3_52655.1'
                     Signature: {'cWW-tSH-cWW-F-cWW-cWW'}
                         NumNT: 11
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 32
                      OwnScore: [-6.7028 -6.7028 -6.7028]
                   OwnSequence: {'UGGA*UAC*GGAA'  'UGGA*UAC*GGAA'  'UGGA*UAC*GGAA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [10 10 10]
            MeanSequenceLength: 10
               DeficitEditData: [8033×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 8033 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  46, J3_52655.1  has acceptance rules AlignmentScore >= -26.7028, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  21.7384
TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences, 8033 random sequences,  321 random matches, 11 NTs, cWW-tSH-cWW-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 321
1 * Deficit + 3 * Core Edit <= 15.0357
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_52842.1'
                     Signature: {'cWW-tHS-F-F-F-cWW-cWW'}
                         NumNT: 11
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 5
                        NumBPh: 0
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: -9.5454
                   OwnSequence: {'CAUCA*UC*GUUAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [7243×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 7243 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  47, J3_52842.1  has acceptance rules AlignmentScore >= -29.5454, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.1572
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 7243 random sequences,  290 random matches, 11 NTs, cWW-tHS-F-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 290
1 * Deficit + 3 * Core Edit <= 18.6118
Motif index 1


ans = 

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

                       MotifID: 'J3_52917.1'
                     Signature: {'cWW-tWW-cHW-tSH-cWW-tSS-F-cSS-cWW'}
                         NumNT: 12
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -10.3210
                   OwnSequence: {'ACUAAUA*UAUC*GUU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 13
            MeanSequenceLength: 13
               DeficitEditData: [3154×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 3154 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  48, J3_52917.1  has acceptance rules AlignmentScore >= -30.3210, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.8525
TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences, 3154 random sequences,  126 random matches, 12 NTs, cWW-tWW-cHW-tSH-cWW-tSS-F-cSS-cWW
Sensitivity 100.00%, Specificity  96.01%, Minimum  96.01% using method 6
Number of false positives with core edit > 0 is 126
1 * Deficit + 3 * Core Edit <= 18.5315
Motif index 1


ans = 

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

                       MotifID: 'J3_56052.2'
                     Signature: {'cWW-F-cWW-cWW-F'}
                         NumNT: 8
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 4
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 32
                      OwnScore: [-5.2465 -4.3992 -4.3992 -4.3992]
                   OwnSequence: {'CGG*CUUG*CG'  'CGG*CUAG*CG'  'CGG*CUAG*CG'  'CGG*CUAG*CG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [8 8 8 8]
            MeanSequenceLength: 8
               DeficitEditData: [6875×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 6875 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  49, J3_56052.2  has acceptance rules AlignmentScore >= -24.3992, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  16.1778
TP   100.00%, TN    95.99%, min    95.99%,   4 3D sequences,     0 alignment sequences, 6856 random sequences,  275 random matches,  8 NTs, cWW-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 275
1 * Deficit + 3 * Core Edit <= 11.7786
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_56708.1'
                     Signature: {'cWW-F-cWW-F-tHW-F-F-F-cWW-F-cWW'}
                         NumNT: 16
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -9.6465
                   OwnSequence: {'AAAACAUAC*GAGAG*CU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [741×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 741 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.1465 because the cutoff seemed overly generous
Group  50, J3_56708.1  has acceptance rules AlignmentScore >= -29.6465, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.5093
TP   100.00%, TN    97.98%, min    97.98%,   1 3D sequences,     0 alignment sequences,  741 random sequences,   15 random matches, 16 NTs, cWW-F-cWW-F-tHW-F-F-F-cWW-F-cWW
Sensitivity 100.00%, Specificity  97.98%, Minimum  97.98% using method 8
Number of false positives with core edit > 0 is 15
1 * Deficit + 3 * Core Edit <= 20.8628
Motif index 1


ans = 

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

                       MotifID: 'J3_58090.1'
                     Signature: {'cWW-tWW-F-F-F-cWW-F-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -10.2033
                   OwnSequence: {'CGUG*CGAUAAGUC*GG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [2226×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2226 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.0696 because the cutoff seemed overly generous
Group  51, J3_58090.1  has acceptance rules AlignmentScore >= -30.2033, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.2033
TP   100.00%, TN    97.17%, min    97.17%,   1 3D sequences,     0 alignment sequences, 2226 random sequences,   63 random matches, 13 NTs, cWW-tWW-F-F-F-cWW-F-F-cWW
Sensitivity 100.00%, Specificity  97.17%, Minimum  97.17% using method 8
Number of false positives with core edit > 0 is 63
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_58453.1'
                     Signature: {'cWW-cWH-F-cWW-tWS-F-F-cWW-F'}
                         NumNT: 14
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 7
                        NumBPh: 1
                         NumBR: 4
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -9.7268
                   OwnSequence: {'UUAAAACC*GUGGG*CAGA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 16
            MeanSequenceLength: 16
               DeficitEditData: [779×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 779 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.4398 because the cutoff seemed overly generous
Group  52, J3_58453.1  has acceptance rules AlignmentScore >= -29.7268, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.7268
TP   100.00%, TN    97.95%, min    97.95%,   1 3D sequences,     0 alignment sequences,  779 random sequences,   16 random matches, 14 NTs, cWW-cWH-F-cWW-tWS-F-F-cWW-F
Sensitivity 100.00%, Specificity  97.95%, Minimum  97.95% using method 8
Number of false positives with core edit > 0 is 16
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_59914.1'
                     Signature: {'cWW-F-cWW-F-cWW-F'}
                         NumNT: 9
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 5
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 30
                      OwnScore: -6.4388
                   OwnSequence: {'UAG*CUU*AAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 8
            MeanSequenceLength: 8
               DeficitEditData: [5443×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 5443 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  53, J3_59914.1  has acceptance rules AlignmentScore >= -26.4388, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  16.2866
TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences, 5408 random sequences,  216 random matches,  9 NTs, cWW-F-cWW-F-cWW-F
Sensitivity 100.00%, Specificity  96.01%, Minimum  96.01% using method 6
Number of false positives with core edit > 0 is 216
1 * Deficit + 3 * Core Edit <= 9.8478
Motif index 1


ans = 

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

                       MotifID: 'J3_64069.1'
                     Signature: {'cWW-tHS-F-F-F-cWW-cWW-F-F'}
                         NumNT: 13
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 34
                      OwnScore: -12.6293
                   OwnSequence: {'GAAC*GUUGAU*AAUGAAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 16
            MeanSequenceLength: 16
               DeficitEditData: [1042×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 1042 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.2628 because the cutoff seemed overly generous
Group  54, J3_64069.1  has acceptance rules AlignmentScore >= -32.6293, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.6293
TP   100.00%, TN    96.55%, min    96.55%,   1 3D sequences,     0 alignment sequences, 1042 random sequences,   36 random matches, 13 NTs, cWW-tHS-F-F-F-cWW-cWW-F-F
Sensitivity 100.00%, Specificity  96.55%, Minimum  96.55% using method 8
Number of false positives with core edit > 0 is 36
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_65070.2'
                     Signature: {'cWW-tWH-cWW-tSH-F-cWW-F'}
                         NumNT: 12
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: [-7.0614 -7.7355 -7.1716]
                   OwnSequence: {'GUGAAAAG*CC*GC'  'GCGAAAAG*CC*GC'  'AUGAAAAG*CG*CU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 11 11]
            MeanSequenceLength: 11
               DeficitEditData: [2085×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 2085 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  55, J3_65070.2  has acceptance rules AlignmentScore >= -27.0614, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  22.0489
TP   100.00%, TN    96.02%, min    96.02%,   3 3D sequences,     0 alignment sequences, 2083 random sequences,   83 random matches, 12 NTs, cWW-tWH-cWW-tSH-F-cWW-F
Sensitivity 100.00%, Specificity  96.02%, Minimum  96.02% using method 6
Number of false positives with core edit > 0 is 83
1 * Deficit + 3 * Core Edit <= 14.9875
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_65990.1'
                     Signature: {'cWW-tHW-F-F-cWW-F-F-F-cWW-F'}
                         NumNT: 14
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -9.3887
                   OwnSequence: {'CUG*UCAACAG*UUAAUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [878×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 878 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  24.7275 because the cutoff seemed overly generous
Group  56, J3_65990.1  has acceptance rules AlignmentScore >= -29.3887, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.5232
TP   100.00%, TN    97.95%, min    97.95%,   1 3D sequences,     0 alignment sequences,  878 random sequences,   18 random matches, 14 NTs, cWW-tHW-F-F-cWW-F-F-F-cWW-F
Sensitivity 100.00%, Specificity  97.95%, Minimum  97.95% using method 8
Number of false positives with core edit > 0 is 18
1 * Deficit + 3 * Core Edit <= 23.1345
Motif index 1


ans = 

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

                       MotifID: 'J3_68440.1'
                     Signature: {'cWW-cWW-F-F-F-cWW-F-F-cWW-F-F-F-F-F-F'}
                         NumNT: 19
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 15
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 50
                      OwnScore: -12.6658
                   OwnSequence: {'CUUGAAAAGCCUG*CA*UAUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 18
            MeanSequenceLength: 18
               DeficitEditData: [13×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 13 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  57, J3_68440.1  has acceptance rules AlignmentScore >= -32.6658, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  37.6658
TP   100.00%, TN    76.92%, min    76.92%,   1 3D sequences,     0 alignment sequences,   13 random sequences,    3 random matches, 19 NTs, cWW-cWW-F-F-F-cWW-F-F-cWW-F-F-F-F-F-F
Sensitivity 100.00%, Specificity  76.92%, Minimum  76.92% using method 1
Number of false positives with core edit > 0 is 3
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_69441.1'
                     Signature: {'cWW-cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW'}
                         NumNT: 14
                  NumBasepairs: 9
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -10.8991
                   OwnSequence: {'CAUC*GUGA*UAUUAAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [898×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 898 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.4065 because the cutoff seemed overly generous
Group  58, J3_69441.1  has acceptance rules AlignmentScore >= -30.8991, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.8991
TP   100.00%, TN    96.33%, min    96.33%,   1 3D sequences,     0 alignment sequences,  898 random sequences,   33 random matches, 14 NTs, cWW-cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW
Sensitivity 100.00%, Specificity  96.33%, Minimum  96.33% using method 8
Number of false positives with core edit > 0 is 33
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_72575.1'
                     Signature: {'cWW-cWW-F-cWW-cSS-cWW-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 2
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -8.2681
                   OwnSequence: {'GGUG*CUUUAC*GAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [2450×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2450 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  59, J3_72575.1  has acceptance rules AlignmentScore >= -28.2681, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.4479
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 2450 random sequences,   98 random matches, 13 NTs, cWW-cWW-F-cWW-cSS-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 98
1 * Deficit + 3 * Core Edit <= 19.1798
Motif index 1


ans = 

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

                       MotifID: 'J3_72804.1'
                     Signature: {'cWW-F-F-F-F-F-tHW-F-F-cWW-cWW-F'}
                         NumNT: 16
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 56
                      OwnScore: -12.1214
                   OwnSequence: {'GCACAGGG*CAAAGC*GUUACC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 19
            MeanSequenceLength: 19
               DeficitEditData: [43×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 43 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  24.0670 because the cutoff seemed overly generous
Group  60, J3_72804.1  has acceptance rules AlignmentScore >= -32.1214, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  35.7064
TP   100.00%, TN    97.67%, min    97.67%,   1 3D sequences,     0 alignment sequences,   43 random sequences,    1 random matches, 16 NTs, cWW-F-F-F-F-F-tHW-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  97.67%, Minimum  97.67% using method 8
Number of false positives with core edit > 0 is 1
1 * Deficit + 3 * Core Edit <= 23.5850
Motif index 1


ans = 

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

                       MotifID: 'J3_75187.1'
                     Signature: {'cWW-cWW-tSH-F-F-F-F-tHS-cWW-cWW'}
                         NumNT: 16
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 1
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -11.0148
                   OwnSequence: {'GAGAUACG*CUG*CUAUGC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 16
            MeanSequenceLength: 16
               DeficitEditData: [425×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 425 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.4284 because the cutoff seemed overly generous
Group  61, J3_75187.1  has acceptance rules AlignmentScore >= -31.0148, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  31.0148
TP   100.00%, TN    97.65%, min    97.65%,   1 3D sequences,     0 alignment sequences,  425 random sequences,   10 random matches, 16 NTs, cWW-cWW-tSH-F-F-F-F-tHS-cWW-cWW
Sensitivity 100.00%, Specificity  97.65%, Minimum  97.65% using method 8
Number of false positives with core edit > 0 is 10
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_79305.1'
                     Signature: {'cWW-cSH-cWW-cWH-F-tSW-F-F-F-F-F-cWW-cWW-F'}
                         NumNT: 19
                  NumBasepairs: 9
                    Structured: 1
                     NumStacks: 15
                        NumBPh: 1
                         NumBR: 3
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 48
                      OwnScore: -10.1205
                   OwnSequence: {'GAGGAAGGAG*CGC*GGACUGC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 19
            MeanSequenceLength: 19
               DeficitEditData: [3×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 3 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  62, J3_79305.1  has acceptance rules AlignmentScore >= -30.1205, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  35.1205
TP   100.00%, TN   100.00%, min   100.00%,   1 3D sequences,     0 alignment sequences,    3 random sequences,    0 random matches, 19 NTs, cWW-cSH-cWW-cWH-F-tSW-F-F-F-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity 100.00%, Minimum 100.00% using method 1
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_82061.2'
                     Signature: {'cWW-F-cWW-F-cWW'}
                         NumNT: 8
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 5
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 32
                      OwnScore: [-6.9256 -9.1070 -6.9789]
                   OwnSequence: {'CCAG*CC*GCG'  'CCCUC*GU*AG'  'GCAG*CC*GCC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [8 8 8]
            MeanSequenceLength: 8
               DeficitEditData: [11760×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 11760 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  63, J3_82061.2  has acceptance rules AlignmentScore >= -26.9256, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  18.2572
TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences, 11760 random sequences,  470 random matches,  8 NTs, cWW-F-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 470
1 * Deficit + 3 * Core Edit <= 11.3316
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_82365.1'
                     Signature: {'cWW-F-F-F-cWW-cWW-F'}
                         NumNT: 10
                  NumBasepairs: 3
                    Structured: 1
                     NumStacks: 6
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: [-7.9822 -7.6785 -8.4819]
                   OwnSequence: {'GGAC*GUUU*AAC'  'AGAC*GGUG*UAU'  'GGAC*GGAG*CGC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [10 10 10]
            MeanSequenceLength: 10
               DeficitEditData: [12513×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 12513 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  64, J3_82365.1  has acceptance rules AlignmentScore >= -27.6785, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  19.4786
TP   100.00%, TN    95.98%, min    95.98%,   3 3D sequences,     0 alignment sequences, 12501 random sequences,  502 random matches, 10 NTs, cWW-F-F-F-cWW-cWW-F
Sensitivity 100.00%, Specificity  95.98%, Minimum  95.98% using method 6
Number of false positives with core edit > 0 is 502
1 * Deficit + 3 * Core Edit <= 11.8001
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_82572.1'
                     Signature: {'cWW-tSH-tWW-F-cWW-tHW-F-F-cWW'}
                         NumNT: 11
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 32
                      OwnScore: [-7.8829 -7.8829]
                   OwnSequence: {'CUUG*CAG*CUUACG'  'CUUG*CAG*CUUACG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [12 12]
            MeanSequenceLength: 12
               DeficitEditData: [7570×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 7570 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  65, J3_82572.1  has acceptance rules AlignmentScore >= -27.8829, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.3085
TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences, 7569 random sequences,  303 random matches, 11 NTs, cWW-tSH-tWW-F-cWW-tHW-F-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 303
1 * Deficit + 3 * Core Edit <= 19.4256
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_83516.1'
                     Signature: {'cWW-F-F-F-tWW-F-tSH-tSS-F-F-F-F-F-cWW-cWW-F-F-F'}
                         NumNT: 22
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 19
                        NumBPh: 5
                         NumBR: 3
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 78
                      OwnScore: [-14.1163 -14.1163 -15.6094]
                   OwnSequence: {'GAAGAACCUUAC*GGCGA*UUUAAUUC'  'GAAGAACCUUAC*GGCUA*UUUAAUUC'  'GGGGAAACUCAC*GGCCG*CUUAAUUU'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [24 24 24]
            MeanSequenceLength: 24
               DeficitEditData: [0×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 0 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
No random sequence matches, so essentially no model-specific cutoff imposed
Decreased cutoff to  25.0000 so that it is possible to reject matches
Group  66, J3_83516.1  has acceptance rules AlignmentScore >= -34.1163, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  39.1163
TP   100.00%, TN      NaN%, min   100.00%,   3 3D sequences,     0 alignment sequences,    0 random sequences,    0 random matches, 22 NTs, cWW-F-F-F-tWW-F-tSH-tSS-F-F-F-F-F-cWW-cWW-F-F-F
Sensitivity 100.00%, Specificity    NaN%, Minimum 100.00% using method 12
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_84189.2'
                     Signature: {'cWW-tSH-tWW-tHH-F-tHW-cWW-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: [-7.9732 -12.3085 -7.9732]
                   OwnSequence: {'CGCAAAC*GUG*CAAG'  'CUAAUG*CAUG*CAAG'  'CGCAAAC*GUG*CAAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [7442×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 7442 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  67, J3_84189.2  has acceptance rules AlignmentScore >= -27.9732, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.2416
TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences, 7442 random sequences,  298 random matches, 13 NTs, cWW-tSH-tWW-tHH-F-tHW-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 298
1 * Deficit + 3 * Core Edit <= 19.2684
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_84625.1'
                     Signature: {'cWW-F-cWW-F-F-F-cWW-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 1
                         NumBR: 2
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: [-8.2692 -8.2692]
                   OwnSequence: {'GAUAAGC*GAUUU*AC'  'GAAAAGC*GAUGU*AC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13]
            MeanSequenceLength: 13
               DeficitEditData: [3760×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 3760 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.8944 because the cutoff seemed overly generous
Group  68, J3_84625.1  has acceptance rules AlignmentScore >= -28.2692, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.2692
TP   100.00%, TN    97.18%, min    97.18%,   2 3D sequences,     0 alignment sequences, 3760 random sequences,  106 random matches, 13 NTs, cWW-F-cWW-F-F-F-cWW-F-cWW
Sensitivity 100.00%, Specificity  97.18%, Minimum  97.18% using method 8
Number of false positives with core edit > 0 is 106
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_85054.2'
                     Signature: {'cWW-tSH-F-tWW-tHS-cWW-cWW-F'}
                         NumNT: 14
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 4
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: [-13.3697 -9.0748 -9.0748 -10.5197]
                   OwnSequence: {'CUAAG*CGCAAAC*GUAG'  'CGAAG*CGUUAAG*CUAG'  'CGAAG*CGUUAAG*CUAG'  'CGGAG*CGUUAAG*CUUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [15 15 15 15]
            MeanSequenceLength: 15
               DeficitEditData: [2424×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

4 sequences from 3D structures
Using 2424 random sequences, 0 from an alignment, and 4 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.3421 because the cutoff seemed overly generous
Group  69, J3_85054.2  has acceptance rules AlignmentScore >= -29.0748, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.0748
TP   100.00%, TN    97.40%, min    97.40%,   4 3D sequences,     0 alignment sequences, 2424 random sequences,   63 random matches, 14 NTs, cWW-tSH-F-tWW-tHS-cWW-cWW-F
Sensitivity 100.00%, Specificity  97.40%, Minimum  97.40% using method 8
Number of false positives with core edit > 0 is 63
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2
Motif index 3
Motif index 4


ans = 

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

                       MotifID: 'J3_86907.1'
                     Signature: {'cWW-F-F-F-tSW-F-tSH-tSS-F-F-F-F-F-F-F-cWW-cWW-F-F-F-F'}
                         NumNT: 26
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 20
                        NumBPh: 3
                         NumBR: 5
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 82
                      OwnScore: -17.9597
                   OwnSequence: {'GAAGAACCUUACC*GGGCGAC*GUUUAAUUC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 28
            MeanSequenceLength: 28
               DeficitEditData: [0×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 0 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
No random sequence matches, so essentially no model-specific cutoff imposed
Decreased cutoff to  25.0000 so that it is possible to reject matches
Group  70, J3_86907.1  has acceptance rules AlignmentScore >= -37.9597, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  42.9597
TP   100.00%, TN      NaN%, min   100.00%,   1 3D sequences,     0 alignment sequences,    0 random sequences,    0 random matches, 26 NTs, cWW-F-F-F-tSW-F-tSH-tSS-F-F-F-F-F-F-F-cWW-cWW-F-F-F-F
Sensitivity 100.00%, Specificity    NaN%, Minimum 100.00% using method 12
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_89044.1'
                     Signature: {'cWW-cSW-F-cWW-cSW-cWW-cHW-F-cWW'}
                         NumNT: 15
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: -9.8314
                   OwnSequence: {'CGCAAUC*GUAG*CGAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [3267×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 3267 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.2583 because the cutoff seemed overly generous
Group  71, J3_89044.1  has acceptance rules AlignmentScore >= -29.8314, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  29.8314
TP   100.00%, TN    96.27%, min    96.27%,   1 3D sequences,     0 alignment sequences, 3267 random sequences,  122 random matches, 15 NTs, cWW-cSW-F-cWW-cSW-cWW-cHW-F-cWW
Sensitivity 100.00%, Specificity  96.27%, Minimum  96.27% using method 8
Number of false positives with core edit > 0 is 122
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_89368.2'
                     Signature: {'cWW-tSH-tHW-F-cWW-tHH-cWW'}
                         NumNT: 13
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 2
                         NumBR: 3
                  NumInstances: 3
                      Truncate: [2×1 double]
                      NumFixed: 34
                      OwnScore: [-7.1631 -6.4218 -6.3368]
                   OwnSequence: {'GGACAG*CUG*CUAAC'  'GGACCG*UUG*CUAAC'  'GGACAG*UUG*CUAAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [13 13 13]
            MeanSequenceLength: 13
               DeficitEditData: [1777×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

3 sequences from 3D structures
Using 1777 random sequences, 0 from an alignment, and 3 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.1137 because the cutoff seemed overly generous
Group  72, J3_89368.2  has acceptance rules AlignmentScore >= -26.3368, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  26.3368
TP   100.00%, TN    97.07%, min    97.07%,   3 3D sequences,     0 alignment sequences, 1777 random sequences,   52 random matches, 13 NTs, cWW-tSH-tHW-F-cWW-tHH-cWW
Sensitivity 100.00%, Specificity  97.07%, Minimum  97.07% using method 8
Number of false positives with core edit > 0 is 52
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2
Motif index 3


ans = 

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

                       MotifID: 'J3_89737.1'
                     Signature: {'cWW-F-cWW-tSS-cWW-F-cWW-cWW'}
                         NumNT: 14
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: -8.8695
                   OwnSequence: {'CCACAG*CGUUC*GUUCG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [920×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 920 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  23.0816 because the cutoff seemed overly generous
Group  73, J3_89737.1  has acceptance rules AlignmentScore >= -28.8695, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.0591
TP   100.00%, TN    98.04%, min    98.04%,   1 3D sequences,     0 alignment sequences,  920 random sequences,   18 random matches, 14 NTs, cWW-F-cWW-tSS-cWW-F-cWW-cWW
Sensitivity 100.00%, Specificity  98.04%, Minimum  98.04% using method 8
Number of false positives with core edit > 0 is 18
1 * Deficit + 3 * Core Edit <= 21.1896
Motif index 1


ans = 

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

                       MotifID: 'J3_90256.1'
                     Signature: {'cWW-cWS-F-F-F-F-F-F-cWW-F-tHS-F-cWW-F'}
                         NumNT: 17
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 2
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 56
                      OwnScore: [-11.0711 -11.0711]
                   OwnSequence: {'GUUAAAACC*GUGGG*CAGAC'  'GUUAAAACC*GUGGG*CAGAC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [18 18]
            MeanSequenceLength: 18
               DeficitEditData: [142×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 142 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  23.0711 because the cutoff seemed overly generous
Group  74, J3_90256.1  has acceptance rules AlignmentScore >= -31.0711, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.4289
TP   100.00%, TN    97.89%, min    97.89%,   2 3D sequences,     0 alignment sequences,  142 random sequences,    3 random matches, 17 NTs, cWW-cWS-F-F-F-F-F-F-cWW-F-tHS-F-cWW-F
Sensitivity 100.00%, Specificity  97.89%, Minimum  97.89% using method 8
Number of false positives with core edit > 0 is 3
1 * Deficit + 3 * Core Edit <= 21.3578
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_90744.1'
                     Signature: {'cWW-F-cWW-F-F-cSS-F-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 8
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -10.1009
                   OwnSequence: {'GAUAAAA*UGCC*GC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [7133×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 7133 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  75, J3_90744.1  has acceptance rules AlignmentScore >= -30.1009, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  27.3911
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 7133 random sequences,  285 random matches, 13 NTs, cWW-F-cWW-F-F-cSS-F-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 285
1 * Deficit + 3 * Core Edit <= 17.2902
Motif index 1


ans = 

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

                       MotifID: 'J3_91491.2'
                     Signature: {'cWW-F-tWW-tHW-cWW-F-cWW'}
                         NumNT: 11
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 6
                        NumBPh: 0
                         NumBR: 3
                  NumInstances: 6
                      Truncate: [2×1 double]
                      NumFixed: 38
                      OwnScore: [-5.7302 -5.7302 -5.9388 -5.9388 -6.4866 -7.1349]
                   OwnSequence: {'CAUAAG*CUC*GAG'  'CAAAAG*CUC*GAG'  'UAGAAG*CUC*GAG'  'UAGAAG*CUC*GAG'  'UAAAAG*CUC*GAA'  'CAUAAG*CUA*UAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 11 11 11 11 11]
            MeanSequenceLength: 11
               DeficitEditData: [7578×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

6 sequences from 3D structures
Using 7578 random sequences, 0 from an alignment, and 6 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  76, J3_91491.2  has acceptance rules AlignmentScore >= -25.7302, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.0711
TP   100.00%, TN    96.00%, min    96.00%,   6 3D sequences,     0 alignment sequences, 7578 random sequences,  303 random matches, 11 NTs, cWW-F-tWW-tHW-cWW-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 303
1 * Deficit + 3 * Core Edit <= 18.3408
Motif index 1
Motif index 2
Motif index 3
Motif index 4
Motif index 5
Motif index 6


ans = 

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

                       MotifID: 'J3_93059.1'
                     Signature: {'cWW-tWH-cWW-tSH-F-cWW-cWW'}
                         NumNT: 13
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 12
                        NumBPh: 1
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -7.9631
                   OwnSequence: {'CUUAAAUG*CUC*GG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [2066×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 2066 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  77, J3_93059.1  has acceptance rules AlignmentScore >= -27.9631, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.7450
TP   100.00%, TN    95.98%, min    95.98%,   1 3D sequences,     0 alignment sequences, 2065 random sequences,   83 random matches, 13 NTs, cWW-tWH-cWW-tSH-F-cWW-cWW
Sensitivity 100.00%, Specificity  95.98%, Minimum  95.98% using method 6
Number of false positives with core edit > 0 is 83
1 * Deficit + 3 * Core Edit <= 16.7819
Motif index 1


ans = 

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

                       MotifID: 'J3_93637.1'
                     Signature: {'cWW-cWW-F-F-F-F-F-cWW-cWW-F-F'}
                         NumNT: 15
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 2
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 52
                      OwnScore: -7.6551
                   OwnSequence: {'UAGUC*GUUGAC*GCUA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 14
            MeanSequenceLength: 14
               DeficitEditData: [1376×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 1376 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  23.9686 because the cutoff seemed overly generous
Group  78, J3_93637.1  has acceptance rules AlignmentScore >= -27.6551, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.0652
TP   100.00%, TN    97.97%, min    97.97%,   1 3D sequences,     0 alignment sequences, 1376 random sequences,   28 random matches, 15 NTs, cWW-cWW-F-F-F-F-F-cWW-cWW-F-F
Sensitivity 100.00%, Specificity  97.97%, Minimum  97.97% using method 8
Number of false positives with core edit > 0 is 28
1 * Deficit + 3 * Core Edit <= 22.4101
Motif index 1


ans = 

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

                       MotifID: 'J3_94515.1'
                     Signature: {'cWW-tWW-F-cWW-F-tHS-F-cWW'}
                         NumNT: 13
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 40
                      OwnScore: -8.7202
                   OwnSequence: {'UCGAAU*AGAG*CAG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 12
            MeanSequenceLength: 12
               DeficitEditData: [7368×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 7368 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  79, J3_94515.1  has acceptance rules AlignmentScore >= -28.7202, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.1543
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 7368 random sequences,  295 random matches, 13 NTs, cWW-tWW-F-cWW-F-tHS-F-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 295
1 * Deficit + 3 * Core Edit <= 19.4341
Motif index 1


ans = 

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

                       MotifID: 'J3_94652.1'
                     Signature: {'cWW-F-F-F-F-F-cWW-cWW'}
                         NumNT: 10
                  NumBasepairs: 4
                    Structured: 1
                     NumStacks: 4
                        NumBPh: 1
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 34
                      OwnScore: -6.9354
                   OwnSequence: {'CGGC*GCUAG*CG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 10
            MeanSequenceLength: 10
               DeficitEditData: [10555×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 10555 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  80, J3_94652.1  has acceptance rules AlignmentScore >= -26.9354, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  24.1867
TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 10555 random sequences,  422 random matches, 10 NTs, cWW-F-F-F-F-F-cWW-cWW
Sensitivity 100.00%, Specificity  96.00%, Minimum  96.00% using method 6
Number of false positives with core edit > 0 is 422
1 * Deficit + 3 * Core Edit <= 17.2513
Motif index 1


ans = 

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

                       MotifID: 'J3_96170.1'
                     Signature: {'cWW-cSH-cWS-tHS-cWH-F-F-cWW-F-tHS-F-cWW-F'}
                         NumNT: 16
                  NumBasepairs: 8
                    Structured: 1
                     NumStacks: 11
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 58
                      OwnScore: -10.5863
                   OwnSequence: {'UUAAAACC*GUGGG*CAGA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 16
            MeanSequenceLength: 16
               DeficitEditData: [471×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 471 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.4381 because the cutoff seemed overly generous
Group  81, J3_96170.1  has acceptance rules AlignmentScore >= -30.5863, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  31.7946
TP   100.00%, TN    98.09%, min    98.09%,   1 3D sequences,     0 alignment sequences,  471 random sequences,    9 random matches, 16 NTs, cWW-cSH-cWS-tHS-cWH-F-F-cWW-F-tHS-F-cWW-F
Sensitivity 100.00%, Specificity  98.09%, Minimum  98.09% using method 8
Number of false positives with core edit > 0 is 9
1 * Deficit + 3 * Core Edit <= 21.2083
Motif index 1


ans = 

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

                       MotifID: 'J3_96372.1'
                     Signature: {'cWW-cSH-cWS-F-F-F-tHW-F-cWW-F-cWW-F'}
                         NumNT: 16
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 0
                         NumBR: 1
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 56
                      OwnScore: [-13.9324 -13.6287]
                   OwnSequence: {'GCACAGGG*CAAAG*UUACC'  'GACAAUAC*GAAAG*CUGCC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [17 17]
            MeanSequenceLength: 17
               DeficitEditData: [719×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 719 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  20.7406 because the cutoff seemed overly generous
Group  82, J3_96372.1  has acceptance rules AlignmentScore >= -33.6287, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  33.6287
TP   100.00%, TN    96.94%, min    96.94%,   2 3D sequences,     0 alignment sequences,  719 random sequences,   22 random matches, 16 NTs, cWW-cSH-cWS-F-F-F-tHW-F-cWW-F-cWW-F
Sensitivity 100.00%, Specificity  96.94%, Minimum  96.94% using method 8
Number of false positives with core edit > 0 is 22
1 * Deficit + 3 * Core Edit <= 20.0000
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_97609.1'
                     Signature: {'cWW-tSH-tHW-F-cWW-tHH-F-cWW-F'}
                         NumNT: 15
                  NumBasepairs: 7
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 2
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: -8.0976
                   OwnSequence: {'GCUG*CUCAC*GGACACC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [493×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 493 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  24.4898 because the cutoff seemed overly generous
Group  83, J3_97609.1  has acceptance rules AlignmentScore >= -28.0976, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  30.2821
TP   100.00%, TN    97.97%, min    97.97%,   1 3D sequences,     0 alignment sequences,  493 random sequences,   10 random matches, 15 NTs, cWW-tSH-tHW-F-cWW-tHH-F-cWW-F
Sensitivity 100.00%, Specificity  97.97%, Minimum  97.97% using method 8
Number of false positives with core edit > 0 is 10
1 * Deficit + 3 * Core Edit <= 22.1845
Motif index 1


ans = 

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

                       MotifID: 'J3_98102.1'
                     Signature: {'cWW-tWH-F-F-tHS-cWW-cWW-cWW-F'}
                         NumNT: 15
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 13
                        NumBPh: 2
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 42
                      OwnScore: -10.2881
                   OwnSequence: {'CCAGAC*GGGUG*UUAGACG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 17
            MeanSequenceLength: 17
               DeficitEditData: [171×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 171 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  25.5685 because the cutoff seemed overly generous
Group  84, J3_98102.1  has acceptance rules AlignmentScore >= -30.2881, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  34.1593
TP   100.00%, TN    98.25%, min    98.25%,   1 3D sequences,     0 alignment sequences,  171 random sequences,    3 random matches, 15 NTs, cWW-tWH-F-F-tHS-cWW-cWW-cWW-F
Sensitivity 100.00%, Specificity  98.25%, Minimum  98.25% using method 8
Number of false positives with core edit > 0 is 3
1 * Deficit + 3 * Core Edit <= 23.8712
Motif index 1


ans = 

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

                       MotifID: 'J3_98298.1'
                     Signature: {'cWW-F-F-F-F-F-F-F-F-tWH-F-F-tHS-cWW-cWW-F-F'}
                         NumNT: 22
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 18
                        NumBPh: 5
                         NumBR: 2
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 76
                      OwnScore: -17.0636
                   OwnSequence: {'UAAUUUGGAG*CGAAG*CAAAUUUGAAA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 25
            MeanSequenceLength: 25
               DeficitEditData: [0×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 0 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
No random sequence matches, so essentially no model-specific cutoff imposed
Decreased cutoff to  25.0000 so that it is possible to reject matches
Group  85, J3_98298.1  has acceptance rules AlignmentScore >= -37.0636, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  42.0636
TP   100.00%, TN      NaN%, min   100.00%,   1 3D sequences,     0 alignment sequences,    0 random sequences,    0 random matches, 22 NTs, cWW-F-F-F-F-F-F-F-F-tWH-F-F-tHS-cWW-cWW-F-F
Sensitivity 100.00%, Specificity    NaN%, Minimum 100.00% using method 12
Number of false positives with core edit > 0 is 0
1 * Deficit + 3 * Core Edit <= 25.0000
Motif index 1


ans = 

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

                       MotifID: 'J3_98484.1'
                     Signature: {'cWW-F-F-tSH-cHW-F-cWW-tSS-cSS-F-cWW-cWW'}
                         NumNT: 16
                  NumBasepairs: 9
                    Structured: 1
                     NumStacks: 10
                        NumBPh: 0
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 46
                      OwnScore: -10.7827
                   OwnSequence: {'CUCC*GUCG*UGUGAUUG'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 15
            MeanSequenceLength: 15
               DeficitEditData: [398×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 398 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  22.9973 because the cutoff seemed overly generous
Group  86, J3_98484.1  has acceptance rules AlignmentScore >= -30.7827, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  32.4897
TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,  398 random sequences,    8 random matches, 16 NTs, cWW-F-F-tSH-cHW-F-cWW-tSS-cSS-F-cWW-cWW
Sensitivity 100.00%, Specificity  97.99%, Minimum  97.99% using method 8
Number of false positives with core edit > 0 is 8
1 * Deficit + 3 * Core Edit <= 21.7070
Motif index 1


ans = 

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

                       MotifID: 'J3_98985.1'
                     Signature: {'cWW-F-cWW-F-F-cSW-F-cWW'}
                         NumNT: 12
                  NumBasepairs: 5
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 3
                         NumBR: 1
                  NumInstances: 2
                      Truncate: [2×1 double]
                      NumFixed: 36
                      OwnScore: [-5.3669 -5.7013]
                   OwnSequence: {'GGAAUCU*AGC*GC'  'GGAAUAU*AGC*GC'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: [11 11]
            MeanSequenceLength: 11
               DeficitEditData: [2766×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

2 sequences from 3D structures
Using 2766 random sequences, 0 from an alignment, and 2 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Group  87, J3_98985.1  has acceptance rules AlignmentScore >= -25.3669, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  22.9589
TP   100.00%, TN    95.99%, min    95.99%,   2 3D sequences,     0 alignment sequences, 2765 random sequences,  111 random matches, 12 NTs, cWW-F-cWW-F-F-cSW-F-cWW
Sensitivity 100.00%, Specificity  95.99%, Minimum  95.99% using method 6
Number of false positives with core edit > 0 is 111
1 * Deficit + 3 * Core Edit <= 17.5920
Motif index 1
Motif index 2


ans = 

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

                       MotifID: 'J3_99170.1'
                     Signature: {'cWW-tSH-tWW-tHW-cWW-F-cWW-F'}
                         NumNT: 13
                  NumBasepairs: 6
                    Structured: 1
                     NumStacks: 9
                        NumBPh: 2
                         NumBR: 0
                  NumInstances: 1
                      Truncate: [2×1 double]
                      NumFixed: 44
                      OwnScore: -7.6503
                   OwnSequence: {'UGAAGUG*CAA*UCUA'}
                  DeficitCoeff: 1
                 CoreEditCoeff: 3
               SequenceLengths: 13
            MeanSequenceLength: 13
               DeficitEditData: [1939×2 double]
              RandomQuantile80: []
              RandomQuantile96: []
              RandomQuantile98: []
                  CutoffMethod: []
              TruePositiveRate: []
              TrueNegativeRate: []
           NumberOf3DSequences: []
    NumberOfAlignmentSequences: []
       NumberOfRandomSequences: []
        NumberOfFalsePositives: []
                 DeficitCutoff: []
                CoreEditCutoff: []
             DeficitEditCutoff: []
                      MinScore: []
                      MaxScore: []
               ScoreEditCutoff: []

1 sequences from 3D structures
Using 1939 random sequences, 0 from an alignment, and 1 from 3D structures
Trying a definition of DefaultMixedScoreCutoff for J3
Decreased cutoff from  21.7068 because the cutoff seemed overly generous
Group  88, J3_99170.1  has acceptance rules AlignmentScore >= -27.6503, CoreEdit <= 5, and   3.0000 * CoreEdit -   1.0000 * AlignmentScore <=  28.1252
TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences, 1939 random sequences,   39 random matches, 13 NTs, cWW-tSH-tWW-tHW-cWW-F-cWW-F
Sensitivity 100.00%, Specificity  97.99%, Minimum  97.99% using method 8
Number of false positives with core edit > 0 is 39
1 * Deficit + 3 * Core Edit <= 20.4750
Motif index 1

  3 (  3.41%) models got the default cutoff from model size
  0 (  0.00%) models had their cutoff set by maximizing TP+TN
  0 (  0.00%) models got the default cutoff plus 2
  0 (  0.00%) models with cutoffs from TP+TN had the cutoff tightened to reduce false positives
  0 (  0.00%) models with default plus 2 had the cutoff tightened to reduce false positives
 39 ( 44.32%) models had cutoff set from random sequences only
  0 (  0.00%) random cutoff models had their cutoff made more generous
 41 ( 46.59%) random cutoff models had their cutoff made more restrictive
  0 (  0.00%) models had no random sequences and so no model-specific cutoff imposed
  0 (  0.00%) models had the cutoff set from alignment sequences only
  1 (  1.14%) models got the minimum cutoff
88 groups, total in this table is 88
Group   1, J3_00584.1  has acceptance rules  -7.7248 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.7248 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.67%, min    97.67%,   1 3D sequences,     0 alignment sequences,  2966 random sequences,   69 random matches, 14 NTs, cWW-F-F-tWH-cWW-tSS-F-tHS-F-cWW
Group   2, J3_02067.1  has acceptance rules  -9.5427 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.5427 - AlignmentScore) +   3.0000 * CoreEdit <=  17.5170, method  6,TP   100.00%, TN    95.99%, min    95.99%,   1 3D sequences,     0 alignment sequences,  8230 random sequences,  330 random matches, 13 NTs, cWW-tSS-F-F-F-cWW-cWW-F-F
Group   3, J3_04858.1  has acceptance rules  -7.8890 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.8890 - AlignmentScore) +   3.0000 * CoreEdit <=  18.2969, method  6,TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences, 10881 random sequences,  435 random matches, 12 NTs, cWW-F-cWW-F-F-F-F-F-cWW
Group   4, J3_05170.1  has acceptance rules  -9.6924 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.6924 - AlignmentScore) +   3.0000 * CoreEdit <=  19.6225, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,   999 random sequences,   40 random matches, 13 NTs, cWW-F-tSH-tWH-cSH-cWW-tWS-F-cWW
Group   5, J3_06335.1  has acceptance rules  -7.8508 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.8508 - AlignmentScore) +   3.0000 * CoreEdit <=  20.8593, method  8,TP   100.00%, TN    98.01%, min    98.01%,   1 3D sequences,     0 alignment sequences,  1761 random sequences,   35 random matches, 14 NTs, cWW-F-F-tSH-cSS-tWH-F-cWW-cWW-F
Group   6, J3_06579.1  has acceptance rules  -8.0717 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.0717 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.94%, min    96.94%,   1 3D sequences,     0 alignment sequences,  3764 random sequences,  115 random matches, 13 NTs, cWW-F-tHS-F-tHS-F-cWW-cWW
Group   7, J3_08394.2  has acceptance rules  -7.8299 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.8299 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method 12,TP   100.00%, TN   100.00%, min   100.00%,   3 3D sequences,     0 alignment sequences,    33 random sequences,    0 random matches, 20 NTs, cWW-F-F-F-tHW-F-F-F-tSS-F-cWW-cWW-F-F-F
Group   8, J3_08465.1  has acceptance rules  -8.1363 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.1363 - AlignmentScore) +   3.0000 * CoreEdit <=  21.8308, method  8,TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,   370 random sequences,    7 random matches, 16 NTs, cWW-cWW-F-F-tHW-F-F-tHH-cWW-cWW
Group   9, J3_11279.1  has acceptance rules -10.1511 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.1511 - AlignmentScore) +   3.0000 * CoreEdit <=  22.6898, method  8,TP   100.00%, TN    97.56%, min    97.56%,   2 3D sequences,     0 alignment sequences,    41 random sequences,    1 random matches, 19 NTs, cWW-tSH-tHW-cSH-tHH-cSS-tWW-F-F-cWW-cWW-F
Group  10, J3_11934.2  has acceptance rules  -6.6474 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.6474 - AlignmentScore) +   3.0000 * CoreEdit <=  20.1412, method  8,TP   100.00%, TN    98.02%, min    98.02%,   4 3D sequences,     0 alignment sequences,  1616 random sequences,   32 random matches, 13 NTs, cWW-F-cWW-F-F-tWW-F-cWW-F
Group  11, J3_13944.1  has acceptance rules  -9.9178 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.9178 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.74%, min    97.74%,   2 3D sequences,     0 alignment sequences,  2303 random sequences,   52 random matches, 13 NTs, cWW-F-F-tSS-F-F-cWW-cWW
Group  12, J3_15893.1  has acceptance rules  -7.7837 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.7837 - AlignmentScore) +   3.0000 * CoreEdit <=  19.4442, method  6,TP   100.00%, TN    95.99%, min    95.99%,   5 3D sequences,     0 alignment sequences,  3817 random sequences,  153 random matches, 14 NTs, cWW-tSH-cSS-tHS-F-cWW-cWW-cWW
Group  13, J3_18709.1  has acceptance rules  -8.6198 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.6198 - AlignmentScore) +   3.0000 * CoreEdit <=  19.2303, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  6006 random sequences,  240 random matches, 12 NTs, cWW-F-tWW-cSH-cWW-cWW-F
Group  14, J3_19256.1  has acceptance rules  -7.3909 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.3909 - AlignmentScore) +   3.0000 * CoreEdit <=  17.4185, method  6,TP   100.00%, TN    95.96%, min    95.96%,   2 3D sequences,     0 alignment sequences,  6256 random sequences,  253 random matches, 12 NTs, cWW-F-F-F-cWW-F-F-cWW-F
Group  15, J3_19286.1  has acceptance rules -10.4085 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.4085 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.96%, min    97.96%,   1 3D sequences,     0 alignment sequences,  1422 random sequences,   29 random matches, 15 NTs, cWW-F-F-tSH-F-cWW-F-F-F-cWW-F
Group  16, J3_19431.1  has acceptance rules  -5.4173 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -5.4173 - AlignmentScore) +   3.0000 * CoreEdit <=  14.4737, method  6,TP   100.00%, TN    95.96%, min    95.96%,   1 3D sequences,     0 alignment sequences,  5793 random sequences,  234 random matches,  9 NTs, cWW-F-cWW-tSS-F-cWW
Group  17, J3_20650.1  has acceptance rules  -7.5675 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.5675 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.69%, min    96.69%,   1 3D sequences,     0 alignment sequences,  8479 random sequences,  281 random matches, 13 NTs, cWW-F-F-F-F-cSS-cWW-cWW-F
Group  18, J3_22198.1  has acceptance rules -10.4869 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.4869 - AlignmentScore) +   3.0000 * CoreEdit <=  15.2619, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 11861 random sequences,  474 random matches, 12 NTs, cWW-cSH-F-cWW-cSS-cWW-F
Group  19, J3_25217.1  has acceptance rules  -6.1782 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.1782 - AlignmentScore) +   3.0000 * CoreEdit <=  15.4840, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 10224 random sequences,  409 random matches,  9 NTs, cWW-F-cWW-F-cWW-F-F
Group  20, J3_25670.1  has acceptance rules  -8.1632 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.1632 - AlignmentScore) +   3.0000 * CoreEdit <=  15.8813, method  6,TP   100.00%, TN    95.81%, min    95.81%,   1 3D sequences,     0 alignment sequences, 11778 random sequences,  493 random matches, 11 NTs, cWW-F-F-F-cWW-F-F-cWW
Group  21, J3_28621.2  has acceptance rules  -7.0605 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.0605 - AlignmentScore) +   3.0000 * CoreEdit <=  16.2071, method  6,TP   100.00%, TN    96.01%, min    96.01%,   6 3D sequences,     0 alignment sequences,  2409 random sequences,   96 random matches, 13 NTs, cWW-tWW-tHS-tSH-cWW-tSS-F-cSS-cWW
Group  22, J3_30104.1  has acceptance rules  -4.5147 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -4.5147 - AlignmentScore) +   3.0000 * CoreEdit <=   9.5000, method 11,TP   100.00%, TN    95.85%, min    95.85%,   1 3D sequences,     0 alignment sequences,  5568 random sequences,  231 random matches,  8 NTs, cWW-F-F-cWW-cWW
Group  23, J3_32030.1  has acceptance rules  -7.8308 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.8308 - AlignmentScore) +   3.0000 * CoreEdit <=  21.4419, method  8,TP   100.00%, TN    97.96%, min    97.96%,   1 3D sequences,     0 alignment sequences,   832 random sequences,   17 random matches, 15 NTs, cWW-tWH-F-F-cWW-tHS-F-F-cWW-F
Group  24, J3_32601.2  has acceptance rules  -7.6711 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.6711 - AlignmentScore) +   3.0000 * CoreEdit <=  18.7312, method  6,TP   100.00%, TN    96.02%, min    96.02%,   4 3D sequences,     0 alignment sequences,  1910 random sequences,   76 random matches, 12 NTs, cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW
Group  25, J3_32852.2  has acceptance rules  -7.4398 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.4398 - AlignmentScore) +   3.0000 * CoreEdit <=  18.3943, method  6,TP   100.00%, TN    95.99%, min    95.99%,   4 3D sequences,     0 alignment sequences,  6466 random sequences,  259 random matches, 12 NTs, cWW-tSH-tHW-F-F-cWW-cWW-F
Group  26, J3_32857.1  has acceptance rules -11.2450 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-11.2450 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.49%, min    97.49%,   1 3D sequences,     0 alignment sequences,  2075 random sequences,   52 random matches, 15 NTs, cWW-F-F-F-F-F-cWW-F-cWW-F-F-F-F
Group  27, J3_33851.1  has acceptance rules  -9.9609 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.9609 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0350, method  8,TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,  2592 random sequences,   52 random matches, 14 NTs, cWW-tSH-F-F-tHS-cWW-cWW-F-F
Group  28, J3_35321.1  has acceptance rules  -9.3308 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.3308 - AlignmentScore) +   3.0000 * CoreEdit <=  19.0208, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  2949 random sequences,  118 random matches, 12 NTs, cWW-cSS-F-F-F-F-cWW-F-cWW
Group  29, J3_36387.1  has acceptance rules  -7.0468 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.0468 - AlignmentScore) +   3.0000 * CoreEdit <=  20.9964, method  8,TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,   424 random sequences,    8 random matches, 16 NTs, cWW-F-F-F-tWW-tHW-tHW-cWW-F-F-cWW
Group  30, J3_36499.1  has acceptance rules  -7.2279 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.2279 - AlignmentScore) +   3.0000 * CoreEdit <=  18.5174, method  6,TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences,  3661 random sequences,  146 random matches, 13 NTs, cWW-tSS-tSH-tHW-tHS-cWW-cWW-F
Group  31, J3_37047.2  has acceptance rules  -8.5525 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.5525 - AlignmentScore) +   3.0000 * CoreEdit <=  22.2254, method  8,TP   100.00%, TN    98.12%, min    98.12%,   4 3D sequences,     0 alignment sequences,   266 random sequences,    5 random matches, 15 NTs, cWW-cSS-cSH-F-tWH-F-cWW-cSH-F-cWW-F
Group  32, J3_37410.1  has acceptance rules  -9.8837 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.8837 - AlignmentScore) +   3.0000 * CoreEdit <=  22.6750, method  8,TP   100.00%, TN    97.79%, min    97.79%,   1 3D sequences,     0 alignment sequences,   136 random sequences,    3 random matches, 18 NTs, cWW-F-F-tSH-tHW-F-F-F-cWW-F-cWW-F-F
Group  33, J3_38151.1  has acceptance rules  -7.0266 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.0266 - AlignmentScore) +   3.0000 * CoreEdit <=   9.7519, method  6,TP   100.00%, TN    95.92%, min    95.92%,   1 3D sequences,     0 alignment sequences, 10559 random sequences,  431 random matches, 10 NTs, cWW-F-F-F-cWW-cWW-F
Group  34, J3_38446.1  has acceptance rules -10.6326 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.6326 - AlignmentScore) +   3.0000 * CoreEdit <=  20.3310, method  8,TP   100.00%, TN    97.47%, min    97.47%,   1 3D sequences,     0 alignment sequences,    79 random sequences,    2 random matches, 17 NTs, cWW-F-cWW-F-F-F-F-F-F-cWS-F-cWW-F
Group  35, J3_38616.1  has acceptance rules -11.1986 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-11.1986 - AlignmentScore) +   3.0000 * CoreEdit <=  21.5250, method  8,TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,   149 random sequences,    3 random matches, 17 NTs, cWW-F-cWW-F-cWW-F-cWW-F-tWW-F-cWW
Group  36, J3_39238.2  has acceptance rules  -8.3588 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.3588 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.71%, min    96.71%,   6 3D sequences,     0 alignment sequences,  4563 random sequences,  150 random matches, 11 NTs, cWW-tWH-cWW-tSW-F-F-cWW
Group  37, J3_41097.1  has acceptance rules  -5.9049 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -5.9049 - AlignmentScore) +   3.0000 * CoreEdit <=  16.4371, method  6,TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences,  7651 random sequences,  306 random matches,  9 NTs, cWW-cWW-F-cWW-cWW
Group  38, J3_42157.1  has acceptance rules  -8.5731 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.5731 - AlignmentScore) +   3.0000 * CoreEdit <=  19.2823, method  6,TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences,  8265 random sequences,  331 random matches, 12 NTs, cWW-tSH-tWW-tHW-F-F-cWW-cWW
Group  39, J3_44724.2  has acceptance rules  -6.7443 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.7443 - AlignmentScore) +   3.0000 * CoreEdit <=  17.3141, method  6,TP   100.00%, TN    96.00%, min    96.00%,   5 3D sequences,     0 alignment sequences,  9171 random sequences,  367 random matches, 12 NTs, cWW-tSH-F-cWW-tHS-cWW-F
Group  40, J3_45941.1  has acceptance rules  -9.8072 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.8072 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.11%, min    96.11%,   1 3D sequences,     0 alignment sequences,  2107 random sequences,   82 random matches, 13 NTs, cWW-cWS-cSH-tWH-F-F-F-F-cWW-cWW-F
Group  41, J3_47248.1  has acceptance rules -12.0999 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-12.0999 - AlignmentScore) +   3.0000 * CoreEdit <=  20.3179, method  8,TP   100.00%, TN    98.11%, min    98.11%,   1 3D sequences,     0 alignment sequences,   371 random sequences,    7 random matches, 17 NTs, cWW-F-F-F-F-F-tHH-F-cWW-cWW-F-F-F
Group  42, J3_47376.1  has acceptance rules  -7.7245 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.7245 - AlignmentScore) +   3.0000 * CoreEdit <=  16.5571, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 11932 random sequences,  477 random matches, 10 NTs, cWW-F-F-cWS-cWW-F-cWW
Group  43, J3_47707.1  has acceptance rules -14.3222 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-14.3222 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method  1,TP   100.00%, TN   100.00%, min   100.00%,   1 3D sequences,     0 alignment sequences,     4 random sequences,    0 random matches, 20 NTs, cWW-F-F-F-F-F-cWW-F-cWW-F-F-cSH-cSH-cWW-F
Group  44, J3_48314.1  has acceptance rules  -7.7472 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.7472 - AlignmentScore) +   3.0000 * CoreEdit <=  15.3226, method  6,TP   100.00%, TN    95.99%, min    95.99%,   1 3D sequences,     0 alignment sequences, 12981 random sequences,  520 random matches, 11 NTs, cWW-cWW-F-cWW-F-cWW-F
Group  45, J3_51910.1  has acceptance rules  -8.7685 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.7685 - AlignmentScore) +   3.0000 * CoreEdit <=  18.5059, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  6928 random sequences,  277 random matches, 12 NTs, cWW-F-cWW-tWS-F-F-cWW-cWW
Group  46, J3_52655.1  has acceptance rules  -6.7028 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.7028 - AlignmentScore) +   3.0000 * CoreEdit <=  15.0357, method  6,TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences,  8033 random sequences,  321 random matches, 11 NTs, cWW-tSH-cWW-F-cWW-cWW
Group  47, J3_52842.1  has acceptance rules  -9.5454 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.5454 - AlignmentScore) +   3.0000 * CoreEdit <=  18.6118, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  7243 random sequences,  290 random matches, 11 NTs, cWW-tHS-F-F-F-cWW-cWW
Group  48, J3_52917.1  has acceptance rules -10.3210 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.3210 - AlignmentScore) +   3.0000 * CoreEdit <=  18.5315, method  6,TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences,  3154 random sequences,  126 random matches, 12 NTs, cWW-tWW-cHW-tSH-cWW-tSS-F-cSS-cWW
Group  49, J3_56052.2  has acceptance rules  -4.3992 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -4.3992 - AlignmentScore) +   3.0000 * CoreEdit <=  11.7786, method  6,TP   100.00%, TN    95.99%, min    95.99%,   4 3D sequences,     0 alignment sequences,  6856 random sequences,  275 random matches,  8 NTs, cWW-F-cWW-cWW-F
Group  50, J3_56708.1  has acceptance rules  -9.6465 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.6465 - AlignmentScore) +   3.0000 * CoreEdit <=  20.8628, method  8,TP   100.00%, TN    97.98%, min    97.98%,   1 3D sequences,     0 alignment sequences,   741 random sequences,   15 random matches, 16 NTs, cWW-F-cWW-F-tHW-F-F-F-cWW-F-cWW
Group  51, J3_58090.1  has acceptance rules -10.2033 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.2033 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.17%, min    97.17%,   1 3D sequences,     0 alignment sequences,  2226 random sequences,   63 random matches, 13 NTs, cWW-tWW-F-F-F-cWW-F-F-cWW
Group  52, J3_58453.1  has acceptance rules  -9.7268 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.7268 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.95%, min    97.95%,   1 3D sequences,     0 alignment sequences,   779 random sequences,   16 random matches, 14 NTs, cWW-cWH-F-cWW-tWS-F-F-cWW-F
Group  53, J3_59914.1  has acceptance rules  -6.4388 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.4388 - AlignmentScore) +   3.0000 * CoreEdit <=   9.8478, method  6,TP   100.00%, TN    96.01%, min    96.01%,   1 3D sequences,     0 alignment sequences,  5408 random sequences,  216 random matches,  9 NTs, cWW-F-cWW-F-cWW-F
Group  54, J3_64069.1  has acceptance rules -12.6293 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-12.6293 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.55%, min    96.55%,   1 3D sequences,     0 alignment sequences,  1042 random sequences,   36 random matches, 13 NTs, cWW-tHS-F-F-F-cWW-cWW-F-F
Group  55, J3_65070.2  has acceptance rules  -7.0614 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.0614 - AlignmentScore) +   3.0000 * CoreEdit <=  14.9875, method  6,TP   100.00%, TN    96.02%, min    96.02%,   3 3D sequences,     0 alignment sequences,  2083 random sequences,   83 random matches, 12 NTs, cWW-tWH-cWW-tSH-F-cWW-F
Group  56, J3_65990.1  has acceptance rules  -9.3887 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.3887 - AlignmentScore) +   3.0000 * CoreEdit <=  23.1345, method  8,TP   100.00%, TN    97.95%, min    97.95%,   1 3D sequences,     0 alignment sequences,   878 random sequences,   18 random matches, 14 NTs, cWW-tHW-F-F-cWW-F-F-F-cWW-F
Group  57, J3_68440.1  has acceptance rules -12.6658 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-12.6658 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method  1,TP   100.00%, TN    76.92%, min    76.92%,   1 3D sequences,     0 alignment sequences,    13 random sequences,    3 random matches, 19 NTs, cWW-cWW-F-F-F-cWW-F-F-cWW-F-F-F-F-F-F
Group  58, J3_69441.1  has acceptance rules -10.8991 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.8991 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.33%, min    96.33%,   1 3D sequences,     0 alignment sequences,   898 random sequences,   33 random matches, 14 NTs, cWW-cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW
Group  59, J3_72575.1  has acceptance rules  -8.2681 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.2681 - AlignmentScore) +   3.0000 * CoreEdit <=  19.1798, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  2450 random sequences,   98 random matches, 13 NTs, cWW-cWW-F-cWW-cSS-cWW-F-cWW
Group  60, J3_72804.1  has acceptance rules -12.1214 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-12.1214 - AlignmentScore) +   3.0000 * CoreEdit <=  23.5850, method  8,TP   100.00%, TN    97.67%, min    97.67%,   1 3D sequences,     0 alignment sequences,    43 random sequences,    1 random matches, 16 NTs, cWW-F-F-F-F-F-tHW-F-F-cWW-cWW-F
Group  61, J3_75187.1  has acceptance rules -11.0148 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-11.0148 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.65%, min    97.65%,   1 3D sequences,     0 alignment sequences,   425 random sequences,   10 random matches, 16 NTs, cWW-cWW-tSH-F-F-F-F-tHS-cWW-cWW
Group  62, J3_79305.1  has acceptance rules -10.1205 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.1205 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method  1,TP   100.00%, TN   100.00%, min   100.00%,   1 3D sequences,     0 alignment sequences,     3 random sequences,    0 random matches, 19 NTs, cWW-cSH-cWW-cWH-F-tSW-F-F-F-F-F-cWW-cWW-F
Group  63, J3_82061.2  has acceptance rules  -6.9256 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.9256 - AlignmentScore) +   3.0000 * CoreEdit <=  11.3316, method  6,TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences, 11760 random sequences,  470 random matches,  8 NTs, cWW-F-cWW-F-cWW
Group  64, J3_82365.1  has acceptance rules  -7.6785 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.6785 - AlignmentScore) +   3.0000 * CoreEdit <=  11.8001, method  6,TP   100.00%, TN    95.98%, min    95.98%,   3 3D sequences,     0 alignment sequences, 12501 random sequences,  502 random matches, 10 NTs, cWW-F-F-F-cWW-cWW-F
Group  65, J3_82572.1  has acceptance rules  -7.8829 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.8829 - AlignmentScore) +   3.0000 * CoreEdit <=  19.4256, method  6,TP   100.00%, TN    96.00%, min    96.00%,   2 3D sequences,     0 alignment sequences,  7569 random sequences,  303 random matches, 11 NTs, cWW-tSH-tWW-F-cWW-tHW-F-F-cWW
Group  66, J3_83516.1  has acceptance rules -14.1163 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-14.1163 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method 12,TP   100.00%, TN      NaN%, min   100.00%,   3 3D sequences,     0 alignment sequences,     0 random sequences,    0 random matches, 22 NTs, cWW-F-F-F-tWW-F-tSH-tSS-F-F-F-F-F-cWW-cWW-F-F-F
Group  67, J3_84189.2  has acceptance rules  -7.9732 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.9732 - AlignmentScore) +   3.0000 * CoreEdit <=  19.2684, method  6,TP   100.00%, TN    96.00%, min    96.00%,   3 3D sequences,     0 alignment sequences,  7442 random sequences,  298 random matches, 13 NTs, cWW-tSH-tWW-tHH-F-tHW-cWW-F-cWW
Group  68, J3_84625.1  has acceptance rules  -8.2692 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.2692 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.18%, min    97.18%,   2 3D sequences,     0 alignment sequences,  3760 random sequences,  106 random matches, 13 NTs, cWW-F-cWW-F-F-F-cWW-F-cWW
Group  69, J3_85054.2  has acceptance rules  -9.0748 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.0748 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.40%, min    97.40%,   4 3D sequences,     0 alignment sequences,  2424 random sequences,   63 random matches, 14 NTs, cWW-tSH-F-tWW-tHS-cWW-cWW-F
Group  70, J3_86907.1  has acceptance rules -17.9597 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-17.9597 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method 12,TP   100.00%, TN      NaN%, min   100.00%,   1 3D sequences,     0 alignment sequences,     0 random sequences,    0 random matches, 26 NTs, cWW-F-F-F-tSW-F-tSH-tSS-F-F-F-F-F-F-F-cWW-cWW-F-F-F-F
Group  71, J3_89044.1  has acceptance rules  -9.8314 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -9.8314 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.27%, min    96.27%,   1 3D sequences,     0 alignment sequences,  3267 random sequences,  122 random matches, 15 NTs, cWW-cSW-F-cWW-cSW-cWW-cHW-F-cWW
Group  72, J3_89368.2  has acceptance rules  -6.3368 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.3368 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    97.07%, min    97.07%,   3 3D sequences,     0 alignment sequences,  1777 random sequences,   52 random matches, 13 NTs, cWW-tSH-tHW-F-cWW-tHH-cWW
Group  73, J3_89737.1  has acceptance rules  -8.8695 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.8695 - AlignmentScore) +   3.0000 * CoreEdit <=  21.1896, method  8,TP   100.00%, TN    98.04%, min    98.04%,   1 3D sequences,     0 alignment sequences,   920 random sequences,   18 random matches, 14 NTs, cWW-F-cWW-tSS-cWW-F-cWW-cWW
Group  74, J3_90256.1  has acceptance rules -11.0711 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-11.0711 - AlignmentScore) +   3.0000 * CoreEdit <=  21.3578, method  8,TP   100.00%, TN    97.89%, min    97.89%,   2 3D sequences,     0 alignment sequences,   142 random sequences,    3 random matches, 17 NTs, cWW-cWS-F-F-F-F-F-F-cWW-F-tHS-F-cWW-F
Group  75, J3_90744.1  has acceptance rules -10.1009 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.1009 - AlignmentScore) +   3.0000 * CoreEdit <=  17.2902, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  7133 random sequences,  285 random matches, 13 NTs, cWW-F-cWW-F-F-cSS-F-F-cWW
Group  76, J3_91491.2  has acceptance rules  -5.7302 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -5.7302 - AlignmentScore) +   3.0000 * CoreEdit <=  18.3408, method  6,TP   100.00%, TN    96.00%, min    96.00%,   6 3D sequences,     0 alignment sequences,  7578 random sequences,  303 random matches, 11 NTs, cWW-F-tWW-tHW-cWW-F-cWW
Group  77, J3_93059.1  has acceptance rules  -7.9631 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.9631 - AlignmentScore) +   3.0000 * CoreEdit <=  16.7819, method  6,TP   100.00%, TN    95.98%, min    95.98%,   1 3D sequences,     0 alignment sequences,  2065 random sequences,   83 random matches, 13 NTs, cWW-tWH-cWW-tSH-F-cWW-cWW
Group  78, J3_93637.1  has acceptance rules  -7.6551 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.6551 - AlignmentScore) +   3.0000 * CoreEdit <=  22.4101, method  8,TP   100.00%, TN    97.97%, min    97.97%,   1 3D sequences,     0 alignment sequences,  1376 random sequences,   28 random matches, 15 NTs, cWW-cWW-F-F-F-F-F-cWW-cWW-F-F
Group  79, J3_94515.1  has acceptance rules  -8.7202 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.7202 - AlignmentScore) +   3.0000 * CoreEdit <=  19.4341, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences,  7368 random sequences,  295 random matches, 13 NTs, cWW-tWW-F-cWW-F-tHS-F-cWW
Group  80, J3_94652.1  has acceptance rules  -6.9354 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -6.9354 - AlignmentScore) +   3.0000 * CoreEdit <=  17.2513, method  6,TP   100.00%, TN    96.00%, min    96.00%,   1 3D sequences,     0 alignment sequences, 10555 random sequences,  422 random matches, 10 NTs, cWW-F-F-F-F-F-cWW-cWW
Group  81, J3_96170.1  has acceptance rules -10.5863 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.5863 - AlignmentScore) +   3.0000 * CoreEdit <=  21.2083, method  8,TP   100.00%, TN    98.09%, min    98.09%,   1 3D sequences,     0 alignment sequences,   471 random sequences,    9 random matches, 16 NTs, cWW-cSH-cWS-tHS-cWH-F-F-cWW-F-tHS-F-cWW-F
Group  82, J3_96372.1  has acceptance rules -13.6287 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-13.6287 - AlignmentScore) +   3.0000 * CoreEdit <=  20.0000, method  8,TP   100.00%, TN    96.94%, min    96.94%,   2 3D sequences,     0 alignment sequences,   719 random sequences,   22 random matches, 16 NTs, cWW-cSH-cWS-F-F-F-tHW-F-cWW-F-cWW-F
Group  83, J3_97609.1  has acceptance rules  -8.0976 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -8.0976 - AlignmentScore) +   3.0000 * CoreEdit <=  22.1845, method  8,TP   100.00%, TN    97.97%, min    97.97%,   1 3D sequences,     0 alignment sequences,   493 random sequences,   10 random matches, 15 NTs, cWW-tSH-tHW-F-cWW-tHH-F-cWW-F
Group  84, J3_98102.1  has acceptance rules -10.2881 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.2881 - AlignmentScore) +   3.0000 * CoreEdit <=  23.8712, method  8,TP   100.00%, TN    98.25%, min    98.25%,   1 3D sequences,     0 alignment sequences,   171 random sequences,    3 random matches, 15 NTs, cWW-tWH-F-F-tHS-cWW-cWW-cWW-F
Group  85, J3_98298.1  has acceptance rules -17.0636 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-17.0636 - AlignmentScore) +   3.0000 * CoreEdit <=  25.0000, method 12,TP   100.00%, TN      NaN%, min   100.00%,   1 3D sequences,     0 alignment sequences,     0 random sequences,    0 random matches, 22 NTs, cWW-F-F-F-F-F-F-F-F-tWH-F-F-tHS-cWW-cWW-F-F
Group  86, J3_98484.1  has acceptance rules -10.7827 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * (-10.7827 - AlignmentScore) +   3.0000 * CoreEdit <=  21.7070, method  8,TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,   398 random sequences,    8 random matches, 16 NTs, cWW-F-F-tSH-cHW-F-cWW-tSS-cSS-F-cWW-cWW
Group  87, J3_98985.1  has acceptance rules  -5.3669 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -5.3669 - AlignmentScore) +   3.0000 * CoreEdit <=  17.5920, method  6,TP   100.00%, TN    95.99%, min    95.99%,   2 3D sequences,     0 alignment sequences,  2765 random sequences,  111 random matches, 12 NTs, cWW-F-cWW-F-F-cSW-F-cWW
Group  88, J3_99170.1  has acceptance rules  -7.6503 - AlignmentScore <=  20.0000, CoreEdit <= 5, and   1.0000 * ( -7.6503 - AlignmentScore) +   3.0000 * CoreEdit <=  20.4750, method  8,TP   100.00%, TN    97.99%, min    97.99%,   1 3D sequences,     0 alignment sequences,  1939 random sequences,   39 random matches, 13 NTs, cWW-tSH-tWW-tHW-cWW-F-cWW-F
