Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014223.1 Corchorus capsularis cultivar CVL-1 contig14244, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 8530
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30


Found at i:2984 original size:51 final size:52

Alignment explanation


    Indices: 2866--2986  Score: 154
    Period size: 51  Copynumber: 2.3  Consensus size: 52

       2856 AATTTCATTT

                              *                  *    *       * *
       2866 GCACCATTACACCTTTAATTATGTAATAGGAATGCATCATATGACTTCAATTT
          1 GCACCATTACACCTTT-ACTATGTAATAGGAATGCATAATATAACTTCAACTG

               *               *                                
       2919 GCATCATTACACCTTTACTGTGTAATAGGAATGCATAATA-AACTTCAACTG
          1 GCACCATTACACCTTTACTATGTAATAGGAATGCATAATATAACTTCAACTG

                     *       
       2970 GCACCATTATACCTTTA
          1 GCACCATTACACCTTTA

       2987 ATACAATAGG


Statistics
Matches: 59,  Mismatches: 9, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  51   23  0.39
  52   21  0.36
  53   15  0.25

ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34


Consensus pattern (52 bp):   
GCACCATTACACCTTTACTATGTAATAGGAATGCATAATATAACTTCAACTG

Found at i:3498 original size:52 final size:52

Alignment explanation


    Indices: 3393--3517  Score: 153
    Period size: 52  Copynumber: 2.4  Consensus size: 52

       3383 CAACAAATTC

                                   *            *    *      *   
       3393 ATTTGCACCATTACACCTTTAACTATGTAATAGGAATGCATTTATGACTTCA
          1 ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCATGTATGACGTCA

                   *       *                               *     
       3445 ATTTGCATCATTACAGCTTTAACCATGTAATAGGAACGCATAGTA-GTCGTCA
          1 ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCAT-GTATGACGTCA

               *         *       
       3497 ATTAGCACCATTATACCTTTA
          1 ATTTGCACCATTACACCTTTA

       3518 GTGTAATAGG


Statistics
Matches: 61,  Mismatches: 11, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  52   59  0.97
  53    2  0.03

ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34


Consensus pattern (52 bp):   
ATTTGCACCATTACACCTTTAACCATGTAATAGGAACGCATGTATGACGTCA

Found at i:5285 original size:52 final size:53

Alignment explanation


    Indices: 5169--5286  Score: 184
    Period size: 53  Copynumber: 2.2  Consensus size: 53

       5159 TCATTTACAC

                                             *              *    
       5169 CATTACACCTTTAACTATGTAATAGGAATGCATCATATGACTTCAATTTGCAT
          1 CATTACACCTTTAACTATGTAATAGGAATGCATAATATGACTTCAATTGGCAT

                        *           *                            
       5222 CATTACACCTTTCACTATGTAATATGAATGCATAATA-GACTTCAATTGGCAT
          1 CATTACACCTTTAACTATGTAATAGGAATGCATAATATGACTTCAATTGGCAT

                 *       
       5274 CATTATACCTTTA
          1 CATTACACCTTTA

       5287 GTATAATAAA


Statistics
Matches: 59,  Mismatches: 6, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  52   25  0.42
  53   34  0.58

ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36


Consensus pattern (53 bp):   
CATTACACCTTTAACTATGTAATAGGAATGCATAATATGACTTCAATTGGCAT

Found at i:7033 original size:29 final size:27

Alignment explanation


    Indices: 6988--7042  Score: 83
    Period size: 29  Copynumber: 2.0  Consensus size: 27

       6978 ATGGAAGAAG

                                       
       6988 AAAAGAAAAAAAAATGGTGGGTAAATC
          1 AAAAGAAAAAAAAATGGTGGGTAAATC

                         *              
       7015 AAAAGTAATAAAAGAATGGTGGGTAAAT
          1 AAAAG-AA-AAAAAAATGGTGGGTAAAT

       7043 GATTGGCAAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  27    5  0.20
  28    2  0.08
  29   18  0.72

ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18


Consensus pattern (27 bp):   
AAAAGAAAAAAAAATGGTGGGTAAATC
Done.