Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006205.1 Corchorus capsularis cultivar CVL-1 contig06224, 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: 18131
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:3773 original size:180 final size:179

Alignment explanation


    Indices: 3525--3987  Score: 465
    Period size: 180  Copynumber: 2.6  Consensus size: 179

       3515 CCGATCAAGA

                              *       *  **       *   *        *    *  *   * 
       3525 TGATTCAAGTGTCT-ATTTAAAGGTTGTTCAATGATCTACAATTTTCATGAAAGG-TTCGAAAAC
          1 TGATTCAAGTGTCTCA-TAAAAGGTTATTTTATGATCTTCAACTTTCATG-CAGGACTCCAAAGC

                                                 *      *               *    
       3588 TAAATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAATAATT-AGTTGTTTCGGTTAACGGGAAT
         64 TAAATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGAAT

               *                     *                  **       
       3652 GGACT-ATCCACTTAATA-TAGCATTACTTTTGCTCCAGATGTCTTATTGAGC
        129 -GAATGATCCACTTAATAGTA-CATAACTTTTGCTCCAGATGTCCGATTGAGC

                                                                             
       3703 TGATTCAAGTGTCTCATAAAAGGTTATTTTAT-ATCATCTACAACTTTCATGCAGGACTCCAAAG
          1 TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATC-T-T-CAACTTTCATGCAGGACTCCAAAG

                                                *            *         *     
       3767 CTAAATTTAATGTTTCAAGTAT-AAAAAATGCTTC-CAAAAATTAACTTTTTTCGGTTAGCGAGA
         63 CTAAATTTAATGTTTCAAGTATCAAAAAA-GCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGA

                   *                   *                        *
       3830 ATGAATGGTCCACTTAATAGTACATAATTTTTGCTCCAGATGTCCGATTGAGG
        127 ATGAATGATCCACTTAATAGTACATAACTTTTGCTCCAGATGTCCGATTGAGC

                          **         *    *              *   *      **       
       3883 TGATTCAAGTGTCTGTTAAAAGGTTGTTTTGTGATCTTCAACTTTTATGTAGGACTTGAAAGCTA
          1 TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATCTTCAACTTTCATGCAGGACTCCAAAGCTA

                 *  *   *  *  *      *              
       3948 AATTTGATTTTTTAAATACCAAAAATGCTTCTGAAAAATT
         66 AATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATT

       3988 TATATTTTAG


Statistics
Matches: 235,  Mismatches: 38, Indels: 23
        0.79            0.13        0.08

Matches are distributed among these distances:
 177    3  0.01
 178   69  0.29
 179   32  0.14
 180  126  0.54
 181    5  0.02

ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Consensus pattern (179 bp):   
TGATTCAAGTGTCTCATAAAAGGTTATTTTATGATCTTCAACTTTCATGCAGGACTCCAAAGCTA
AATTTAATGTTTCAAGTATCAAAAAAGCTTCTGAAAAATTAACTTGTTTCGGTTAACGAGAATGA
ATGATCCACTTAATAGTACATAACTTTTGCTCCAGATGTCCGATTGAGC

Found at i:13914 original size:11 final size:12

Alignment explanation


    Indices: 13898--13930  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      13888 TAATGAACCA

                        
      13898 TAAACGAAT-TT
          1 TAAACGAATATT

                   *    
      13909 TAAACGAGTATT
          1 TAAACGAATATT

                      
      13921 TAAACGAATA
          1 TAAACGAATA

      13931 ATAAACGAGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  11    8  0.42
  12   11  0.58

ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30


Consensus pattern (12 bp):   
TAAACGAATATT

Found at i:13947 original size:23 final size:23

Alignment explanation


    Indices: 13897--13947  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

      13887 TTAATGAACC

                      **           
      13897 ATAAACGAATTTTAAACGAGTAT
          1 ATAAACGAATAATAAACGAGTAT

            *                       
      13920 TTAAACGAATAATAAACGAGCTA-
          1 ATAAACGAATAATAAACGAG-TAT

                 
      13943 ATAAA
          1 ATAAA

      13948 TGAACATTTA


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  23   21  0.91
  24    2  0.09

ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25


Consensus pattern (23 bp):   
ATAAACGAATAATAAACGAGTAT

Found at i:15968 original size:105 final size:106

Alignment explanation


    Indices: 15788--16049  Score: 404
    Period size: 107  Copynumber: 2.5  Consensus size: 106

      15778 TAATTTTCTA

                      *    * **                                              
      15788 ACCCTTAAAAGAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                                               *     
      15851 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
         66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT

                                                                   * *       
      15891 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                             *               *        
      15956 TTTCTAAAACCCTATAATAATAAATTATTAATTTTGAAATTT
         66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT

                                  *                             
      15998 ACCCTTAAAATAAAAATAAAATCTTAATTTGGGGCTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA

      16050 AGACTAAACT


Statistics
Matches: 145,  Mismatches: 10, Indels: 4
        0.91            0.06        0.03

Matches are distributed among these distances:
 103   26  0.18
 104   15  0.10
 105   36  0.25
 107   68  0.47

ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40


Consensus pattern (106 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT

Done.