Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012547.1 Corchorus capsularis cultivar CVL-1 contig12568, 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: 23388
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:9950 original size:33 final size:33

Alignment explanation


    Indices: 9905--10066  Score: 200
    Period size: 33  Copynumber: 4.9  Consensus size: 33

       9895 TTTGCCCTTA

                          *          *       
       9905 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT
          1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT

                   *                  *      
       9938 GCCACGGTGGAGCCGCCCCACTAGGATGGCTCT
          1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT

                  *      *      *            
       9971 GCCACGACGGAGCAGCCCCATTAGGACGGCTCT
          1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT

                   * *    *     *     *      
      10004 GCCACGGTGTAGCCACCCCATTAGGATGGCT-T
          1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT

                                           
      10036 AGCCACGGCGGAGCCGCCCCACTAGGACGGC
          1 -GCCACGGCGGAGCCGCCCCACTAGGACGGC

      10067 AAGGCTATTT


Statistics
Matches: 108,  Mismatches: 20, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  32    1  0.01
  33  107  0.99

ACGTcount: A:0.17, C:0.38, G:0.32, T:0.13


Consensus pattern (33 bp):   
GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT

Found at i:9990 original size:66 final size:66

Alignment explanation


    Indices: 9901--10066  Score: 244
    Period size: 66  Copynumber: 2.5  Consensus size: 66

       9891 CACTTTTGCC

                              *          *                     *             
       9901 CTTAGCCACGGCGGAGCCTCCCCACTAGGGCGGCTCTGCCACGGTGGAGCCGCCCCACTAGGATG
          1 CTTAGCCACGGCGGAGCCGCCCCACTAGGACGGCTCTGCCACGGTGGAGCCACCCCACTAGGATG

             
       9966 G
         66 G

                       *      *      *                     *          *      
       9967 CTCT-GCCACGACGGAGCAGCCCCATTAGGACGGCTCTGCCACGGTGTAGCCACCCCATTAGGAT
          1 CT-TAGCCACGGCGGAGCCGCCCCACTAGGACGGCTCTGCCACGGTGGAGCCACCCCACTAGGAT

              
      10031 GG
         65 GG

                                              
      10033 CTTAGCCACGGCGGAGCCGCCCCACTAGGACGGC
          1 CTTAGCCACGGCGGAGCCGCCCCACTAGGACGGC

      10067 AAGGCTATTT


Statistics
Matches: 87,  Mismatches: 11, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
  65    1  0.01
  66   85  0.98
  67    1  0.01

ACGTcount: A:0.17, C:0.37, G:0.31, T:0.14


Consensus pattern (66 bp):   
CTTAGCCACGGCGGAGCCGCCCCACTAGGACGGCTCTGCCACGGTGGAGCCACCCCACTAGGATG
G

Found at i:18038 original size:354 final size:354

Alignment explanation


    Indices: 17395--18060  Score: 879
    Period size: 354  Copynumber: 1.9  Consensus size: 354

      17385 AGATCAAAAT

                *                   *            *                      **   
      17395 TAGATAGTGCAGCTGACATGGATTGTTCTCACAATGTTGCTGAGCAGACTAATGCTGCTGTTGAT
          1 TAGACAGTGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGAT

                                                                             
      17460 GATGACAGCACAAACAAACATGCAGCTAACTTGCCAGGATCTATTCAGAGTGTAAATCATTCTCC
         66 GATGACAGCACAAACAAACATGCAGCTAACTTGCCAGGATCTATTCAGAGTGTAAATCATTCTCC

               *           *                      *   *  *                   
      17525 ACCGAACATGGAAACTAATAAAGTAAAAGGCAGAAGAAGCAAGAATGAAGTAAATGTCAGCCAAT
        131 ACCAAACATGGAAACCAATAAAGTAAAAGGCAGAAGAAACAAAAACGAAGTAAATGTCAGCCAAT

              ** *  *         *        *        *           *          *     
      17590 ACTTTGTTGGAACTAAAATAACCAGAAGTAATGTTCGGATGACAAAATTCAGTCAGAAAGAGAAC
        196 ACGATCTTAGAACTAAAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAGAAC

              *                 * *         *         *                      
      17655 TTTAAGGATGGATTTTCTACGACGCACAAGGATAGAGCTTCAGGAATGGAGCAAAAGCTGAATAG
        261 TTAAAGGATGGATTTTCTACAAAGCACAAGGACAGAGCTTCAAGAATGGAGCAAAAGCTGAATAG

                                         
      17720 GAAGAAGCCACACAATGAAAGATTGAAGG
        326 GAAGAAGCCACACAATGAAAGATTGAAGG

                        *                    *     *                         
      17749 TAGACAGTGCAGTTGACATGGATTCTTCTCACACTGTAGTTGAGCAGACTAATGCTGCTGCCGAT
          1 TAGACAGTGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGAT

                ***     *       *              *       *                     
      17814 GATGGTGGCACACACAAGA-GTGCAGCTAACTTGCGAGGATCTTTTCAGAGTGTAAATCATTCTC
         66 GATGACAGCACAAACAA-ACATGCAGCTAACTTGCCAGGATCTATTCAGAGTGTAAATCATTCTC

              *    *                         *                               
      17878 CATCAAATACT-GAAACCAATAAAG-AAAATGGTAGAAGAAACAAAAACGAAGTAAATGTCAGCC
        130 CACCAAACA-TGGAAACCAATAAAGTAAAA-GGCAGAAGAAACAAAAACGAAGTAAATGTCAGCC

            *                 *    *        *          *   *                 
      17941 CATACGATCTTAGAACTAGAACATCCAGAAATCATGTTCAGATTACAGAATGCAGTCAGAAAAAG
        193 AATACGATCTTAGAACTAAAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAG

                      *                             *              
      18006 AACTTAAAGGCTGGATTTTCTACAAAGCACAAGGACAGAGTTTCAAGAATGGAGC
        258 AACTTAAAGGATGGATTTTCTACAAAGCACAAGGACAGAGCTTCAAGAATGGAGC

      18061 TTCAAGATGA


Statistics
Matches: 264,  Mismatches: 45, Indels: 6
        0.84            0.14        0.02

Matches are distributed among these distances:
 353    4  0.02
 354  258  0.98
 355    2  0.01

ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22


Consensus pattern (354 bp):   
TAGACAGTGCAGCTGACATGGATTCTTCTCACAATGTAGCTGAGCAGACTAATGCTGCTGCCGAT
GATGACAGCACAAACAAACATGCAGCTAACTTGCCAGGATCTATTCAGAGTGTAAATCATTCTCC
ACCAAACATGGAAACCAATAAAGTAAAAGGCAGAAGAAACAAAAACGAAGTAAATGTCAGCCAAT
ACGATCTTAGAACTAAAACAACCAGAAATAATGTTCAGATGACAAAATGCAGTCAGAAAAAGAAC
TTAAAGGATGGATTTTCTACAAAGCACAAGGACAGAGCTTCAAGAATGGAGCAAAAGCTGAATAG
GAAGAAGCCACACAATGAAAGATTGAAGG
Done.