Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21251

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: 2688
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26


Found at i:712 original size:132 final size:131

Alignment explanation


    Indices: 352--783  Score: 470
    Period size: 132  Copynumber: 3.3  Consensus size: 131

        342 GGTAGAAGGT

                 *     *                     *                *              
        352 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTGATGGTGAAATGCTTGATGAAAA
          1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA

                       **        **       * * *  *      *           *        
        417 TAGATCTACTGGCTCTCATAGTGAGGAGCAAGATCAGCACTTATTGGTAGAAGGGCGACGTAATG
         66 TAGATCTACTGATTCTCATAGCAAGGAGCACGGTGAGAACTTATCGGTAGAA-GGCCACGTAATG

             *
        482 GT
        130 GA

            *    *     *  *      *                                  *        
        484 TGCTATGAGAAGGAACAAAATGCATCCAGAGA---T-A--GTGATGGTGATATGCTCGATGAAAA
          1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA

                             *                                               
        543 TAGATCTACTGATTCTCGTAGCAAGGAGCACGGTGAGAAGC-TATCGGTAGAAGGCCAACGTAAT
         66 TAGATCTACTGATTCTCATAGCAAGGAGCACGGTGAGAA-CTTATCGGTAGAAGGCC-ACGTAAT

               
        607 GGA
        129 GGA

                                   *                              *         *
        610 CGCTACGAGAAAGATCAAAATACTTCCAGAGATGGTGATGGTGATGGTGATATGGTTGATGAAAG
          1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA

               *    *                                                        
        675 TAGGTCTATTGATTCTCATAGCAAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCA--TAATGG
         66 TAGATCTACTGATTCTCATAGCAAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG

              
        738 TA
        131 -A

                     **        * * *                     
        740 -GCTACGAGGCAGATCAAATTGCGTCCAGAGATGGTGATGGTGAT
          1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGAT

        784 ATGGTTGATG


Statistics
Matches: 256,  Mismatches: 34, Indels: 23
        0.82            0.11        0.07

Matches are distributed among these distances:
 125    3  0.01
 126   98  0.38
 127    1  0.00
 128    1  0.00
 129   47  0.18
 130    2  0.01
 131    2  0.01
 132  102  0.40

ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24


Consensus pattern (131 bp):   
CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
TAGATCTACTGATTCTCATAGCAAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG
A
Done.