Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12500

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, 627

Length: 1046
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.27


Found at i:647 original size:36 final size:36

Alignment explanation


    Indices: 607--724  Score: 200
    Period size: 36  Copynumber: 3.3  Consensus size: 36

        597 ACTGCCACCA

                                                
        607 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT

                                   *            
        643 CCAGCTCCACTTATTCCAAACCCCTTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT

                    *              *            
        679 CCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT

                 *    
        715 CCAGCCCCAC
          1 CCAGCTCCAC

        725 CGGCTCCACT


Statistics
Matches: 77,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   77  1.00

ACGTcount: A:0.19, C:0.47, G:0.06, T:0.27


Consensus pattern (36 bp):   
CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT

Found at i:857 original size:45 final size:45

Alignment explanation


    Indices: 676--863  Score: 250
    Period size: 45  Copynumber: 4.2  Consensus size: 45

        666 CTTTCAGCCT

                       *                 *           *  *
        676 CCTCCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCTCCAGCC
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

              *  *                       *               
        721 CCACCGGCTCCACTTATTCCAAACCCTTTTCAGCCTCCTCCCGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

              *  *                                       
        766 CCACCGGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

                        *    *        *            * *   
        811 CCTCCAGCTCCATTTATCCCAAACCCCTTCCAGCCTCCTTCGGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

                    
        856 CCTCCAGC
          1 CCTCCAGC

        864 ACCTCCAGCA


Statistics
Matches: 130,  Mismatches: 13, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45  130  1.00

ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24


Consensus pattern (45 bp):   
CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

Done.