Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10008102

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, 631

Length: 1053
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.27


Found at i:653 original size:36 final size:35

Alignment explanation


    Indices: 613--730  Score: 191
    Period size: 36  Copynumber: 3.3  Consensus size: 35

        603 ACTGCCACCA

                                                
        613 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAACCC-TTTCAGCCTCCT

                                                
        649 CCAGCTCCACTTATTCCAAATCCCTTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAA-CCCTTTCAGCCTCCT

                    *                           
        685 CCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCT
          1 CCAGCTCCACTTATTCCAAACCC-TTTCAGCCTCCT

                 *    
        721 CCAGCACCAC
          1 CCAGCTCCAC

        731 CGGCTCCACT


Statistics
Matches: 77,  Mismatches: 3, Indels: 4
        0.92            0.04        0.05

Matches are distributed among these distances:
  35    3  0.04
  36   71  0.92
  37    3  0.04

ACGTcount: A:0.20, C:0.46, G:0.06, T:0.28


Consensus pattern (35 bp):   
CCAGCTCCACTTATTCCAAACCCTTTCAGCCTCCT

Found at i:864 original size:45 final size:45

Alignment explanation


    Indices: 682--869  Score: 259
    Period size: 45  Copynumber: 4.2  Consensus size: 45

        672 CTTTCAGCCT

                       *                 *           *   
        682 CCTCCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCTCCAGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

              *  *                       *               
        727 CCACCGGCTCCACTTATTCCAAACCCTTTTCAGCCTCCTCCCGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

              *  *                                       
        772 CCACCGGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

                        *    *  *     *              *   
        817 CCTCCAGCTCCATTTATCCCGAACCCCTTCCAGCCTCCTCCGGCA
          1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA

                    
        862 CCTCCAGC
          1 CCTCCAGC

        870 ACCTCCAGCA


Statistics
Matches: 131,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  45  131  1.00

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


Consensus pattern (45 bp):   
CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
Done.