Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_37326

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: 2913
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28


Found at i:647 original size:24 final size:24

Alignment explanation


    Indices: 416--645  Score: 268
    Period size: 24  Copynumber: 9.5  Consensus size: 24

        406 TCAACACAGT

                *                   
        416 CTGCGTTTGGTGCCACAAGCACCC
          1 CTGCCTTTGGTGCCACAAGCACCC

                *                   
        440 CTGCGTTTGGTGCCACAAGCACCC
          1 CTGCCTTTGGTGCCACAAGCACCC

                *              *  *    
        464 CTGCGTTTGGTGCCGCCACCAGTACCC
          1 CTGCCTTTGGT---GCCACAAGCACCC

                            *  *    
        491 CTGCCTTTGGTGCCACTAGTACCC
          1 CTGCCTTTGGTGCCACAAGCACCC

                   *                
        515 CTGCCTTCGGTGCCACAAGCACCC
          1 CTGCCTTTGGTGCCACAAGCACCC

                                     
        539 CTG-CTTTCGGTGCCACAAGCACCC
          1 CTGCCTTT-GGTGCCACAAGCACCC

                                     
        563 CTG-CTTTCGGTGCCACAAGCACCC
          1 CTGCCTTT-GGTGCCACAAGCACCC

                             ** *    
        587 CTG-CTTTCGGTGCCACTGGTACCC
          1 CTGCCTTT-GGTGCCACAAGCACCC

             *         *            
        611 CAGCCTTTGGTTCCACAAGCACCC
          1 CTGCCTTTGGTGCCACAAGCACCC

                       
        635 CTGCCTTTGGT
          1 CTGCCTTTGGT

        646 TCAACTGGAA


Statistics
Matches: 184,  Mismatches: 17, Indels: 10
        0.87            0.08        0.05

Matches are distributed among these distances:
  23    3  0.02
  24  156  0.85
  25    4  0.02
  27   21  0.11

ACGTcount: A:0.14, C:0.40, G:0.23, T:0.23


Consensus pattern (24 bp):   
CTGCCTTTGGTGCCACAAGCACCC

Found at i:733 original size:24 final size:24

Alignment explanation


    Indices: 700--761  Score: 63
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        690 GTCTAATGCC

                 *        *         
        700 CCAGCATTTGGAGCTTCAAGCACA
          1 CCAGCTTTTGGAGCATCAAGCACA

              *               *     *
        724 CCTGCTTTTGGCA-CATCTAGCACT
          1 CCAGCTTTTGG-AGCATCAAGCACA

                          
        748 CCAGCTTTTGGAGC
          1 CCAGCTTTTGGAGC

        762 GTCTTCTACT


Statistics
Matches: 30,  Mismatches: 6, Indels: 4
        0.75            0.15        0.10

Matches are distributed among these distances:
  23    1  0.03
  24   28  0.93
  25    1  0.03

ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27


Consensus pattern (24 bp):   
CCAGCTTTTGGAGCATCAAGCACA
Done.