Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29507

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, 892

Length: 1488
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27


Found at i:153 original size:24 final size:24

Alignment explanation


    Indices: 121--178  Score: 71
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        111 GGTGCAGAAT

                     * *        *   
        121 CATCATCATTTTCAACAACAGCAA
          1 CATCATCATCTGCAACAACAACAA

                             *      
        145 CATCATCATCTGCAACAGCAACAA
          1 CATCATCATCTGCAACAACAACAA

                 *    
        169 CATCAACATC
          1 CATCATCATC

        179 AACAGCAGTG


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21


Consensus pattern (24 bp):   
CATCATCATCTGCAACAACAACAA

Found at i:181 original size:21 final size:21

Alignment explanation


    Indices: 136--185  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        126 TCATTTTCAA

                       *     *   
        136 CAACAGCAACATCATCATCTG
          1 CAACAGCAACAACATCAACTG

                                  
        157 CAACAGCAACAACATCAACAT-
          1 CAACAGCAACAACATCAAC-TG

                    
        178 CAACAGCA
          1 CAACAGCA

        186 GTGGCTCAGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  21   25  0.96
  22    1  0.04

ACGTcount: A:0.46, C:0.34, G:0.08, T:0.12


Consensus pattern (21 bp):   
CAACAGCAACAACATCAACTG
Done.