Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_40725

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, 844

Length: 1407
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27


Found at i:1205 original size:39 final size:39

Alignment explanation


    Indices: 1084--1206  Score: 140
    Period size: 39  Copynumber: 3.2  Consensus size: 39

       1074 CCCGAAGTCT

                                      **           
       1084 TATTCTCGCTCAAGCAGTTTTCAGCAGGATCCATCTCCG
          1 TATTCTCGCTCAAGCAGTTTTCAGCAAAATCCATCTCCG

                   **   *         *                *
       1123 TATTCTCAATC-TGCCAGTTTTAAGCAAAATCCATCTCCC
          1 TATTCTCGCTCAAG-CAGTTTTCAGCAAAATCCATCTCCG

                                          ** *     
       1162 TATTCTCGCTCAAGCAGTTTTCAGCAAAATATACCTCCG
          1 TATTCTCGCTCAAGCAGTTTTCAGCAAAATCCATCTCCG

                  
       1201 TATTCT
          1 TATTCT

       1207 GGATATGATA


Statistics
Matches: 67,  Mismatches: 15, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  38    1  0.01
  39   65  0.97
  40    1  0.01

ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33


Consensus pattern (39 bp):   
TATTCTCGCTCAAGCAGTTTTCAGCAAAATCCATCTCCG
Done.