Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12370

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: 3429
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27


Found at i:3076 original size:57 final size:54

Alignment explanation


    Indices: 3015--3151  Score: 139
    Period size: 57  Copynumber: 2.4  Consensus size: 54

       3005 AGCAGCTTTT

                              *                          *      *    
       3015 ACAGCAACAGTATCAGCAACAGCCACAGCTGCTACAAGTGCAACAGCAATATCTTCA
          1 ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTAC-A--GCAACAACAATATATTCA

                      *   *   *                 *             *      
       3072 ACAGCAACAATTACCCTATCAGCAGCCACAGCTGCTGCAGCAACAACAATTTATTCA
          1 ACAGCAAC-AGTA-TC-AGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

                          *        
       3129 ACAGCAACAGTATCTGCAGCAGC
          1 ACAGCAACAGTATCAGCAGCAGC

       3152 AGCAGCAACA


Statistics
Matches: 65,  Mismatches: 12, Indels: 9
        0.76            0.14        0.10

Matches are distributed among these distances:
  54    7  0.11
  55    1  0.02
  56    3  0.05
  57   31  0.48
  58    3  0.05
  59    2  0.03
  60   18  0.28

ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17


Consensus pattern (54 bp):   
ACAGCAACAGTATCAGCAGCAGCCACAGCTGCTACAGCAACAACAATATATTCA

Done.