Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25510

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: 3756
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29


Found at i:2908 original size:69 final size:69

Alignment explanation


    Indices: 2793--2948  Score: 278
    Period size: 69  Copynumber: 2.3  Consensus size: 69

       2783 CTGCAACCAG

                                                     *         *             
       2793 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTTTATGAAGAAGAAGCAAGCAATAA
          1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA

                
       2858 TTAA
         66 TTAA

                                                                             
       2862 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
          1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA

                
       2927 TTAA
         66 TTAA

                               
       2931 AATTCAGAG-CAATTTCCG
          1 AATTCAGAGTC-ATTTCCG

       2949 ACTGCAAAAA


Statistics
Matches: 84,  Mismatches: 2, Indels: 2
        0.95            0.02        0.02

Matches are distributed among these distances:
  68    1  0.01
  69   83  0.99

ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27


Consensus pattern (69 bp):   
AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
TTAA
Done.