Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08755

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: 3341
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25


Found at i:2766 original size:33 final size:33

Alignment explanation


    Indices: 2724--2812  Score: 142
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       2714 GGATTCTGGA

                                             
       2724 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
          1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

                                   *         
       2757 GGCCGTGGTGGAATGAGGGATGGGGGCTTTGGT
          1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

              *        *     *     
       2790 GGACGTGGTGGCATGAGAGATGG
          1 GGCCGTGGTGGAATGAGGGATGG

       2813 TTTTGGCGGT


Statistics
Matches: 52,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  33   52  1.00

ACGTcount: A:0.16, C:0.09, G:0.53, T:0.22


Consensus pattern (33 bp):   
GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT

Found at i:3158 original size:63 final size:63

Alignment explanation


    Indices: 3059--3214  Score: 226
    Period size: 63  Copynumber: 2.5  Consensus size: 63

       3049 GCTATGAGCG

                              *                  **            *            
       3059 GAAGGATGTTGCAAAGCGGGCATTTGATTCTCCTCCTGGTTCCAACGAACATAACTT-GCAACA
          1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCG-AACA

                        *                                               *  
       3122 GAAGGATGTTGCGAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAGCA
          1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA

                                           
       3185 GAAGGATGTTGCAAAGC-AGGCATTTGATTC
          1 GAAGGATGTTGCAAAGCGA-GCATTTGATTC

       3215 ACCTGGTGCA


Statistics
Matches: 84,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
  62    1  0.01
  63   82  0.98
  64    1  0.01

ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25


Consensus pattern (63 bp):   
GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
Done.