Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20124

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, 846

Length: 1410
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26


Found at i:1035 original size:24 final size:24

Alignment explanation


    Indices: 1003--1082  Score: 115
    Period size: 24  Copynumber: 3.3  Consensus size: 24

        993 GTATGGTGGG

                                   *
       1003 TATGGTGGACCAGGTTCAACTGGC
          1 TATGGTGGACCAGGTTCAACTGGT

                          *   *     
       1027 TATGGTGGACCAGGATCAGCTGGT
          1 TATGGTGGACCAGGTTCAACTGGT

                 *                * 
       1051 TATGGCGGACCAGGTTCAACTGTT
          1 TATGGTGGACCAGGTTCAACTGGT

                    
       1075 TATGGTGG
          1 TATGGTGG

       1083 GTTGAGTGGT


Statistics
Matches: 48,  Mismatches: 8, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   48  1.00

ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28


Consensus pattern (24 bp):   
TATGGTGGACCAGGTTCAACTGGT

Found at i:1131 original size:27 final size:27

Alignment explanation


    Indices: 1078--1131  Score: 63
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1068 AACTGTTTAT

                         *   **        
       1078 GGTGGGTTGAGTGGTGCTGGTGCAGGG
          1 GGTGGGTTGAGTGCTGCAAGTGCAGGG

                     *            *    
       1105 GGTGGGTTGGGTGCTGCAAGTGGAGGG
          1 GGTGGGTTGAGTGCTGCAAGTGCAGGG

       1132 TCTTCATTGT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  27   22  1.00

ACGTcount: A:0.09, C:0.07, G:0.59, T:0.24


Consensus pattern (27 bp):   
GGTGGGTTGAGTGCTGCAAGTGCAGGG
Done.