Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15897

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: 3642
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26


Found at i:1177 original size:93 final size:93

Alignment explanation


    Indices: 1018--1297  Score: 434
    Period size: 93  Copynumber: 3.0  Consensus size: 93

       1008 ATTACATGGT

                  *       *                                 *      *     *   
       1018 GGTGTTGCAACTCACGCAGAACATTTTATGCAAGCTAAAGAAACTGAGGCCAGTGTTGAGGCCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                                       *
       1083 GGTTGCTTCTAAAATGATTTCTTCTGCG
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

                        *    *                                               
       1111 GGTGTTACAACTAATGCTGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       1176 GGTTGCTTCTCAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             *               *  *                                           *
       1204 GATGTTACAACTCATGCCGAGCATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCT
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       1269 GGTTGCTTCTGAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             
       1297 G
          1 G

       1298 ACCATGATGT


Statistics
Matches: 172,  Mismatches: 15, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  93  172  1.00

ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29


Consensus pattern (93 bp):   
GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
GGTTGCTTCTAAAATGATTTCTTCTGCA

Done.