Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23084

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: 1980
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34


Found at i:1031 original size:105 final size:105

Alignment explanation


    Indices: 890--1195  Score: 405
    Period size: 105  Copynumber: 2.9  Consensus size: 105

        880 AATATGTTGA

                         *          **             *     ***                 
        890 TTGATGCACATTGCAAGGAGGGGACAATTTCTGAAGCTGTAGATACCATTGACACAATGAGAAAG
          1 TTGATGCACATTGTAAGGAGGGGATGATTTCTGAAGCTGAAGATATTGTTGACACAATGAGAAAG

                                                    
        955 CAAGGCATTGAGCCTAATGTTGTTACATATAGTATATTGG
         66 CAAGGCATTGAGCCTAATGTTGTTACATATAGTATATTGG

                               *         *        *             *       *    
        995 TTGATGCACATTGTAAGGAAGGGATGATTCCTGAAGCTAAAGATATTGTTGAGACAATGATAAAG
          1 TTGATGCACATTGTAAGGAGGGGATGATTTCTGAAGCTGAAGATATTGTTGACACAATGAGAAAG

                                   *  *             
       1060 CAAGGCATTGAGCCTAATGTTGTCACGTATAGTATATTGG
         66 CAAGGCATTGAGCCTAATGTTGTTACATATAGTATATTGG

             *       *                *   *                       *      *  *
       1100 TCGATGCACTTTGTAAGGAGGGGATGGTTTTTGAAGCTGAAGATATTGTTGACAAAATGAGCAAT
          1 TTGATGCACATTGTAAGGAGGGGATGATTTCTGAAGCTGAAGATATTGTTGACACAATGAGAAAG

                           *          *    
       1165 CAAGGCATTGAGCCTGATGTTGTTACCTATA
         66 CAAGGCATTGAGCCTAATGTTGTTACATATA

       1196 ATGCATTGAT


Statistics
Matches: 172,  Mismatches: 29, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
 105  172  1.00

ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29


Consensus pattern (105 bp):   
TTGATGCACATTGTAAGGAGGGGATGATTTCTGAAGCTGAAGATATTGTTGACACAATGAGAAAG
CAAGGCATTGAGCCTAATGTTGTTACATATAGTATATTGG
Done.