Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23023

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, 300

Length: 501
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30


Found at i:325 original size:132 final size:132

Alignment explanation


    Indices: 93--341  Score: 338
    Period size: 132  Copynumber: 1.9  Consensus size: 132

         83 TCCTCGCCAA

                    *     *                    *                      *  *   
         93 GAGTGGATTTGCATTAGTCTTCACATTGGCTCACCTAAGGGAAGCTCAAGCTACCATAGCCGCAA
          1 GAGTGGATCTGCATCAGTCTTCACATTGGCTCACCCAAGGGAAGCTCAAGCTACCATAACCACAA

                   *                   *                   *                 
        158 GCTTCAATATAAGGTGTCCTTCTTTCAGGACTCTTCTGTCCTTGTTCGTACAAGATCTCCTCGTT
         66 GCTTCAAAATAAGGTGTCCTTCTTTCAAGACTCTTCTGTCCTTGTTCATACAAGATCTCCTCGTT

              
        223 AG
        131 AG

                                   **                *          *       *    
        225 GAGTGGATCTGCATCAGTCTTCATGTTGGCTCACCCAAGGGCAGCTCAAGCTGCCATAACTACAA
          1 GAGTGGATCTGCATCAGTCTTCACATTGGCTCACCCAAGGGAAGCTCAAGCTACCATAACCACAA

                       *                   *      *              
        290 GCTTCAAAATAGGGTGTCCTT-TTCTCAAGATTCTTCTTTCCTTGTTCATACA
         66 GCTTCAAAATAAGGTGTCCTTCTT-TCAAGACTCTTCTGTCCTTGTTCATACA

        342 GGGTAGTTAC


Statistics
Matches: 100,  Mismatches: 16, Indels: 2
        0.85            0.14        0.02

Matches are distributed among these distances:
 131    2  0.02
 132   98  0.98

ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32


Consensus pattern (132 bp):   
GAGTGGATCTGCATCAGTCTTCACATTGGCTCACCCAAGGGAAGCTCAAGCTACCATAACCACAA
GCTTCAAAATAAGGTGTCCTTCTTTCAAGACTCTTCTGTCCTTGTTCATACAAGATCTCCTCGTT
AG
Done.