Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_28705

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: 2340
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22


Found at i:563 original size:120 final size:121

Alignment explanation


    Indices: 344--623  Score: 348
    Period size: 120  Copynumber: 2.3  Consensus size: 121

        334 AATTCTTCCG

                *     *              *     *                          *  **  
        344 AGTCTAGTAGCGAGGAAGATTCATCTTCTGACGAAGAAGCTCCTGCTCAGAAGAAAAATCCTGTA
          1 AGTCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGCTCCTGCTCAGAAGAAAAAACCCATA

                            * * *                                   
        409 GTTGCTAAAAAGGCCTGTGTTCCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTC
         66 GTTGCTAAAAAGGCCTCTATACCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTC

             *                                     *                         
        465 -TTCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGTTCCTGCTCAGAAGAAAAAACCCATA
          1 AGTCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGCTCCTGCTCAGAAGAAAAAACCCATA

                          *        *      *           *        *     
        529 GTTGCT-AAAAGTGGCTCTATACTAGCTGCTAAGACAGTGAAGGCTGATAGTAGTTC
         66 GTTGCTAAAAAG-GCCTCTATACCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTC

                  *                       *        
        585 AGAGTCTAGTAGTGAGGAAGATTCATCCTCCGATGAAGA
          1 --AGTCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGA

        624 GCGTGTTGCA


Statistics
Matches: 135,  Mismatches: 20, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 119    5  0.04
 120   97  0.72
 123   33  0.24

ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24


Consensus pattern (121 bp):   
AGTCAAGTAGTGAGGAAGATTCATCCTCTGATGAAGAAGCTCCTGCTCAGAAGAAAAAACCCATA
GTTGCTAAAAAGGCCTCTATACCAGCTGCCAAGACAGTGAAAGCTGATAGCAGTTC
Done.