Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29365

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: 2127
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27


Found at i:1664 original size:39 final size:39

Alignment explanation


    Indices: 1489--1667  Score: 182
    Period size: 39  Copynumber: 4.6  Consensus size: 39

       1479 TTTTGCTATT

                                            * *    *
       1489 TCAGGGCCAAAGAGGAAAAT-AGAAGATTCCTATGATTTT
          1 TCAGGGCCAAAGA-GAAAATCAGAAGATTCCTGTAATTTC

                  *     *     *          *   *  *  
       1528 TCAGGGGCAAAGCGAAAACCAGAAGATTCTTGTGATGTC
          1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC

                  *                *        *     * 
       1567 TCAGGGGCAAAGAGAAAAT-ATGGAGATTCCTCTAATTCC
          1 TCAGGGCCAAAGAGAAAATCA-GAAGATTCCTGTAATTTC

                 *              *                 *
       1606 TCAGGACCAAAGAGAAAATCTGAAGATTCCTGTAATTTA
          1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC

                                   
       1645 TCAGGGCCAAAGAGAAAATCAGA
          1 TCAGGGCCAAAGAGAAAATCAGA

       1668 GGACTCTTCC


Statistics
Matches: 113,  Mismatches: 24, Indels: 6
        0.79            0.17        0.04

Matches are distributed among these distances:
  38    6  0.05
  39  107  0.95

ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22


Consensus pattern (39 bp):   
TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
Done.