Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04793

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: 3963
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25


Found at i:860 original size:120 final size:120

Alignment explanation


    Indices: 643--1005  Score: 494
    Period size: 120  Copynumber: 3.0  Consensus size: 120

        633 CCTTGATTTT

                       *                          *                          
        643 AGGTCAAAAGATAATGAGGGCTCTGAAATGGCTGTAGCCGATGATGGTGATTGCAATGGAGATGG
          1 AGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATGG

                          *                                 **     
        708 TTTAGCTAATGATAATGCTGAGGCCACTGTCTCTGAAGCCAACGTTATCAATTCC
         66 TTTAGCTAATGATAGTGCTGAGGCCACTGTCTCTGAAGCCAACGTTATTGATTCC

                                   **    **                    *          ***
        763 AGGTCAAAAGAGAATGAGGGCTCCAAAATAACTGTAGCTGATGATGGTGATAGCAATGGAGACAA
          1 AGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATGG

                               *  *    *             *             
        828 TTTAGCTAATGATAGTGCTAAGACCACAGTCTCTGAAGCCAGCGTTATTGATTCC
         66 TTTAGCTAATGATAGTGCTGAGGCCACTGTCTCTGAAGCCAACGTTATTGATTCC

            *               *                          *               *     
        883 TGGTCAAAAGAGAATGCGGGCTCTGAAATGGCTGTAGCTGATGGTGGTGATTGCAATGCCA-ATG
          1 AGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATG-GAGATG

                 *                            *        *            
        947 GTTTATCTAATGATAGTGCTGAGGCCACTGTCTCCGAAGCCAATGTTATTGATTCC
         65 GTTTAGCTAATGATAGTGCTGAGGCCACTGTCTCTGAAGCCAACGTTATTGATTCC

               
       1003 AGG
          1 AGG

       1006 AATGAACATA


Statistics
Matches: 205,  Mismatches: 37, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
 120  204  1.00
 121    1  0.00

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26


Consensus pattern (120 bp):   
AGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGATGGTGATTGCAATGGAGATGG
TTTAGCTAATGATAGTGCTGAGGCCACTGTCTCTGAAGCCAACGTTATTGATTCC
Done.