Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_28057

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: 2244
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22


Found at i:506 original size:3 final size:3

Alignment explanation


    Indices: 481--533  Score: 52
    Period size: 3  Copynumber: 17.3  Consensus size: 3

        471 TAGTGGCGGT

                  *              *                        *       *   * 
        481 AGG AGT AGG AGAG AGG TGG AGG AGG AGG AGG AGG AAG AGG ACG AAG
          1 AGG AGG AGG AG-G AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG

                     
        527 AGG AGG A
          1 AGG AGG A

        534 AATAGTGACG


Statistics
Matches: 40,  Mismatches: 9, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
   3   37  0.93
   4    3  0.08

ACGTcount: A:0.38, C:0.02, G:0.57, T:0.04


Consensus pattern (3 bp):   
AGG

Done.