Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18429

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, 396

Length: 660
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25


Found at i:404 original size:3 final size:3

Alignment explanation


    Indices: 396--448  Score: 63
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        386 ATACAGATGT

                                        *        * *                    
        396 AGA AGA AGA AGA AGA AGA AG- CGA AGGA TGT AGA AGA AGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA

                      
        441 AGA AGA AG
          1 AGA AGA AG

        449 CAAAGGAAGA


Statistics
Matches: 42,  Mismatches: 6, Indels: 4
        0.81            0.12        0.08

Matches are distributed among these distances:
   2    1  0.02
   3   39  0.93
   4    2  0.05

ACGTcount: A:0.58, C:0.02, G:0.36, T:0.04


Consensus pattern (3 bp):   
AGA

Done.