Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03740

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: 2787
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23


Found at i:1750 original size:48 final size:48

Alignment explanation


    Indices: 1654--1754  Score: 116
    Period size: 48  Copynumber: 2.1  Consensus size: 48

       1644 GAGGCAACAA

                                      *     *          *    
       1654 AGGGAAAGAGAAGAGGAAGAGAGAGAGCAAAGGAGGCGTGAAGTAGAG
          1 AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG

                    *  *                          *           
       1702 AGGGAAAGGGAGGA-GAAGGAGAGAGAACAAAGAAGGCTTG-AGAAAGAG
          1 AGGGAAAGAGAAGAGGAA-GAGAGAGAACAAAGAAGGCGTGAAG-AAGAG

                 
       1750 AGGGA
          1 AGGGA

       1755 GCGAATTAGG


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  47    5  0.11
  48   40  0.89

ACGTcount: A:0.47, C:0.04, G:0.46, T:0.04


Consensus pattern (48 bp):   
AGGGAAAGAGAAGAGGAAGAGAGAGAACAAAGAAGGCGTGAAGAAGAG
Done.