Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2040

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, 682

Length: 1137
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24


Found at i:62 original size:13 final size:13

Alignment explanation


    Indices: 44--92  Score: 71
    Period size: 13  Copynumber: 3.7  Consensus size: 13

         34 ATAGGTACAT

                    *    
         44 AAAAAAAAGTTCG
          1 AAAAAAAAATTCG

                       * 
         57 AAAAAAAAATTTG
          1 AAAAAAAAATTCG

                         
         70 AAAAAAAAATTCG
          1 AAAAAAAAATTCG

                      
         83 AAAGAAAAAA
          1 AAA-AAAAAA

         93 GAAGAAGAAG


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  13   26  0.81
  14    6  0.19

ACGTcount: A:0.71, C:0.04, G:0.10, T:0.14


Consensus pattern (13 bp):   
AAAAAAAAATTCG
Done.