Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2039

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: 39585
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29


Found at i:4077 original size:21 final size:21

Alignment explanation


    Indices: 4037--4099  Score: 62
    Period size: 20  Copynumber: 3.1  Consensus size: 21

       4027 TATATATAAT

                           * *   
       4037 ATAATT-TTTAAA-TGTCAAA
          1 ATAATTATTTAAATTTTAAAA

                                   
       4056 ATAA-TATTTAAAATTTTTAAAA
          1 ATAATTATTT-AAA-TTTTAAAA

                                 
       4078 A-AATTATTTAAATTTTAAAA
          1 ATAATTATTTAAATTTTAAAA

              
       4098 AT
          1 AT

       4100 TTGAAAAAGC


Statistics
Matches: 36,  Mismatches: 2, Indels: 10
        0.75            0.04        0.21

Matches are distributed among these distances:
  18    1  0.03
  19    7  0.19
  20   12  0.33
  21    5  0.14
  22   11  0.31

ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44


Consensus pattern (21 bp):   
ATAATTATTTAAATTTTAAAA

Found at i:37791 original size:2 final size:2

Alignment explanation


    Indices: 37784--37809  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      37774 CACCACCTAT

                                                  
      37784 AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG

      37810 CAACCTCTAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.