Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1438

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: 14448
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:787 original size:19 final size:19

Alignment explanation


    Indices: 742--792  Score: 60
    Period size: 13  Copynumber: 3.0  Consensus size: 19

        732 CAGTTCTAAA

                               
        742 TTCTATAAGGAAATTCTAT
          1 TTCTATAAGGAAATTCTAT

                               
        761 TTC--T----AAATTCTAT
          1 TTCTATAAGGAAATTCTAT

                               
        774 TTCTATAAGGAAATTCTAT
          1 TTCTATAAGGAAATTCTAT

        793 AAGGTTAAAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 12
        0.68            0.00        0.32

Matches are distributed among these distances:
  13   12  0.46
  15    1  0.04
  17    1  0.04
  19   12  0.46

ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45


Consensus pattern (19 bp):   
TTCTATAAGGAAATTCTAT

Found at i:12033 original size:22 final size:22

Alignment explanation


    Indices: 12007--12051  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      11997 CATAAATTTT

                             *    
      12007 TTTTTTATTTAAAAATTCTAAA
          1 TTTTTTATTTAAAAATTATAAA

                                  
      12029 TTTTTTATTTAAAAATTATAAA
          1 TTTTTTATTTAAAAATTATAAA

             
      12051 T
          1 T

      12052 ATAAATAAGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56


Consensus pattern (22 bp):   
TTTTTTATTTAAAAATTATAAA
Done.