Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2781

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: 16040
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2378 original size:17 final size:19

Alignment explanation


    Indices: 2341--2378  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2331 TAAAATAAAA

                        *      
       2341 ATATTAATTTATTTAAATT
          1 ATATTAATTTATATAAATT

                               
       2360 ATATTAATTT-TAT-AATT
          1 ATATTAATTTATATAAATT

              
       2377 AT
          1 AT

       2379 GTCAAAGTCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    6  0.33
  18    2  0.11
  19   10  0.56

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (19 bp):   
ATATTAATTTATATAAATT

Found at i:15890 original size:20 final size:21

Alignment explanation


    Indices: 15865--15905  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      15855 AATATTTTAA

                                 
      15865 ATTAT-GGCTTGAAATTGTTG
          1 ATTATGGGCTTGAAATTGTTG

                                 
      15885 ATTATGGGCTTGAAATTGTTG
          1 ATTATGGGCTTGAAATTGTTG

      15906 GAATTGAGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    5  0.25
  21   15  0.75

ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44


Consensus pattern (21 bp):   
ATTATGGGCTTGAAATTGTTG

Done.