Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3456

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, 446

Length: 744
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25


Found at i:473 original size:20 final size:20

Alignment explanation


    Indices: 448--502  Score: 67
    Period size: 19  Copynumber: 2.8  Consensus size: 20

        438 GCGAAAATAC

                            *   
        448 AAAAGAAAAGAAAAATGAAA
          1 AAAAGAAAAGAAAAATCAAA

                          *     
        468 AAAAG-AAAGAAAATTCAAA
          1 AAAAGAAAAGAAAAATCAAA

                     *      
        487 AAAAGAGAATGAAAAA
          1 AAAAGA-AAAGAAAAA

        503 AATGAGAAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  19   17  0.59
  20    5  0.17
  21    7  0.24

ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07


Consensus pattern (20 bp):   
AAAAGAAAAGAAAAATCAAA

Found at i:480 original size:36 final size:33

Alignment explanation


    Indices: 429--504  Score: 89
    Period size: 36  Copynumber: 2.2  Consensus size: 33

        419 AATGAGAGAA

                     **                         
        429 AAAAAAAGAGCGAAAATACAAAAGAAAAGAAAAATG
          1 AAAAAAAGAAAGAAAATAC-AAA-AAAAG-AAAATG

                             *          *    
        465 AAAAAAAGAAAGAAAATTCAAAAAAAGAGAATG
          1 AAAAAAAGAAAGAAAATACAAAAAAAGAAAATG

                   
        498 AAAAAAA
          1 AAAAAAA

        505 TGAGAAAAGC


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  33   12  0.33
  34    5  0.14
  35    3  0.08
  36   16  0.44

ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07


Consensus pattern (33 bp):   
AAAAAAAGAAAGAAAATACAAAAAAAGAAAATG

Found at i:534 original size:15 final size:16

Alignment explanation


    Indices: 497--534  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

        487 AAAAGAGAAT

                  *         
        497 GAAAAAAATGAGAAAA
          1 GAAAAAGATGAGAAAA

             *              
        513 GCAAAAGATGA-AAAA
          1 GAAAAAGATGAGAAAA

                   
        528 GAAAAAG
          1 GAAAAAG

        535 TGATTGAAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05


Consensus pattern (16 bp):   
GAAAAAGATGAGAAAA
Done.