Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6038.1

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: 14527
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:1824 original size:30 final size:31

Alignment explanation


    Indices: 1790--1886  Score: 101
    Period size: 30  Copynumber: 3.2  Consensus size: 31

       1780 AGCTCACTCC

                          *                
       1790 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
          1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT

                             * *   * * *   
       1820 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
          1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT

            *                           *  
       1850 CAGCTCAACTTT-AGCTCACGAGCTAAATCT
          1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT

                   
       1880 TAGCTCA
          1 TAGCTCA

       1887 TTTTAGTTTA


Statistics
Matches: 51,  Mismatches: 14, Indels: 4
        0.74            0.20        0.06

Matches are distributed among these distances:
  30   47  0.92
  31    4  0.08

ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29


Consensus pattern (31 bp):   
TAGCTCAACTTTCAGCTCACGAGCTAAACCT

Found at i:5698 original size:20 final size:20

Alignment explanation


    Indices: 5652--5698  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       5642 AGCTCGTTTC

                      *         
       5652 CAGCTCACTCGAGCTCAAGT
          1 CAGCTCACTCAAGCTCAAGT

              *               * 
       5672 CAACTCACTCAAGCTCAATT
          1 CAGCTCACTCAAGCTCAAGT

                   
       5692 CAGCTCA
          1 CAGCTCA

       5699 ATTTTAACCC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21


Consensus pattern (20 bp):   
CAGCTCACTCAAGCTCAAGT

Found at i:8388 original size:48 final size:47

Alignment explanation


    Indices: 8309--8414  Score: 135
    Period size: 48  Copynumber: 2.2  Consensus size: 47

       8299 GAGTGTCATG

                                    *                        
       8309 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
          1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC

                                                      *     *
       8357 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
          1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC

                      
       8405 GAAAAAGAAA
          1 GAAAAAGAAA

       8415 GAAAAGACAA


Statistics
Matches: 52,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  48   40  0.77
  49    8  0.15
  50    4  0.08

ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14


Consensus pattern (47 bp):   
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC

Found at i:10131 original size:20 final size:20

Alignment explanation


    Indices: 10085--10131  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      10075 AGCTCGTTTC

                      *         
      10085 CAGCTCACTCGAGCTCAAGT
          1 CAGCTCACTCAAGCTCAAGT

              *               * 
      10105 CAACTCACTCAAGCTCAATT
          1 CAGCTCACTCAAGCTCAAGT

                   
      10125 CAGCTCA
          1 CAGCTCA

      10132 ATCTTAACCC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21


Consensus pattern (20 bp):   
CAGCTCACTCAAGCTCAAGT

Found at i:14015 original size:20 final size:19

Alignment explanation


    Indices: 13975--14035  Score: 63
    Period size: 20  Copynumber: 3.1  Consensus size: 19

      13965 ACCAATAAAA

                                 
      13975 TAAATGAGCT-GAATTGTAGC
          1 TAAATGAGCTCG-ATTG-AGC

                                
      13995 TAAATTGAGCTCGATTGAGC
          1 TAAA-TGAGCTCGATTGAGC

                                 
      14015 TGAAATGAGCTC-ATTTGAGC
          1 T-AAATGAGCTCGA-TTGAGC

             
      14035 T
          1 T

      14036 GGTCGGAGTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 8
        0.82            0.00        0.18

Matches are distributed among these distances:
  19    1  0.03
  20   22  0.59
  21   13  0.35
  22    1  0.03

ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31


Consensus pattern (19 bp):   
TAAATGAGCTCGATTGAGC

Done.