Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1367

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: 1906
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27


Found at i:787 original size:10 final size:10

Alignment explanation


    Indices: 772--824  Score: 83
    Period size: 9  Copynumber: 5.4  Consensus size: 10

        762 TGAGTTCAGA

                      
        772 CAAAAAAAAT
          1 CAAAAAAAAT

                      
        782 C-AAAAAAAT
          1 CAAAAAAAAT

                      
        791 CAAAAAAAAT
          1 CAAAAAAAAT

                      
        801 C-AAAAAAAT
          1 CAAAAAAAAT

                       
        810 CAAAAAAAAAT
          1 C-AAAAAAAAT

                
        821 CAAA
          1 CAAA

        825 GTCAAAATAG


Statistics
Matches: 40,  Mismatches: 0, Indels: 6
        0.87            0.00        0.13

Matches are distributed among these distances:
   9   18  0.45
  10   13  0.32
  11    9  0.22

ACGTcount: A:0.79, C:0.11, G:0.00, T:0.09


Consensus pattern (10 bp):   
CAAAAAAAAT

Found at i:796 original size:19 final size:19

Alignment explanation


    Indices: 772--824  Score: 97
    Period size: 19  Copynumber: 2.7  Consensus size: 19

        762 TGAGTTCAGA

                               
        772 CAAAAAAAATCAAAAAAAT
          1 CAAAAAAAATCAAAAAAAT

                               
        791 CAAAAAAAATCAAAAAAAT
          1 CAAAAAAAATCAAAAAAAT

                           
        810 CAAAAAAAAATCAAA
          1 C-AAAAAAAATCAAA

        825 GTCAAAATAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  19   20  0.61
  20   13  0.39

ACGTcount: A:0.79, C:0.11, G:0.00, T:0.09


Consensus pattern (19 bp):   
CAAAAAAAATCAAAAAAAT

Found at i:858 original size:15 final size:15

Alignment explanation


    Indices: 838--873  Score: 56
    Period size: 15  Copynumber: 2.4  Consensus size: 15

        828 AAAATAGAAA

                            
        838 AAAAAG-AGAAAAAGG
          1 AAAAAGAAGAAAAA-G

                           
        853 AAAAAGAAGAAAAAG
          1 AAAAAGAAGAAAAAG

                  
        868 AAAAAG
          1 AAAAAG

        874 GAGAGGTCAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  15   13  0.65
  16    7  0.35

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (15 bp):   
AAAAAGAAGAAAAAG

Found at i:1693 original size:21 final size:23

Alignment explanation


    Indices: 1667--1719  Score: 92
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       1657 ATTTTGGGTC

                                   
       1667 AAAAAATGATG-ATG-AAAATGA
          1 AAAAAATGATGAATGAAAAATGA

                                   
       1688 AAAAAATGATGAATGAAAAATGA
          1 AAAAAATGATGAATGAAAAATGA

                     
       1711 AAAAAATGA
          1 AAAAAATGA

       1720 AAAAGTAAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  21   11  0.37
  22    3  0.10
  23   16  0.53

ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17


Consensus pattern (23 bp):   
AAAAAATGATGAATGAAAAATGA

Found at i:1729 original size:23 final size:23

Alignment explanation


    Indices: 1681--1732  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1671 AATGATGATG

                            **     
       1681 AAAATGAAAAAAATGATGAATGA
          1 AAAATGAAAAAAATGAAAAATGA

                                    
       1704 AAAATGAAAAAAATGAAAAA-GTA
          1 AAAATGAAAAAAATGAAAAATG-A

                  
       1727 AAAATG
          1 AAAATG

       1733 GAGAGGCTAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  22    1  0.04
  23   25  0.96

ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15


Consensus pattern (23 bp):   
AAAATGAAAAAAATGAAAAATGA

Found at i:1841 original size:21 final size:22

Alignment explanation


    Indices: 1815--1862  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1805 GCTCAAATAT

                                  
       1815 TGATCAGAAT-GGGGCATAAAG
          1 TGATCAGAATAGGGGCATAAAG

                    *         **  
       1836 TGATCAGATTAGGGGCATGTAG
          1 TGATCAGAATAGGGGCATAAAG

                 
       1858 TGATC
          1 TGATC

       1863 TTACTATACC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  21    9  0.39
  22   14  0.61

ACGTcount: A:0.31, C:0.10, G:0.33, T:0.25


Consensus pattern (22 bp):   
TGATCAGAATAGGGGCATAAAG

Done.