Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold837

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: 5499
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.29

Warning! 867 characters in sequence are not A, C, G, or T


Found at i:3668 original size:20 final size:21

Alignment explanation


    Indices: 3630--3678  Score: 59
    Period size: 19  Copynumber: 2.4  Consensus size: 21

       3620 ATTTAAAAAT

                                 
       3630 ATTTTTATATTTACTTTTAAA
          1 ATTTTTATATTTACTTTTAAA

                                  
       3651 ATTTTTA-ATTTA-TATTT-AA
          1 ATTTTTATATTTACT-TTTAAA

            *        
       3670 CTTTTTATA
          1 ATTTTTATA

       3679 ATCCATATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19    9  0.36
  20    9  0.36
  21    7  0.28

ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63


Consensus pattern (21 bp):   
ATTTTTATATTTACTTTTAAA

Found at i:5108 original size:20 final size:22

Alignment explanation


    Indices: 5073--5130  Score: 63
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       5063 ACAAAATATA

                                   
       5073 TTTAT-ATTTA-ATTTTAAAC-T
          1 TTTATAATTTATA-TTTAAACTT

                                   
       5093 TTT-TAATTTATATTT-AACTTT
          1 TTTATAATTTATATTTAAAC-TT

                             
       5114 TTTATAATTTATATTTA
          1 TTTATAATTTATATTTA

       5131 CTAAATTTTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 9
        0.78            0.00        0.22

Matches are distributed among these distances:
  19    4  0.12
  20   11  0.34
  21    5  0.16
  22   12  0.38

ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64


Consensus pattern (22 bp):   
TTTATAATTTATATTTAAACTT

Found at i:5459 original size:112 final size:112

Alignment explanation


    Indices: 5262--5483  Score: 444
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       5252 AACCCCAAAA

                                                                             
       5262 AGAAACTCAAAATTAACAAATTTATAAATCCAAAAAAATGGTTGGGTTGACGACACCAACTATAA
          1 AGAAACTCAAAATTAACAAATTTATAAATCCAAAAAAATGGTTGGGTTGACGACACCAACTATAA

                                                           
       5327 CAGCCTTACTCTTTGCTATCTAGATAGTGCCCATTTTAGGCTCTACT
         66 CAGCCTTACTCTTTGCTATCTAGATAGTGCCCATTTTAGGCTCTACT

                                                                             
       5374 AGAAACTCAAAATTAACAAATTTATAAATCCAAAAAAATGGTTGGGTTGACGACACCAACTATAA
          1 AGAAACTCAAAATTAACAAATTTATAAATCCAAAAAAATGGTTGGGTTGACGACACCAACTATAA

                                                         
       5439 CAGCCTTACTCTTTGCTATCTAGATAGTGCCCATTTTAGGCTCTA
         66 CAGCCTTACTCTTTGCTATCTAGATAGTGCCCATTTTAGGCTCTA

       5484 GTGTTCTCAT


Statistics
Matches: 110,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 112  110  1.00

ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29


Consensus pattern (112 bp):   
AGAAACTCAAAATTAACAAATTTATAAATCCAAAAAAATGGTTGGGTTGACGACACCAACTATAA
CAGCCTTACTCTTTGCTATCTAGATAGTGCCCATTTTAGGCTCTACT
Done.