Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4067

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, 356

Length: 594
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Found at i:549 original size:13 final size:13

Alignment explanation


    Indices: 504--559  Score: 80
    Period size: 13  Copynumber: 4.4  Consensus size: 13

        494 AAAAAAATTC

                      *  
        504 AAAAAAAATTCGA
          1 AAAAAAAATTTGA

                         
        517 AAAAAAAATTTG-
          1 AAAAAAAATTTGA

                         
        529 -AAAAAAATTTGA
          1 AAAAAAAATTTGA

                          
        541 AAAAAAAATTGTGA
          1 AAAAAAAATT-TGA

                 
        555 AAAAA
          1 AAAAA

        560 GAGAGAGCTA


Statistics
Matches: 39,  Mismatches: 1, Indels: 5
        0.87            0.02        0.11

Matches are distributed among these distances:
  11   11  0.28
  13   20  0.51
  14    8  0.21

ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20


Consensus pattern (13 bp):   
AAAAAAAATTTGA

Found at i:557 original size:24 final size:24

Alignment explanation


    Indices: 493--559  Score: 98
    Period size: 24  Copynumber: 2.8  Consensus size: 24

        483 TAGTTTCTCG

                      **            
        493 AAAAAAAATTCAAAAAAAATTCGA
          1 AAAAAAAATTTGAAAAAAATTCGA

                                 *  
        517 AAAAAAAATTTGAAAAAAATTTGA
          1 AAAAAAAATTTGAAAAAAATTCGA

                               
        541 AAAAAAAATTGTGAAAAAA
          1 AAAAAAAATT-TGAAAAAA

        560 GAGAGAGCTA


Statistics
Matches: 39,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  24   31  0.79
  25    8  0.21

ACGTcount: A:0.70, C:0.03, G:0.07, T:0.19


Consensus pattern (24 bp):   
AAAAAAAATTTGAAAAAAATTCGA

Found at i:559 original size:12 final size:11

Alignment explanation


    Indices: 494--546  Score: 61
    Period size: 11  Copynumber: 4.6  Consensus size: 11

        484 AGTTTCTCGA

                     **
        494 AAAAAAATTCA
          1 AAAAAAATTTG

                     * 
        505 AAAAAAATTCG
          1 AAAAAAATTTG

                         
        516 AAAAAAAAATTTG
          1 --AAAAAAATTTG

                       
        529 AAAAAAATTTG
          1 AAAAAAATTTG

                   
        540 AAAAAAA
          1 AAAAAAA

        547 AATTGTGAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  11   28  0.74
  13   10  0.26

ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19


Consensus pattern (11 bp):   
AAAAAAATTTG
Done.