Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold501

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: 21747
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:10617 original size:12 final size:11

Alignment explanation


    Indices: 10576--10616  Score: 64
    Period size: 11  Copynumber: 3.6  Consensus size: 11

      10566 TAGTTTCTCG

                   *    
      10576 AAAAAAACTCGA
          1 AAAAAAATTC-A

                       
      10588 AAAAAAATTCA
          1 AAAAAAATTCA

                       
      10599 AAAAAAATTCA
          1 AAAAAAATTCA

                   
      10610 AAAAAAA
          1 AAAAAAA

      10617 AGTTTCCATT


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  11   19  0.68
  12    9  0.32

ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12


Consensus pattern (11 bp):   
AAAAAAATTCA

Found at i:10677 original size:15 final size:15

Alignment explanation


    Indices: 10652--10693  Score: 68
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      10642 GGATATCAAG

                           
      10652 TTGTG-AAAAAAAAA
          1 TTGTGAAAAAAAAAA

              *            
      10666 TTTTGAAAAAAAAAA
          1 TTGTGAAAAAAAAAA

                         
      10681 TTGTGAAAAAAAA
          1 TTGTGAAAAAAAA

      10694 GAGAGCTAGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  14    4  0.16
  15   21  0.84

ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24


Consensus pattern (15 bp):   
TTGTGAAAAAAAAAA

Found at i:18709 original size:14 final size:14

Alignment explanation


    Indices: 18690--18730  Score: 75
    Period size: 14  Copynumber: 3.0  Consensus size: 14

      18680 ACTAGCTCTC

                          
      18690 TTTTTTTTTCACAA
          1 TTTTTTTTTCACAA

                          
      18704 TTTTTTTTTCACAA
          1 TTTTTTTTTCACAA

                          
      18718 -TTTTTTTTCACAA
          1 TTTTTTTTTCACAA

      18731 CTTGATATCC


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  13   13  0.48
  14   14  0.52

ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63


Consensus pattern (14 bp):   
TTTTTTTTTCACAA

Found at i:18815 original size:12 final size:12

Alignment explanation


    Indices: 18769--18814  Score: 67
    Period size: 12  Copynumber: 3.9  Consensus size: 12

      18759 GGAAACTAGT

                        
      18769 TTTTTTTTC-AA
          1 TTTTTTTTCGAA

                    *   
      18780 TTTTTTTTTGAA
          1 TTTTTTTTCGAA

                       *
      18792 TTTTTTTTCGAG
          1 TTTTTTTTCGAA

                       
      18804 TTTTTTTTCGA
          1 TTTTTTTTCGA

      18815 GAAACTACTA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  11    8  0.26
  12   23  0.74

ACGTcount: A:0.13, C:0.07, G:0.09, T:0.72


Consensus pattern (12 bp):   
TTTTTTTTCGAA
Done.