Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004488.1 Corchorus capsularis cultivar CVL-1 contig04496, whole genome shotgun sequence

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, 831

Length: 1386
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Found at i:683 original size:11 final size:11

Alignment explanation


    Indices: 653--713  Score: 65
    Period size: 10  Copynumber: 5.7  Consensus size: 11

        643 TTGATTTAAT

                      *
        653 ATTTAAAT-GG
          1 ATTTAAATAGA

                       
        663 ATTT-AATAGA
          1 ATTTAAATAGA

                       
        673 ATTTAAATAGA
          1 ATTTAAATAGA

                      **
        684 ATTTTAAAT-TT
          1 A-TTTAAATAGA

                       
        695 ATTTAAATAGA
          1 ATTTAAATAGA

                    
        706 ATTTAAAT
          1 ATTTAAAT

        714 TTAATAAAAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 7
        0.78            0.09        0.13

Matches are distributed among these distances:
   9    3  0.07
  10   16  0.38
  11   16  0.38
  12    7  0.17

ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44


Consensus pattern (11 bp):   
ATTTAAATAGA

Found at i:712 original size:21 final size:22

Alignment explanation


    Indices: 673--716  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        663 ATTTAATAGA

                                  
        673 ATTTAAATAGAATTTTAAATTT
          1 ATTTAAATAGAATTTTAAATTT

                                  
        695 ATTTAAATAGAA-TTTAAATTT
          1 ATTTAAATAGAATTTTAAATTT

             
        716 A
          1 A

        717 ATAAAAATAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  21   10  0.45
  22   12  0.55

ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48


Consensus pattern (22 bp):   
ATTTAAATAGAATTTTAAATTT

Found at i:724 original size:22 final size:22

Alignment explanation


    Indices: 677--725  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        667 AATAGAATTT

                                **
        677 AAATAGAATTTTAAATTTATTT
          1 AAATAGAATTTTAAATTTATAA

                                   
        699 AAATAGAA-TTTAAATTTAATAA
          1 AAATAGAATTTTAAATTT-ATAA

                 
        721 AAATA
          1 AAATA

        726 AAAAATAAGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  21    9  0.38
  22   15  0.62

ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41


Consensus pattern (22 bp):   
AAATAGAATTTTAAATTTATAA
Done.