Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005186.1 Corchorus capsularis cultivar CVL-1 contig05204, 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, 1000

Length: 2579
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:574 original size:29 final size:30

Alignment explanation


    Indices: 541--604  Score: 85
    Period size: 29  Copynumber: 2.2  Consensus size: 30

        531 TAAGCAAATA

                    *  *        **        
        541 GACAATTTGCATCCTAAACTTTAATTT-TG
          1 GACAATTTACACCCTAAACTACAATTTATG

                                          
        570 GACAATTTACACCCTAAACTACAATTTATG
          1 GACAATTTACACCCTAAACTACAATTTATG

                 
        600 GACAA
          1 GACAA

        605 CATGCACCCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  29   23  0.77
  30    7  0.23

ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33


Consensus pattern (30 bp):   
GACAATTTACACCCTAAACTACAATTTATG

Found at i:613 original size:30 final size:29

Alignment explanation


    Indices: 548--613  Score: 69
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        538 ATAGACAATT

                *        **            **
        548 TGCATCCTAAACTTTAATTTTGGACAATT
          1 TGCACCCTAAACTACAATTTTGGACAACA

             *                            
        577 TACACCCTAAACTACAATTTATGGACAACA
          1 TGCACCCTAAACTACAATTT-TGGACAACA

                   
        607 TGCACCC
          1 TGCACCC

        614 CAATTGGATG


Statistics
Matches: 29,  Mismatches: 7, Indels: 1
        0.78            0.19        0.03

Matches are distributed among these distances:
  29   16  0.55
  30   13  0.45

ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30


Consensus pattern (29 bp):   
TGCACCCTAAACTACAATTTTGGACAACA

Found at i:776 original size:29 final size:29

Alignment explanation


    Indices: 744--814  Score: 81
    Period size: 31  Copynumber: 2.4  Consensus size: 29

        734 ATAGTTAAAG

                                          
        744 GTGCAAATTGTCCA-AAATTAAAGTTTAGA
          1 GTGCAAATTGTCCATAAA-TAAAGTTTAGA

                   *          *           *
        773 GTGCAAAGTGTCCATTTACATAAAGTTTAGG
          1 GTGCAAATTGTCCA--TAAATAAAGTTTAGA

                       
        804 GTGCAAATTGT
          1 GTGCAAATTGT

        815 ACATTAAGCC


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  29   13  0.37
  31   20  0.57
  32    2  0.06

ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32


Consensus pattern (29 bp):   
GTGCAAATTGTCCATAAATAAAGTTTAGA
Done.