Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000297.1 Corchorus capsularis cultivar CVL-1 contig00297, 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, 682

Length: 1138
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28


Found at i:631 original size:21 final size:21

Alignment explanation


    Indices: 605--646  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        595 GCACAAGTGA

                   *             
        605 CCGGCCATGCGACTTGGAGAT
          1 CCGGCCACGCGACTTGGAGAT

                                 
        626 CCGGCCACGCGACTTGGAGAT
          1 CCGGCCACGCGACTTGGAGAT

        647 GCCCGCGCAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17


Consensus pattern (21 bp):   
CCGGCCACGCGACTTGGAGAT

Found at i:671 original size:33 final size:33

Alignment explanation


    Indices: 626--732  Score: 119
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        616 ACTTGGAGAT

                         *                   
        626 CCGGCCACGCGACTTGGAGATGCCCGCGCAACA
          1 CCGGCCACGCGACATGGAGATGCCCGCGCAACA

                   *             *         *  
        659 CCGGCCATGCGACATGGAGATACCCAGC-CATCA
          1 CCGGCCACGCGACATGGAGATGCCC-GCGCAACA

                             **          *   
        692 CCGGCCACGCGACATGGCCATGCCCG-GCCACA
          1 CCGGCCACGCGACATGGAGATGCCCGCGCAACA

                     
        724 CCTGGCCAC
          1 CC-GGCCAC

        733 ATGACTTGGC


Statistics
Matches: 61,  Mismatches: 10, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  32    6  0.10
  33   53  0.87
  34    2  0.03

ACGTcount: A:0.21, C:0.42, G:0.27, T:0.09


Consensus pattern (33 bp):   
CCGGCCACGCGACATGGAGATGCCCGCGCAACA

Found at i:743 original size:33 final size:33

Alignment explanation


    Indices: 706--769  Score: 110
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        696 CCACGCGACA

                              *              
        706 TGGCCATGCCCGGCCACACCTGGCCACATGACT
          1 TGGCCATGCCCGGCCACAACTGGCCACATGACT

                                      *    
        739 TGGCCATGCCCGGCCACAACTGGCCATATGA
          1 TGGCCATGCCCGGCCACAACTGGCCACATGA

        770 TCCTTTAGCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.20, C:0.39, G:0.25, T:0.16


Consensus pattern (33 bp):   
TGGCCATGCCCGGCCACAACTGGCCACATGACT
Done.