Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013344.1 Corchorus capsularis cultivar CVL-1 contig13365, 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: 11698
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:120 original size:33 final size:33

Alignment explanation


    Indices: 39--161  Score: 133
    Period size: 33  Copynumber: 3.7  Consensus size: 33

         29 CCGCGCAACA

                                              *
         39 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC

                                             *
         74 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC

                 *           **         *     
        107 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC

                        *         
        140 CCGGCCACAACCAGCCACGCGA
          1 CCGGCCACAACCGGCCACGCGA

        162 TCCTTTGTCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 8
        0.81            0.11        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   65  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.24, C:0.41, G:0.27, T:0.07


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGC

Found at i:7150 original size:38 final size:38

Alignment explanation


    Indices: 7047--7156  Score: 150
    Period size: 39  Copynumber: 2.9  Consensus size: 38

       7037 TCGAGTCTAG

                                         *        
       7047 CCAACAG-TTAACCCCCTGAGGCACGGGTTCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                   *           *                   
       7084 CCAATCAATTTAACCCCCTAAGGCACGGGTCCACTCTTA
          1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                            *  *  *           
       7123 CCAACAGTTTAACCCCATGTGGTACGGGTCCACT
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT

       7157 ATGCACAGCC


Statistics
Matches: 63,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  37    4  0.06
  38   27  0.43
  39   32  0.51

ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

Found at i:8763 original size:18 final size:17

Alignment explanation


    Indices: 8734--8768  Score: 61
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       8724 TTTCATATAG

                             
       8734 GAATTTCATTTAGATTT
          1 GAATTTCATTTAGATTT

                              
       8751 GAATTTGCATTTAGATTT
          1 GAATTT-CATTTAGATTT

       8769 AGTGGATTGC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51


Consensus pattern (17 bp):   
GAATTTCATTTAGATTT
Done.