Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008725.1 Corchorus capsularis cultivar CVL-1 contig08746, 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: 4954
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30


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

Alignment explanation


    Indices: 70--193  Score: 153
    Period size: 33  Copynumber: 3.7  Consensus size: 33

         60 CCGCGCAACA

                                               
         70 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT

                                              
        105 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT

                 *           **         *    *
        138 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGT

                                   
        171 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACGCGAC

        194 CCTTTGTCTA


Statistics
Matches: 78,  Mismatches: 8, Indels: 8
        0.83            0.09        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   68  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGT

Found at i:1962 original size:21 final size:21

Alignment explanation


    Indices: 1919--1968  Score: 55
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1909 TGGCAGCTGG

                        *     *  
       1919 GCGCCCAGGCCGTAGGCCTCA
          1 GCGCCCAGGCCGCAGGCCACA

                   *      *      
       1940 GCGCCCATGCCGCATGCCACA
          1 GCGCCCAGGCCGCAGGCCACA

              *     
       1961 GCCCCCAG
          1 GCGCCCAG

       1969 CCTATTCTAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.16, C:0.48, G:0.28, T:0.08


Consensus pattern (21 bp):   
GCGCCCAGGCCGCAGGCCACA
Done.