Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013025.1 Corchorus capsularis cultivar CVL-1 contig13046, 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: 6201
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30


Found at i:48 original size:8 final size:8

Alignment explanation


    Indices: 35--68  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

         25 CACCTTCTTG

                    
         35 AAAAATTC
          1 AAAAATTC

                    
         43 AAAAATTC
          1 AAAAATTC

                 *   
         51 AGAAACTTC
          1 A-AAAATTC

                    
         60 AAAAATTC
          1 AAAAATTC

             
         68 A
          1 A

         69 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:159 original size:5 final size:5

Alignment explanation


    Indices: 142--171  Score: 51
    Period size: 5  Copynumber: 5.8  Consensus size: 5

        132 GTTATATCGA

                                               
        142 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
          1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA

        172 AAATTTTCGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   5   19  0.79
   6    5  0.21

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
AAAAT

Found at i:5594 original size:33 final size:33

Alignment explanation


    Indices: 5541--5663  Score: 135
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       5531 CCGCACAACA

                                              *
       5541 CCGGCCACAAGACC-GCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC

                                             *
       5575 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC

                 *           **         *     
       5608 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC

                                   
       5641 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACGCGAC

       5664 CCTTTGCCTA


Statistics
Matches: 76,  Mismatches: 9, Indels: 9
        0.81            0.10        0.10

Matches are distributed among these distances:
  32    5  0.07
  33   63  0.83
  34    7  0.09
  35    1  0.01

ACGTcount: A:0.24, C:0.42, G:0.27, T:0.07


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.