Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005315.1 Corchorus capsularis cultivar CVL-1 contig05333, 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: 8410
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:150 original size:23 final size:23

Alignment explanation


    Indices: 117--170  Score: 99
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        107 TGCAAAACAG

                                    
        117 AAAAGACACGATCAAACAATCATC
          1 AAAAG-CACGATCAAACAATCATC

                                   
        141 AAAAGCACGATCAAACAATCATC
          1 AAAAGCACGATCAAACAATCATC

                   
        164 AAAAGCA
          1 AAAAGCA

        171 GGAAAGGAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  23   25  0.83
  24    5  0.17

ACGTcount: A:0.56, C:0.24, G:0.09, T:0.11


Consensus pattern (23 bp):   
AAAAGCACGATCAAACAATCATC

Found at i:544 original size:24 final size:25

Alignment explanation


    Indices: 512--574  Score: 94
    Period size: 24  Copynumber: 2.6  Consensus size: 25

        502 CGTTATCTCA

                         *           
        512 GGAAACCATCAGCGAATAC-AAAAG
          1 GGAAACCATCAGCAAATACAAAAAG

                                     
        536 GGAAACCATCAGCAAATACAAAAAG
          1 GGAAACCATCAGCAAATACAAAAAG

             *             
        561 GAAAACCA-CAGCAA
          1 GGAAACCATCAGCAA

        575 GCAAGCAAAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  24   24  0.67
  25   12  0.33

ACGTcount: A:0.54, C:0.22, G:0.17, T:0.06


Consensus pattern (25 bp):   
GGAAACCATCAGCAAATACAAAAAG

Found at i:833 original size:45 final size:45

Alignment explanation


    Indices: 751--874  Score: 187
    Period size: 45  Copynumber: 2.8  Consensus size: 45

        741 GAAAACGTGC

                      *  *     *          *  *           
        751 AGGAGATCAAGGAAAG-TTAGGCTCCATGACTGTCAAATGCTTTA
          1 AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCCAAATGCTTTA

                                   *                     
        795 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
          1 AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCCAAATGCTTTA

                                               
        840 AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCC
          1 AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCC

        875 GAGTGCACAA


Statistics
Matches: 72,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  44   14  0.19
  45   58  0.81

ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24


Consensus pattern (45 bp):   
AGGAGATCAAAGAGAGCTTTGGCTCCATGATTGCCAAATGCTTTA
Done.