Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003184.1 Corchorus capsularis cultivar CVL-1 contig03192, 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, 619

Length: 1032
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24


Found at i:208 original size:56 final size:53

Alignment explanation


    Indices: 141--255  Score: 176
    Period size: 54  Copynumber: 2.1  Consensus size: 53

        131 GAAAGGGGGC

                                                                   
        141 AATCAGTAATTAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAATAGTAATCAGT
          1 AATCAGTAATTAAGT-AAAAGAGATTAATC-AGAGTCAAAGTAATAGTAATCAGT

                                               *  *   *           
        196 AAATCAGTAATTAAGTAAAAGAGATTAATCAGAGTTAAGGTAGTAGTAATCAGT
          1 -AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT

                  
        250 AATCAG
          1 AATCAG

        256 GTAAAAGATA


Statistics
Matches: 56,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  53    6  0.11
  54   21  0.38
  55   14  0.25
  56   15  0.27

ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26


Consensus pattern (53 bp):   
AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT

Found at i:624 original size:21 final size:21

Alignment explanation


    Indices: 569--638  Score: 79
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        559 TATCTAAAAA

                    *           *
        569 AGTAAAATGGTAATCAGTAAA
          1 AGTAAAATAGTAATCAGTAAG

                    *             
        590 ATGTAAAAGA-TAATCAGTAAG
          1 A-GTAAAATAGTAATCAGTAAG

                           *     
        611 AGTAAAATAGTAATCGGTAAG
          1 AGTAAAATAGTAATCAGTAAG

              *    
        632 AGCAAAA
          1 AGTAAAA

        639 GCGATAATAG


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  20    7  0.17
  21   28  0.68
  22    6  0.15

ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21


Consensus pattern (21 bp):   
AGTAAAATAGTAATCAGTAAG

Found at i:755 original size:29 final size:28

Alignment explanation


    Indices: 730--794  Score: 89
    Period size: 27  Copynumber: 2.4  Consensus size: 28

        720 GTAAAAAGTG

                                        
        730 GTAATAAATAAAAGAGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                 ***                    
        758 GTAATTGGTAAAA-AGAGTAAGAAAAGA
          1 GTAATAAATAAAAGAGAGTAAGAAAAGA

                       
        785 GTAA-AAATAA
          1 GTAATAAATAA

        795 TAAAAGTAGC


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  26    3  0.10
  27   18  0.58
  28   10  0.32

ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17


Consensus pattern (28 bp):   
GTAATAAATAAAAGAGAGTAAGAAAAGA

Done.