Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010160.1 Corchorus capsularis cultivar CVL-1 contig10181, 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: 14892
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:672 original size:7 final size:7

Alignment explanation


    Indices: 660--696  Score: 56
    Period size: 7  Copynumber: 5.3  Consensus size: 7

        650 CAGAAGGCTG

                   
        660 TCCAGTT
          1 TCCAGTT

                   
        667 TCCAGTT
          1 TCCAGTT

              *    
        674 TCTAGTT
          1 TCCAGTT

                   
        681 TCCAGTT
          1 TCCAGTT

             *     
        688 TTCAGTT
          1 TCCAGTT

              
        695 TC
          1 TC

        697 AACTTTCAAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.14, C:0.24, G:0.14, T:0.49


Consensus pattern (7 bp):   
TCCAGTT

Found at i:703 original size:21 final size:21

Alignment explanation


    Indices: 660--703  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        650 CAGAAGGCTG

                            * *  
        660 TCCAGTTTCCAGTTTCTAGTT
          1 TCCAGTTTCCAGTTTCAACTT

                    *            
        681 TCCAGTTTTCAGTTTCAACTT
          1 TCCAGTTTCCAGTTTCAACTT

              
        702 TC
          1 TC

        704 AATTGCCATT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.16, C:0.25, G:0.11, T:0.48


Consensus pattern (21 bp):   
TCCAGTTTCCAGTTTCAACTT

Found at i:9610 original size:30 final size:30

Alignment explanation


    Indices: 9574--9635  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       9564 TTCAATATCT

                                          
       9574 TTTTATAATTAATAAATAAAAGTTTAATGA
          1 TTTTATAATTAATAAATAAAAGTTTAATGA

                          *               
       9604 TTTTATAATTAATAGATAAAAGTTTAATGA
          1 TTTTATAATTAATAAATAAAAGTTTAATGA

              
       9634 TT
          1 TT

       9636 AAAAATTATA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45


Consensus pattern (30 bp):   
TTTTATAATTAATAAATAAAAGTTTAATGA

Found at i:10676 original size:28 final size:27

Alignment explanation


    Indices: 10613--10691  Score: 122
    Period size: 27  Copynumber: 2.9  Consensus size: 27

      10603 ATTACGGACG

                                       
      10613 CCCAGGGGCATTTTGGTCATTTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

                                       
      10640 CCCAGGGGCATTTTGGTCATTTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

             **            *         
      10667 CTTAGGGGGCATTTTAGTCATTTTT
          1 CCCA-GGGGCATTTTGGTCATTTTT

      10692 AAGTTCACCT


Statistics
Matches: 48,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  27   29  0.60
  28   19  0.40

ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41


Consensus pattern (27 bp):   
CCCAGGGGCATTTTGGTCATTTTTGCA

Found at i:12078 original size:13 final size:13

Alignment explanation


    Indices: 12060--12091  Score: 64
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      12050 AGATACACTG

                         
      12060 CAGACTGGCAGTA
          1 CAGACTGGCAGTA

                         
      12073 CAGACTGGCAGTA
          1 CAGACTGGCAGTA

                  
      12086 CAGACT
          1 CAGACT

      12092 ACCAAGAGAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16


Consensus pattern (13 bp):   
CAGACTGGCAGTA

Found at i:13838 original size:33 final size:33

Alignment explanation


    Indices: 13796--13858  Score: 101
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      13786 TGATAATAAA

                          *                   
      13796 AATTAAATCTTTATTTAGTAAGG-GTTGAGTTCT
          1 AATTAAATCTTTATGTAGT-AGGAGTTGAGTTCT

                                          
      13829 AATTAAATCTTTATGTAGTAGGAGTTGAGT
          1 AATTAAATCTTTATGTAGTAGGAGTTGAGT

      13859 CCTAGTAATT


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  32    3  0.11
  33   25  0.89

ACGTcount: A:0.32, C:0.05, G:0.21, T:0.43


Consensus pattern (33 bp):   
AATTAAATCTTTATGTAGTAGGAGTTGAGTTCT

Found at i:14872 original size:39 final size:38

Alignment explanation


    Indices: 14801--14892  Score: 141
    Period size: 39  Copynumber: 2.4  Consensus size: 38

      14791 ATTAAGGCAG

                                              *   
      14801 TAGTAATCAGT-AAATCAATAATTAAGAGTCAAAGTAA
          1 TAGTAATCAGTAAAATCAATAATTAAGAGTCAAAATAA

                            *                      
      14838 TAGTAATCAGTAAAATTAATAAATTAAGAGTCAAAATAA
          1 TAGTAATCAGTAAAATCAAT-AATTAAGAGTCAAAATAA

                     *      
      14877 TAGTAATCATTAAAAT
          1 TAGTAATCAGTAAAAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  37   11  0.22
  38    7  0.14
  39   32  0.64

ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29


Consensus pattern (38 bp):   
TAGTAATCAGTAAAATCAATAATTAAGAGTCAAAATAA
Done.