Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007880.1 Corchorus capsularis cultivar CVL-1 contig07901, 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: 2942
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:996 original size:30 final size:32

Alignment explanation


    Indices: 941--1012  Score: 112
    Period size: 30  Copynumber: 2.3  Consensus size: 32

        931 CATGCATCCA

                                       *    
        941 TCATGCATCATCCCCTTCTTTTGTATTTGTGC
          1 TCATGCATCATCCCCTTCTTTTGTATTAGTGC

                                           *
        973 TCATGCATCAT-CCCTTC-TTTGTATTAGTGT
          1 TCATGCATCATCCCCTTCTTTTGTATTAGTGC

                      
       1003 TCATGCATCA
          1 TCATGCATCA

       1013 GTCATGCATT


Statistics
Matches: 38,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  30   21  0.55
  31    6  0.16
  32   11  0.29

ACGTcount: A:0.17, C:0.26, G:0.12, T:0.44


Consensus pattern (32 bp):   
TCATGCATCATCCCCTTCTTTTGTATTAGTGC

Found at i:2099 original size:12 final size:12

Alignment explanation


    Indices: 2076--2122  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

       2066 AGAGGAAGAT

                        
       2076 AAAAAA-AAAAG
          1 AAAAAAGAAAAG

               *        
       2087 AAAGAAGAAAAG
          1 AAAAAAGAAAAG

                        *
       2099 AAAAAAGAACAAT
          1 AAAAAAGAA-AAG

                 *     
       2112 AAAAAGGAAAA
          1 AAAAAAGAAAA

       2123 AAGAGAAATC


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  11    5  0.17
  12   15  0.50
  13   10  0.33

ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02


Consensus pattern (12 bp):   
AAAAAAGAAAAG

Found at i:2102 original size:19 final size:22

Alignment explanation


    Indices: 2055--2107  Score: 76
    Period size: 19  Copynumber: 2.5  Consensus size: 22

       2045 AAATTCCCAT

                                  
       2055 AAAAAAAAAGAAGAGGAAGATA
          1 AAAAAAAAAGAAGAGGAAGATA

                                  
       2077 AAAAAAAAAGAA-A-GAAGA-A
          1 AAAAAAAAAGAAGAGGAAGATA

              *         
       2096 AAGAAAAAAGAA
          1 AAAAAAAAAGAA

       2108 CAATAAAAAG


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  19   12  0.40
  20    5  0.17
  21    1  0.03
  22   12  0.40

ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02


Consensus pattern (22 bp):   
AAAAAAAAAGAAGAGGAAGATA
Done.