Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013613.1 Corchorus capsularis cultivar CVL-1 contig13634, 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: 15633
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:6332 original size:22 final size:22

Alignment explanation


    Indices: 6307--6349  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6297 AATTGATTAG

                                  
       6307 CAAAAACCCTAGTACCACTTGT
          1 CAAAAACCCTAGTACCACTTGT

                                 
       6329 CAAAAACCCTAGTACCACTTG
          1 CAAAAACCCTAGTACCACTTG

       6350 ATCCAATTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.37, C:0.33, G:0.09, T:0.21


Consensus pattern (22 bp):   
CAAAAACCCTAGTACCACTTGT

Found at i:9642 original size:24 final size:24

Alignment explanation


    Indices: 9607--9653  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       9597 ATCGGGACAA

                   *    *           
       9607 AGAGTTTTGGTCTTGATGGTCATT
          1 AGAGTTTCGGTCCTGATGGTCATT

                                   
       9631 AGAGTTTCGGTCCTGATGGTCAT
          1 AGAGTTTCGGTCCTGATGGTCAT

       9654 GATTGATGTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40


Consensus pattern (24 bp):   
AGAGTTTCGGTCCTGATGGTCATT

Found at i:11819 original size:10 final size:10

Alignment explanation


    Indices: 11806--11833  Score: 56
    Period size: 10  Copynumber: 2.8  Consensus size: 10

      11796 GATTATATTC

                      
      11806 AGTCCATATA
          1 AGTCCATATA

                      
      11816 AGTCCATATA
          1 AGTCCATATA

                    
      11826 AGTCCATA
          1 AGTCCATA

      11834 ATTGGAGTTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29


Consensus pattern (10 bp):   
AGTCCATATA

Found at i:13260 original size:33 final size:33

Alignment explanation


    Indices: 13222--13328  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      13212 GGTGCGAGTG

                    *            *           
      13222 ACCGGCCATGCGACTTGGAGAAGACCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGACCGGCCAAC

                           *       *       * 
      13255 ACCGGCCACGCGACTCGGAGATGCCCGGCCACC
          1 ACCGGCCACGCGACTTGGAGATGACCGGCCAAC

                          *    *   *         
      13288 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGATGACCGGCCAAC

                     
      13320 AACCGGCCA
          1 -ACCGGCCA

      13329 TCGCTTAGCG


Statistics
Matches: 63,  Mismatches: 10, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   62  0.98

ACGTcount: A:0.23, C:0.40, G:0.29, T:0.07


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGACCGGCCAAC
Done.