Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009227.1 Corchorus capsularis cultivar CVL-1 contig09248, 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: 22974
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:161 original size:2 final size:2

Alignment explanation


    Indices: 154--189  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        144 TTTTCCATCA

                                                                 
        154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        190 GTAGCTTTCG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:13624 original size:2 final size:2

Alignment explanation


    Indices: 13614--13654  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      13604 TAGTGTGTCA

                                                                          
      13614 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13655 CATGGATGAC


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:19983 original size:38 final size:38

Alignment explanation


    Indices: 19923--19997  Score: 132
    Period size: 38  Copynumber: 2.0  Consensus size: 38

      19913 TGGGCCTTAG

                                                  
      19923 ACTTTGGGCTAAGCAGACTAAAAGTGTATAGATAATAC
          1 ACTTTGGGCTAAGCAGACTAAAAGTGTATAGATAATAC

                         *   *                   
      19961 ACTTTGGGCTAAGTAGAGTAAAAGTGTATAGATAATA
          1 ACTTTGGGCTAAGCAGACTAAAAGTGTATAGATAATA

      19998 TAGAGGCAGT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   35  1.00

ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28


Consensus pattern (38 bp):   
ACTTTGGGCTAAGCAGACTAAAAGTGTATAGATAATAC

Found at i:21777 original size:19 final size:19

Alignment explanation


    Indices: 21753--21790  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      21743 AGCAACCCCG

                               
      21753 TAGGTGACTCCATAAGCAC
          1 TAGGTGACTCCATAAGCAC

                  *            
      21772 TAGGTGGCTCCATAAGCAC
          1 TAGGTGACTCCATAAGCAC

      21791 CCAACAACCC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21


Consensus pattern (19 bp):   
TAGGTGACTCCATAAGCAC
Done.