Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005341.1 Corchorus capsularis cultivar CVL-1 contig05359, 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: 13788
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:7372 original size:13 final size:13

Alignment explanation


    Indices: 7356--7380  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7346 TAACCATTCC

                         
       7356 CTTTAGATTTTAT
          1 CTTTAGATTTTAT

                        
       7369 CTTTAGATTTTA
          1 CTTTAGATTTTA

       7381 ACCATCAATG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60


Consensus pattern (13 bp):   
CTTTAGATTTTAT

Found at i:11205 original size:2 final size:2

Alignment explanation


    Indices: 11198--11228  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      11188 ATATTACTAT

                                                          
      11198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11229 CCTACCCATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:13454 original size:40 final size:40

Alignment explanation


    Indices: 13396--13472  Score: 109
    Period size: 40  Copynumber: 1.9  Consensus size: 40

      13386 GTCCCTCCTA

                    *              *                
      13396 ATAATTAAGGAAACAAATTAAATTCAGGTTTAGCCCCCTG
          1 ATAATTAAAGAAACAAATTAAATCCAGGTTTAGCCCCCTG

                      *  *            *          
      13436 ATAATTAAAGTAAGAAATTAAATCCATGTTTAGCCCC
          1 ATAATTAAAGAAACAAATTAAATCCAGGTTTAGCCCC

      13473 TAGTTATAAA


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  40   32  1.00

ACGTcount: A:0.42, C:0.17, G:0.13, T:0.29


Consensus pattern (40 bp):   
ATAATTAAAGAAACAAATTAAATCCAGGTTTAGCCCCCTG

Found at i:13593 original size:13 final size:13

Alignment explanation


    Indices: 13575--13604  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      13565 ACACGTCAGG

                         
      13575 AGGGACAAATTGA
          1 AGGGACAAATTGA

                        *
      13588 AGGGACAAATTGG
          1 AGGGACAAATTGA

                
      13601 AGGG
          1 AGGG

      13605 CCATGTAGCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.40, C:0.07, G:0.40, T:0.13


Consensus pattern (13 bp):   
AGGGACAAATTGA
Done.