Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015177.1 Corchorus capsularis cultivar CVL-1 contig15198, 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: 7311
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:3617 original size:22 final size:22

Alignment explanation


    Indices: 3586--3640  Score: 76
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       3576 TGCTCGATTA

                 *         *      
       3586 ATGTTCGTTTAAT-ATTCGTTT
          1 ATGTTTGTTTAATAACTCGTTT

                                   
       3607 ATTGTTTGTTTAATAACTCGTTT
          1 A-TGTTTGTTTAATAACTCGTTT

                       
       3630 ATGTTTGTTTA
          1 ATGTTTGTTTA

       3641 TTAAGATTAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  21    1  0.03
  22   21  0.70
  23    8  0.27

ACGTcount: A:0.20, C:0.07, G:0.15, T:0.58


Consensus pattern (22 bp):   
ATGTTTGTTTAATAACTCGTTT

Found at i:6527 original size:6 final size:6

Alignment explanation


    Indices: 6518--6550  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       6508 AAAGCAAAGC

                                                  
       6518 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       6551 GCAGATTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:6576 original size:13 final size:13

Alignment explanation


    Indices: 6547--6593  Score: 60
    Period size: 13  Copynumber: 3.7  Consensus size: 13

       6537 AATCTAAATC

                   *     
       6547 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                 *       
       6559 TAAAGTAAATTAA
          1 TAAAGCAAATTAA

                   *     
       6572 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                     
       6585 TAAAGCAAA
          1 TAAAGCAAA

       6594 CAATATTTAT


Statistics
Matches: 29,  Mismatches: 5, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  12    9  0.31
  13   20  0.69

ACGTcount: A:0.57, C:0.06, G:0.13, T:0.23


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:6598 original size:25 final size:25

Alignment explanation


    Indices: 6547--6598  Score: 70
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       6537 AATCTAAATC

                             *    *  
       6547 TAAAGCAGATTATAAAGTAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       6572 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

              
       6597 TA
          1 TA

       6599 TTTATAAAGC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25   15  0.62
  26    9  0.38

ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.