Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012226.1 Corchorus capsularis cultivar CVL-1 contig12247, 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: 5359
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:608 original size:35 final size:36

Alignment explanation


    Indices: 562--1006  Score: 322
    Period size: 35  Copynumber: 12.9  Consensus size: 36

        552 CTGTGCGGTC

                 *                              
        562 TTTCAGGAAGTTTTCAGA-GATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

                                *   *           
        597 TTTCAAGAAGTTTT-AGA-GGTCAAAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

              *          *      *               
        631 TTCCAAGAAGTTTCCAGA-GGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

              *                 *               
        666 TTCCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

             *                                  
        701 TATCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

              *                                 
        736 TTCCAAGAAG---T-------T-AGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

                                                 *  
        761 TTTCAAGAAGTTTTCAGAGGTCAGA-CAGAGTTGATCGCA
          1 TTTCAAGAAGTTTTCAGA---C-GATCAGAGTTGATCTCA

                    *                          *  
        800 TTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCACA
          1 -TTTCAAGAAGTTTT-CAGACGATCAGAGTTGATCTCA

                          *                   *  
        835 TTTTC-AGAAGTTTCCA-ACGATCAGAGTTGATCACA
          1 -TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

                    *                       *  *  
        870 TTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGGTCGCA
          1 -TTTCAAGAAGTTTT-CAGACGATCAGAGTTGATCTCA

                    *     *                   *  
        905 TTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCACA
          1 -TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

                    *     *     *       *        
        940 TTTTC-AGTAGTTTCCA-ACAATCAGAGGTGATCTCA
          1 -TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

                      *    *  *              
        975 TTTCAAGAA-ATTTCCGATGATCAGAGTTGATC
          1 TTTCAAGAAGTTTTCAGACGATCAGAGTTGATC

       1007 CAGAGGAGTT


Statistics
Matches: 351,  Mismatches: 35, Indels: 48
        0.81            0.08        0.11

Matches are distributed among these distances:
  25   22  0.06
  26    1  0.00
  28    1  0.00
  32    1  0.00
  34   42  0.12
  35  252  0.72
  36    6  0.02
  38    5  0.01
  39   17  0.05
  40    4  0.01

ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Consensus pattern (36 bp):   
TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA

Found at i:757 original size:25 final size:25

Alignment explanation


    Indices: 723--772  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        713 TTCAGAGATC

                                     
        723 AGAGTTGATCTCATTCCAAGAAGTT
          1 AGAGTTGATCTCATTCCAAGAAGTT

                           *         
        748 AGAGTTGATCTCATTTCAAGAAGTT
          1 AGAGTTGATCTCATTCCAAGAAGTT

        773 TTCAGAGGTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34


Consensus pattern (25 bp):   
AGAGTTGATCTCATTCCAAGAAGTT

Found at i:1488 original size:23 final size:23

Alignment explanation


    Indices: 1461--1507  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1451 CAATAGACAC

                                   
       1461 ACGGACTAGATAGAGGGACGGAT
          1 ACGGACTAGATAGAGGGACGGAT

                                   
       1484 ACGGACTAGATAGAGGGACGGAT
          1 ACGGACTAGATAGAGGGACGGAT

             
       1507 A
          1 A

       1508 GAGAGACAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.36, C:0.13, G:0.38, T:0.13


Consensus pattern (23 bp):   
ACGGACTAGATAGAGGGACGGAT
Done.