Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010197.1 Corchorus capsularis cultivar CVL-1 contig10218, 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: 12152
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:5916 original size:21 final size:20

Alignment explanation


    Indices: 5885--5934  Score: 55
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       5875 TAAGGCCTAT

                *       *        
       5885 GAAAGAGAGCAAGAGCAAAAA
          1 GAAAAAGAGCAACAG-AAAAA

             *               *  
       5906 GCAAAAGAGCAACAGAAGAA
          1 GAAAAAGAGCAACAGAAAAA

                     
       5926 GAAAAAGAG
          1 GAAAAAGAG

       5935 TGAGCAACAG


Statistics
Matches: 24,  Mismatches: 5, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  20   12  0.50
  21   12  0.50

ACGTcount: A:0.62, C:0.10, G:0.28, T:0.00


Consensus pattern (20 bp):   
GAAAAAGAGCAACAGAAAAA

Found at i:5944 original size:24 final size:24

Alignment explanation


    Indices: 5912--5968  Score: 96
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       5902 AAAAGCAAAA

                                  * 
       5912 GAGCAACAGAAGAAGAAAAAGAGT
          1 GAGCAACAGAAGAAGAAAAAGAAT

                     *              
       5936 GAGCAACAGCAGAAGAAAAAGAAT
          1 GAGCAACAGAAGAAGAAAAAGAAT

                     
       5960 GAGCAACAG
          1 GAGCAACAG

       5969 GAAAAAGCAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.56, C:0.12, G:0.28, T:0.04


Consensus pattern (24 bp):   
GAGCAACAGAAGAAGAAAAAGAAT

Found at i:5980 original size:24 final size:24

Alignment explanation


    Indices: 5891--5980  Score: 57
    Period size: 24  Copynumber: 3.9  Consensus size: 24

       5881 CTATGAAAGA

                  *  *              
       5891 GAGCAAGAGCAAAAAGC-AA-AA-
          1 GAGCAACAGGAAAAAGCAAAGAAT

                        *    *     * 
       5912 GAGCAACA-GAAGAAGAAAAAGAGT
          1 GAGCAACAGGAAAAAG-CAAAGAAT

                          *           
       5936 GAGCAACAGCAGAAGAA--AAAGAAT
          1 GAGCAACAG--GAAAAAGCAAAGAAT

                                 
       5960 GAGCAACAGGAAAAAGCAAAG
          1 GAGCAACAGGAAAAAGCAAAG

       5981 GACATTAGCG


Statistics
Matches: 53,  Mismatches: 7, Indels: 15
        0.71            0.09        0.20

Matches are distributed among these distances:
  20    5  0.09
  21    7  0.13
  22    7  0.13
  23    1  0.02
  24   27  0.51
  27    6  0.11

ACGTcount: A:0.59, C:0.12, G:0.27, T:0.02


Consensus pattern (24 bp):   
GAGCAACAGGAAAAAGCAAAGAAT
Done.