Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000176.1 Corchorus capsularis cultivar CVL-1 contig00176, 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: 3409
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31


Found at i:1583 original size:21 final size:21

Alignment explanation


    Indices: 1557--1606  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1547 GAAGAAGAAA

                         *  *    
       1557 AAGAAGAAAGTGAGAACGAGG
          1 AAGAAGAAAGTGAAAAAGAGG

                  *          *   
       1578 AAGAAGGAAGTGAAAAATAGG
          1 AAGAAGAAAGTGAAAAAGAGG

                    
       1599 AAGAAGAA
          1 AAGAAGAA

       1607 GGAGCTGCTG


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.58, C:0.02, G:0.34, T:0.06


Consensus pattern (21 bp):   
AAGAAGAAAGTGAAAAAGAGG

Found at i:1636 original size:18 final size:18

Alignment explanation


    Indices: 1598--1638  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1588 TGAAAAATAG

                      *     * 
       1598 GAAGAAGAAGGAGCTGCT
          1 GAAGAAGAAGAAGCTGAT

                        *     
       1616 GAAGAAGAAGAATCTGAT
          1 GAAGAAGAAGAAGCTGAT

                 
       1634 GAAGA
          1 GAAGA

       1639 GGTTGATGAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.46, C:0.07, G:0.34, T:0.12


Consensus pattern (18 bp):   
GAAGAAGAAGAAGCTGAT
Done.