Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004814.1 Corchorus capsularis cultivar CVL-1 contig04832, 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: 1996
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:197 original size:32 final size:32

Alignment explanation


    Indices: 152--212  Score: 104
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        142 GAAACTGGTA

                    *                       
        152 ATCAACTTGATTCAGTGTAATTAAGTAAAGTG
          1 ATCAACTTAATTCAGTGTAATTAAGTAAAGTG

                              *          
        184 ATCAACTTAATTCAGTGTTATTAAGTAAA
          1 ATCAACTTAATTCAGTGTAATTAAGTAAA

        213 TTCAGTGATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36


Consensus pattern (32 bp):   
ATCAACTTAATTCAGTGTAATTAAGTAAAGTG

Found at i:1767 original size:22 final size:22

Alignment explanation


    Indices: 1739--1780  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1729 AGAGTCAGTA

                           *      
       1739 TTGAGAGAGAATTCATAGAGTG
          1 TTGAGAGAGAATTCAGAGAGTG

                     *          
       1761 TTGAGAGAGGATTCAGAGAG
          1 TTGAGAGAGAATTCAGAGAG

       1781 AATTCAGAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.36, C:0.05, G:0.36, T:0.24


Consensus pattern (22 bp):   
TTGAGAGAGAATTCAGAGAGTG

Found at i:1778 original size:11 final size:11

Alignment explanation


    Indices: 1742--1792  Score: 57
    Period size: 11  Copynumber: 4.6  Consensus size: 11

       1732 GTCAGTATTG

                       
       1742 AGAGAGAATTC
          1 AGAGAGAATTC

             *    **  *
       1753 ATAGAGTGTTG
          1 AGAGAGAATTC

                  *    
       1764 AGAGAGGATTC
          1 AGAGAGAATTC

                       
       1775 AGAGAGAATTC
          1 AGAGAGAATTC

                   
       1786 AGAGAGA
          1 AGAGAGA

       1793 GAGACTGAGT


Statistics
Matches: 31,  Mismatches: 9, Indels: 0
        0.77            0.22        0.00

Matches are distributed among these distances:
  11   31  1.00

ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20


Consensus pattern (11 bp):   
AGAGAGAATTC

Done.