Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007437.1 Corchorus capsularis cultivar CVL-1 contig07458, 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: 3699
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26


Found at i:1705 original size:18 final size:18

Alignment explanation


    Indices: 1682--1747  Score: 62
    Period size: 18  Copynumber: 3.5  Consensus size: 18

       1672 ATAATGATCT

                              
       1682 ACAAAATCCCTCTCAATC
          1 ACAAAATCCCTCTCAATC

                       *  *      *
       1700 ACAAAAT-CCTGTAAATGATAT
          1 ACAAAATCCCTCT-CA--AT-C

                              
       1721 ACAAAATCCCTCTCAATC
          1 ACAAAATCCCTCTCAATC

                     
       1739 ACAAAATCC
          1 ACAAAATCC

       1748 TGTAAAATTG


Statistics
Matches: 37,  Mismatches: 6, Indels: 10
        0.70            0.11        0.19

Matches are distributed among these distances:
  17    4  0.11
  18   17  0.46
  19    2  0.05
  20    2  0.05
  21    8  0.22
  22    4  0.11

ACGTcount: A:0.44, C:0.30, G:0.03, T:0.23


Consensus pattern (18 bp):   
ACAAAATCCCTCTCAATC

Found at i:1728 original size:39 final size:39

Alignment explanation


    Indices: 1674--1753  Score: 151
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       1664 AAGACAAAAT

                  *                                
       1674 AATGATCTACAAAATCCCTCTCAATCACAAAATCCTGTA
          1 AATGATATACAAAATCCCTCTCAATCACAAAATCCTGTA

                                                   
       1713 AATGATATACAAAATCCCTCTCAATCACAAAATCCTGTA
          1 AATGATATACAAAATCCCTCTCAATCACAAAATCCTGTA

              
       1752 AA
          1 AA

       1754 ATTGCAAGAA


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.44, C:0.26, G:0.05, T:0.25


Consensus pattern (39 bp):   
AATGATATACAAAATCCCTCTCAATCACAAAATCCTGTA

Found at i:1842 original size:28 final size:28

Alignment explanation


    Indices: 1802--1861  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       1792 AAAGAAGGGC

                    *           *       
       1802 AAAACAAATATGCAATTACAGCCAACAA
          1 AAAACAAACATGCAATTACAACCAACAA

                                        
       1830 AAAACAAACATGCAATTACAACCAACAA
          1 AAAACAAACATGCAATTACAACCAACAA

                
       1858 AAAA
          1 AAAA

       1862 GCAAGCCAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.62, C:0.22, G:0.05, T:0.12


Consensus pattern (28 bp):   
AAAACAAACATGCAATTACAACCAACAA
Done.