Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005792.1 Corchorus capsularis cultivar CVL-1 contig05810, 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: 2219
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30


Found at i:1660 original size:50 final size:48

Alignment explanation


    Indices: 1573--1719  Score: 127
    Period size: 51  Copynumber: 3.0  Consensus size: 48

       1563 AATTTGCAAA

                       **                **           *     * 
       1573 TAAAAGATTGAAGCTTTAAGTAATTAGTAGGTAAAAATGTCATCTTTGGG
          1 TAAAAGATTGATTCTTTAAGT-ATTAGTAAAT-AAAATGTCACCTTTGAG

                                                   * *        *
       1623 TAAAAGATTGATTCTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGAT
          1 TAAAAGATTGATTCTTTA-AGT-ATTAGTAAATAAAA-TGTCACCTTTGAG

                    *                                 *     
       1674 TAAAAGATCGAATT-TTTAAGT-TTAGTAAATAAAATGTCACATTTGA
          1 TAAAAGATTG-ATTCTTTAAGTATTAGTAAATAAAATGTCACCTTTGA

       1720 ATTAGAAGTT


Statistics
Matches: 80,  Mismatches: 14, Indels: 9
        0.78            0.14        0.09

Matches are distributed among these distances:
  47    9  0.11
  48   13  0.16
  50   23  0.29
  51   32  0.40
  52    3  0.04

ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37


Consensus pattern (48 bp):   
TAAAAGATTGATTCTTTAAGTATTAGTAAATAAAATGTCACCTTTGAG

Found at i:1739 original size:48 final size:48

Alignment explanation


    Indices: 1647--1739  Score: 107
    Period size: 48  Copynumber: 1.9  Consensus size: 48

       1637 TTTAGAGTGA

                           *    *                  *        
       1647 TTAGTAAATAAAATTTTAACCTTTGATTAAAAGATCGAATTTTTAAGT
          1 TTAGTAAATAAAATTGTAACATTTGATTAAAAGATCGAACTTTTAAGT

                             *            *   * *         
       1695 TTAGTAAATAAAA-TGTCACATTTGAATTAGAAGTTTGAACTTTTA
          1 TTAGTAAATAAAATTGTAACATTTG-ATTAAAAGATCGAACTTTTA

       1740 GGCCATTAGT


Statistics
Matches: 37,  Mismatches: 7, Indels: 2
        0.80            0.15        0.04

Matches are distributed among these distances:
  47    8  0.22
  48   29  0.78

ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41


Consensus pattern (48 bp):   
TTAGTAAATAAAATTGTAACATTTGATTAAAAGATCGAACTTTTAAGT
Done.