Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021836.1 Corchorus olitorius cultivar O-4 contig21869, 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, 984

Length: 1641
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30


Found at i:746 original size:21 final size:23

Alignment explanation


    Indices: 720--784  Score: 80
    Period size: 23  Copynumber: 2.9  Consensus size: 23

        710 CAAGAAATTC

                                   
        720 AAAAAAAAATC-A-ATCAAAAAT
          1 AAAAAAAAATCAAGATCAAAAAT

                                   
        741 AAAAAAAAATCAAGATCAAAAAT
          1 AAAAAAAAATCAAGATCAAAAAT

            *   **       *       
        764 CAAATCAAATCAAAATCAAAA
          1 AAAAAAAAATCAAGATCAAAA

        785 GAGAATTGAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   11  0.29
  22    1  0.03
  23   26  0.68

ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14


Consensus pattern (23 bp):   
AAAAAAAAATCAAGATCAAAAAT

Found at i:761 original size:17 final size:17

Alignment explanation


    Indices: 737--778  Score: 52
    Period size: 17  Copynumber: 2.5  Consensus size: 17

        727 AATCAATCAA

                             
        737 AAAT-AAAAA-AAAATC
          1 AAATCAAAAATAAAATC

                        *     
        752 AAGATCAAAAATCAAATC
          1 AA-ATCAAAAATAAAATC

                     
        770 AAATCAAAA
          1 AAATCAAAA

        779 TCAAAAGAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  15    2  0.09
  16    2  0.09
  17   12  0.52
  18    7  0.30

ACGTcount: A:0.71, C:0.12, G:0.02, T:0.14


Consensus pattern (17 bp):   
AAATCAAAAATAAAATC

Found at i:1449 original size:50 final size:50

Alignment explanation


    Indices: 1374--1521  Score: 206
    Period size: 50  Copynumber: 3.0  Consensus size: 50

       1364 GTTTTATAAC

                                                 *            
       1374 AAGATTCCTTTCCATTTATGAGTTCAAGATCAAAATTTGCTTTTCAAAAT
          1 AAGATTCCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAT

                  *            *                           ** 
       1424 AAGATTTCTTTCCATTTATAAGTTCAAGATCAAAATTCGCTTTTCAAGGT
          1 AAGATTCCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAT

                  * *     *  *     *                        
       1474 AAGATTGCATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
          1 AAGATTCCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAA

       1522 GGGCATTTAA


Statistics
Matches: 86,  Mismatches: 12, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  50   86  1.00

ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37


Consensus pattern (50 bp):   
AAGATTCCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
Done.