Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013288.1 Corchorus olitorius cultivar O-4 contig13321, 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: 14748
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1080 original size:29 final size:29

Alignment explanation


    Indices: 1024--1081  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       1014 CTTGAAATAA

                               * *       
       1024 ATCTTCAATGGTCTTCAAGTCTCCAATTT
          1 ATCTTCAATGGTCTTCAAGACACCAATTT

                                    *     
       1053 ATCTTCAAATGGTCTTCAA-ACACGAATTT
          1 ATCTTC-AATGGTCTTCAAGACACCAATTT

       1082 CGCATCTCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29   13  0.52
  30   12  0.48

ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38


Consensus pattern (29 bp):   
ATCTTCAATGGTCTTCAAGACACCAATTT

Found at i:5778 original size:31 final size:32

Alignment explanation


    Indices: 5726--5815  Score: 92
    Period size: 31  Copynumber: 2.8  Consensus size: 32

       5716 ATTTCAGCGG

                       *  * *         *     
       5726 TTTGGTCCGACATGGCCTTGCCACATTGCA-T
          1 TTTGGTCCGACGTGACATTGCCACATGGCATT

                      *             *        
       5757 TTTGGTCCGATGTGACATTGCCACGTGGCATTT
          1 TTTGGTCCGACGTGACATTGCCACATGGCA-TT

                          *  *        
       5790 TTTGGTCCGACGTGGCAATGCCACAT
          1 TTTGGTCCGACGTGACATTGCCACAT

       5816 CAGGAGCATG


Statistics
Matches: 47,  Mismatches: 10, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  31   24  0.51
  33   23  0.49

ACGTcount: A:0.17, C:0.26, G:0.26, T:0.32


Consensus pattern (32 bp):   
TTTGGTCCGACGTGACATTGCCACATGGCATT

Found at i:10697 original size:19 final size:18

Alignment explanation


    Indices: 10664--10699  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10654 TGGAAATAAT

                              
      10664 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      10682 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      10700 TAGGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:11590 original size:18 final size:18

Alignment explanation


    Indices: 11555--11589  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      11545 CTCCTCTATC

                     *        
      11555 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
      11573 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

      11590 TTTAATTACC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT
Done.