Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017708.1 Corchorus olitorius cultivar O-4 contig17741, 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: 31450
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:7674 original size:19 final size:19

Alignment explanation


    Indices: 7654--7690  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       7644 AATTAATTAT

                               
       7654 TTTA-ATATTATATTTTTA
          1 TTTATATATTATATTTTTA

                               
       7672 TTTATATATTATATTTTTA
          1 TTTATATATTATATTTTTA

       7691 CTTAAAAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (19 bp):   
TTTATATATTATATTTTTA

Found at i:7701 original size:19 final size:19

Alignment explanation


    Indices: 7660--7701  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       7650 TTATTTTAAT

                        *   * *
       7660 ATTATATTTTTATTTATAT
          1 ATTATATTTTTACTTAAAA

                               
       7679 ATTATATTTTTACTTAAAA
          1 ATTATATTTTTACTTAAAA

                
       7698 ATTA
          1 ATTA

       7702 CTCCTAATTA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (19 bp):   
ATTATATTTTTACTTAAAA

Found at i:14123 original size:12 final size:12

Alignment explanation


    Indices: 14108--14133  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      14098 AATAAAAAGT

                        
      14108 ACAATAGTACAA
          1 ACAATAGTACAA

                        
      14120 ACAATAGTACAA
          1 ACAATAGTACAA

              
      14132 AC
          1 AC

      14134 CTATCCATAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15


Consensus pattern (12 bp):   
ACAATAGTACAA

Found at i:15741 original size:21 final size:22

Alignment explanation


    Indices: 15705--15745  Score: 66
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      15695 TATTAGAGGA

                                  
      15705 TAAAAGGAAATTAAAAAAAATC
          1 TAAAAGGAAATTAAAAAAAATC

                     *          
      15727 TAAAAGG-ATTTAAAAAAAA
          1 TAAAAGGAAATTAAAAAAAA

      15746 AACACAGGAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20


Consensus pattern (22 bp):   
TAAAAGGAAATTAAAAAAAATC

Found at i:15819 original size:28 final size:29

Alignment explanation


    Indices: 15788--15842  Score: 94
    Period size: 28  Copynumber: 1.9  Consensus size: 29

      15778 TATATATATA

                 *                       
      15788 TTTTTTAATCCTTATAGA-TTTTCTTTTC
          1 TTTTTAAATCCTTATAGATTTTTCTTTTC

                                       
      15816 TTTTTAAATCCTTATAGATTTTTCTTT
          1 TTTTTAAATCCTTATAGATTTTTCTTT

      15843 AATTTCCTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28   17  0.68
  29    8  0.32

ACGTcount: A:0.20, C:0.13, G:0.04, T:0.64


Consensus pattern (29 bp):   
TTTTTAAATCCTTATAGATTTTTCTTTTC

Done.