Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018876.1 Corchorus olitorius cultivar O-4 contig18909, 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: 10010
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:8051 original size:23 final size:24

Alignment explanation


    Indices: 8017--8063  Score: 71
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       8007 ATGGTTGAAT

                                     
       8017 GAGAAGAAGAAGATCGAAAA-AACA
          1 GAGAAGAAGAAGATC-AAAACAACA

                                    
       8041 GAGAA-AAGAAGATCAAAACAACA
          1 GAGAAGAAGAAGATCAAAACAACA

       8064 AAAAACATAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  22    4  0.18
  23   13  0.59
  24    5  0.23

ACGTcount: A:0.64, C:0.11, G:0.21, T:0.04


Consensus pattern (24 bp):   
GAGAAGAAGAAGATCAAAACAACA

Found at i:9681 original size:20 final size:19

Alignment explanation


    Indices: 9641--9678  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       9631 TATGAATGAA

                           *   
       9641 AAAATAGCCACGTGGCATT
          1 AAAATAGCCACGTGGAATT

                               
       9660 AAAATAGCCACGTGGAATT
          1 AAAATAGCCACGTGGAATT

       9679 TAATTGAATT


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

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21


Consensus pattern (19 bp):   
AAAATAGCCACGTGGAATT

Found at i:9786 original size:21 final size:21

Alignment explanation


    Indices: 9744--9793  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       9734 ACCGTTTAGC

                            **   
       9744 TTTTCTTTTCCTTTGTTTTTT
          1 TTTTCTTTTCCTTTGTCATTT

                                  
       9765 TTTTCTTTTCCCTTT-TCATTT
          1 TTTTCTTTT-CCTTTGTCATTT

                    
       9786 TTCTTCTT
          1 TT-TTCTT

       9794 CTTCAACCCG


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

Matches are distributed among these distances:
  21   15  0.60
  22   10  0.40

ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76


Consensus pattern (21 bp):   
TTTTCTTTTCCTTTGTCATTT

Found at i:9786 original size:22 final size:21

Alignment explanation


    Indices: 9744--9793  Score: 57
    Period size: 22  Copynumber: 2.3  Consensus size: 21

       9734 ACCGTTTAGC

                            *    
       9744 TTTTCTTTTCCTTTGTTTTTT
          1 TTTTCTTTTCCTTTGTATTTT

                                   
       9765 TTTTCTTTTCCCTTT-TCATTTT
          1 TTTTCTTTT-CCTTTGT-ATTTT

             *     
       9787 TCTTCTT
          1 TTTTCTT

       9794 CTTCAACCCG


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

Matches are distributed among these distances:
  21   10  0.40
  22   15  0.60

ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76


Consensus pattern (21 bp):   
TTTTCTTTTCCTTTGTATTTT
Done.