Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023575.1 Corchorus olitorius cultivar O-4 contig23608, 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: 19464
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31


Found at i:6147 original size:46 final size:46

Alignment explanation


    Indices: 6080--6174  Score: 165
    Period size: 46  Copynumber: 2.1  Consensus size: 46

       6070 GGGTGAATTT

                                                          
       6080 TTGTTGTTAAGATTAGTTTTATTAGACGAACAAAACTGATTTGAAA
          1 TTGTTGTTAAGATTAGTTTTATTAGACGAACAAAACTGATTTGAAA

                                           *               
       6126 TTGTTGTTGAA-ATTAGTTTTATTAGACGAATAAAACTGATTTGAAA
          1 TTGTTGTT-AAGATTAGTTTTATTAGACGAACAAAACTGATTTGAAA

               
       6172 TTG
          1 TTG

       6175 CTTTTGAGCT


Statistics
Matches: 47,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  46   45  0.96
  47    2  0.04

ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41


Consensus pattern (46 bp):   
TTGTTGTTAAGATTAGTTTTATTAGACGAACAAAACTGATTTGAAA

Found at i:6560 original size:29 final size:30

Alignment explanation


    Indices: 6511--6607  Score: 97
    Period size: 29  Copynumber: 3.2  Consensus size: 30

       6501 AAGTACCTAA

                     **                   
       6511 TTAGTCCCTGTACTATTGAAAAAAATCAAT
          1 TTAGTCCCTCAACTATTGAAAAAAATCAAT

                      * *        ****     
       6541 TTAGTCCCTCCATTA-TGAAATGTGTCAAT
          1 TTAGTCCCTCAACTATTGAAAAAAATCAAT

                                    *      
       6570 TTAGTCCCTCAACTATTGAAAAGAGATCAAT
          1 TTAGTCCCTCAACTATTGAAAA-AAATCAAT

                   
       6601 TTAGTCC
          1 TTAGTCC

       6608 GATTTGAAAC


Statistics
Matches: 52,  Mismatches: 13, Indels: 3
        0.76            0.19        0.04

Matches are distributed among these distances:
  29   23  0.44
  30   17  0.33
  31   12  0.23

ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34


Consensus pattern (30 bp):   
TTAGTCCCTCAACTATTGAAAAAAATCAAT

Found at i:9542 original size:25 final size:25

Alignment explanation


    Indices: 9514--9587  Score: 130
    Period size: 25  Copynumber: 3.0  Consensus size: 25

       9504 CTCAACAATC

                        *            
       9514 TTGAGCACTCTCACTCGATCTCTAT
          1 TTGAGCACTCTCGCTCGATCTCTAT

                             *       
       9539 TTGAGCACTCTCGCTCGGTCTCTAT
          1 TTGAGCACTCTCGCTCGATCTCTAT

                                    
       9564 TTGAGCACTCTCGCTCGATCTCTA
          1 TTGAGCACTCTCGCTCGATCTCTA

       9588 CAAACCAATC


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  25   46  1.00

ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35


Consensus pattern (25 bp):   
TTGAGCACTCTCGCTCGATCTCTAT

Found at i:10041 original size:12 final size:12

Alignment explanation


    Indices: 10024--10072  Score: 53
    Period size: 12  Copynumber: 4.1  Consensus size: 12

      10014 CTTCTTTTTT

                      * 
      10024 CCACGACCACGA
          1 CCACGACCACCA

                        
      10036 CCACGACCACCA
          1 CCACGACCACCA

               * *  * * 
      10048 CCATGGCCTCTA
          1 CCACGACCACCA

                        
      10060 CCACGACCACCA
          1 CCACGACCACCA

             
      10072 C
          1 C

      10073 TGCCACGGCC


Statistics
Matches: 28,  Mismatches: 9, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  12   28  1.00

ACGTcount: A:0.29, C:0.53, G:0.12, T:0.06


Consensus pattern (12 bp):   
CCACGACCACCA
Done.