Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018559.1 Corchorus olitorius cultivar O-4 contig18592, 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: 12976
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30


Found at i:2475 original size:23 final size:23

Alignment explanation


    Indices: 2447--2491  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2437 TCCAACTTCC

                                   
       2447 AAAATTCAAATTTTGAAATTTCA
          1 AAAATTCAAATTTTGAAATTTCA

                   *              
       2470 AAAATTCTAATTTTGAAATTTC
          1 AAAATTCAAATTTTGAAATTTC

       2492 GCACCAAAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42


Consensus pattern (23 bp):   
AAAATTCAAATTTTGAAATTTCA

Found at i:5811 original size:12 final size:12

Alignment explanation


    Indices: 5794--5820  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       5784 GGAATGTGAG

                        
       5794 TTTTCTTTGTAA
          1 TTTTCTTTGTAA

                        
       5806 TTTTCTTTGTAA
          1 TTTTCTTTGTAA

               
       5818 TTT
          1 TTT

       5821 ATTTGTTTGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70


Consensus pattern (12 bp):   
TTTTCTTTGTAA

Found at i:10459 original size:23 final size:23

Alignment explanation


    Indices: 10433--10481  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      10423 AGAAATTTAG

                      *   * *      
      10433 CTTTATAGAGTTGATTGTTTAAA
          1 CTTTATAGAGATGACTATTTAAA

                                   
      10456 CTTTATAGAGATGACTATTTAAA
          1 CTTTATAGAGATGACTATTTAAA

               
      10479 CTT
          1 CTT

      10482 AGAAATTTAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45


Consensus pattern (23 bp):   
CTTTATAGAGATGACTATTTAAA

Found at i:10919 original size:13 final size:13

Alignment explanation


    Indices: 10901--10925  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10891 GAGTAAAAGA

                         
      10901 CCCCCCCCCCCTC
          1 CCCCCCCCCCCTC

                        
      10914 CCCCCCCCCCCT
          1 CCCCCCCCCCCT

      10926 AAAAAAAAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.00, C:0.92, G:0.00, T:0.08


Consensus pattern (13 bp):   
CCCCCCCCCCCTC

Found at i:12723 original size:11 final size:11

Alignment explanation


    Indices: 12709--12742  Score: 68
    Period size: 11  Copynumber: 3.1  Consensus size: 11

      12699 TAAAGGAAAA

                       
      12709 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
      12720 AGCTAGGAAGG
          1 AGCTAGGAAGG

                       
      12731 AGCTAGGAAGG
          1 AGCTAGGAAGG

             
      12742 A
          1 A

      12743 CCCTACTCCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.38, C:0.09, G:0.44, T:0.09


Consensus pattern (11 bp):   
AGCTAGGAAGG
Done.