Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024301.1 Corchorus olitorius cultivar O-4 contig24334, 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: 5958
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38


Found at i:5691 original size:16 final size:16

Alignment explanation


    Indices: 5661--5699  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       5651 CCATTAGTAG

                      *      
       5661 ATTTTATTACTAATTTA
          1 ATTTT-TTACCAATTTA

                           *
       5678 ATTTTTTACCAATTTT
          1 ATTTTTTACCAATTTA

                  
       5694 ATTTTT
          1 ATTTTT

       5700 ATGTAGCATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  16   15  0.75
  17    5  0.25

ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64


Consensus pattern (16 bp):   
ATTTTTTACCAATTTA

Found at i:5889 original size:78 final size:78

Alignment explanation


    Indices: 5801--5956  Score: 303
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       5791 GATCTAGTAC

                                                *                            
       5801 TGATTTAGTTAATTAATATGTAAATTAATTATAATTGCTTTAATTTGACCAAGTTTCAAATCAGT
          1 TGATTTAGTTAATTAATATGTAAATTAATTATAATTACTTTAATTTGACCAAGTTTCAAATCAGT

                         
       5866 TGATCTCAAAAAA
         66 TGATCTCAAAAAA

                                                                             
       5879 TGATTTAGTTAATTAATATGTAAATTAATTATAATTACTTTAATTTGACCAAGTTTCAAATCAGT
          1 TGATTTAGTTAATTAATATGTAAATTAATTATAATTACTTTAATTTGACCAAGTTTCAAATCAGT

                         
       5944 TGATCTCAAAAAA
         66 TGATCTCAAAAAA

       5957 AA


Statistics
Matches: 77,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  78   77  1.00

ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41


Consensus pattern (78 bp):   
TGATTTAGTTAATTAATATGTAAATTAATTATAATTACTTTAATTTGACCAAGTTTCAAATCAGT
TGATCTCAAAAAA
Done.