Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011490.1 Corchorus olitorius cultivar O-4 contig11523, 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: 33701
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--27  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

                                                    
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

         28 AAAAGCATGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:6395 original size:29 final size:29

Alignment explanation


    Indices: 6356--6437  Score: 157
    Period size: 29  Copynumber: 2.9  Consensus size: 29

       6346 GGCTTCAGGC

                                         
       6356 AGATTCCACATCTCACAAACATTTCTCAG
          1 AGATTCCACATCTCACAAACATTTCTCAG

                                         
       6385 AGATTCCACATCTCACAAACATTTCTCAG
          1 AGATTCCACATCTCACAAACATTTCTCAG

                                     
       6414 AGATTCCACATCTCA-AAACATTTC
          1 AGATTCCACATCTCACAAACATTTC

       6438 CTAGAGAAAT


Statistics
Matches: 53,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  28    9  0.17
  29   44  0.83

ACGTcount: A:0.35, C:0.30, G:0.06, T:0.28


Consensus pattern (29 bp):   
AGATTCCACATCTCACAAACATTTCTCAG

Found at i:6750 original size:9 final size:9

Alignment explanation


    Indices: 6736--6761  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       6726 TCAGTCAAGA

                     
       6736 ACAGATCTC
          1 ACAGATCTC

                     
       6745 ACAGATCTC
          1 ACAGATCTC

                    
       6754 ACAGATCT
          1 ACAGATCT

       6762 GATCCAGTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.35, C:0.31, G:0.12, T:0.23


Consensus pattern (9 bp):   
ACAGATCTC

Found at i:13891 original size:20 final size:20

Alignment explanation


    Indices: 13843--13893  Score: 59
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      13833 AGCAATAATC

                                 
      13843 ACAAAGAATAAACAACAACAA
          1 ACAAAGAA-AAACAACAACAA

               *                 
      13864 ACACAGAAAAAGCAAC-ACAA
          1 ACAAAGAAAAA-CAACAACAA

            *         
      13884 TCAAAGAAAA
          1 ACAAAGAAAA

      13894 GGACAAAATG


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  20   15  0.58
  21   11  0.42

ACGTcount: A:0.69, C:0.20, G:0.08, T:0.04


Consensus pattern (20 bp):   
ACAAAGAAAAACAACAACAA
Done.