Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008133.1 Corchorus olitorius cultivar O-4 contig08160, 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, 672

Length: 1121
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40


Found at i:618 original size:105 final size:102

Alignment explanation


    Indices: 478--683  Score: 326
    Period size: 105  Copynumber: 2.0  Consensus size: 102

        468 CTTAAATTTT

                                                *                            
        478 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTGTAAGTA-CT
          1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC-T-T-A-TACCT

                                                *     
        542 ATTTTATTTTTACCATTTTACT-ATTTTAATTAAAATACTTC
         62 ATTTTATTTTTACCATTTTACTAATTTT-ATTAAAAAACTTC

                                                                             
        583 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
          1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT

                    *                           
        648 TATTTTTATCATTTTACTAATTTTATTAAAAAACTT
         66 TATTTTTACCATTTTACTAATTTTATTAAAAAACTT

        684 AGATATATTA


Statistics
Matches: 96,  Mismatches: 3, Indels: 7
        0.91            0.03        0.07

Matches are distributed among these distances:
 101    2  0.02
 102   35  0.36
 103    6  0.06
 104    1  0.01
 105   52  0.54

ACGTcount: A:0.34, C:0.13, G:0.02, T:0.50


Consensus pattern (102 bp):   
TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
TATTTTTACCATTTTACTAATTTTATTAAAAAACTTC

Found at i:625 original size:23 final size:26

Alignment explanation


    Indices: 566--625  Score: 63
    Period size: 23  Copynumber: 2.4  Consensus size: 26

        556 ATTTTACTAT

                                       
        566 TTTAATTAAAATACTTCTATAGTTTTA
          1 TTTAATTAAAATACTTCTATA-TTTTA

            * *  *                    
        593 CTCAACTAAAA-AC-TCTAT-TTTTA
          1 TTTAATTAAAATACTTCTATATTTTA

                      
        616 TTTAATTAAA
          1 TTTAATTAAA

        626 TCTAATATCC


Statistics
Matches: 27,  Mismatches: 6, Indels: 4
        0.73            0.16        0.11

Matches are distributed among these distances:
  23   12  0.44
  25    5  0.19
  26    2  0.07
  27    8  0.30

ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47


Consensus pattern (26 bp):   
TTTAATTAAAATACTTCTATATTTTA

Found at i:657 original size:23 final size:23

Alignment explanation


    Indices: 631--674  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        621 TTAAATCTAA

                *                   
        631 TATCCTTATACCT-ATTTTATTTT
          1 TATCATTATA-CTAATTTTATTTT

                   *             
        654 TATCATTTTACTAATTTTATT
          1 TATCATTATACTAATTTTATT

        675 AAAAAACTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61


Consensus pattern (23 bp):   
TATCATTATACTAATTTTATTTT
Done.