Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009569.1 Corchorus olitorius cultivar O-4 contig09601, 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: 6999
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Found at i:3670 original size:53 final size:54

Alignment explanation


    Indices: 3564--3676  Score: 192
    Period size: 53  Copynumber: 2.1  Consensus size: 54

       3554 AATGAAGTAC

                                                                   
       3564 TATTTCACCAAAAAAGAAAATGAAGTATACTAGCTAAATATATGTTCATATTATA
          1 TATTTCACCAAAAAAGAAAATGAAG-ATACTAGCTAAATATATGTTCATATTATA

                              *             *                     
       3619 TATTTCACCAAAAAAGAATATGAAG-TACTAGTTAAATATATGTTCATATTATA
          1 TATTTCACCAAAAAAGAAAATGAAGATACTAGCTAAATATATGTTCATATTATA

                 
       3672 TATTT
          1 TATTT

       3677 TAATTATATT


Statistics
Matches: 56,  Mismatches: 2, Indels: 2
        0.93            0.03        0.03

Matches are distributed among these distances:
  53   32  0.57
  55   24  0.43

ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36


Consensus pattern (54 bp):   
TATTTCACCAAAAAAGAAAATGAAGATACTAGCTAAATATATGTTCATATTATA

Found at i:5389 original size:19 final size:19

Alignment explanation


    Indices: 5354--5405  Score: 61
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       5344 AGAAAATTTC

                                  
       5354 CATTACACTCAAAATT-GATAT
          1 CATTACAC-C-AAATTGGA-AT

                               
       5375 CATTACACCAAATTGGAAT
          1 CATTACACCAAATTGGAAT

            *           
       5394 TATTACACCAAA
          1 CATTACACCAAA

       5406 CAGTTATTAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  19   18  0.62
  20    3  0.10
  21    8  0.28

ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29


Consensus pattern (19 bp):   
CATTACACCAAATTGGAAT
Done.