Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009898.1 Corchorus olitorius cultivar O-4 contig09930, 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: 2847
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38


Found at i:2389 original size:80 final size:80

Alignment explanation


    Indices: 2252--2400  Score: 246
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       2242 CAGTGATTAT

                                        *             *                      
       2252 AGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTTAATATCTTTATAATTACTTTAT
          1 AGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATCTTTATAATTACTTTAT

                           
       2317 TTTTTCAAAATATAG
         66 TTTTTCAAAATATAG

                                             *                          *    
       2332 AGTTTTATTCTACTAAAAAACTCTATTTTCATTTAATTAAATTCAATAT-TTTATAATTATTTTA
          1 AGTTTTATTCTACT-AAAAACTCTATTTTCATTCAATTAAATTCAATATCTTTATAATTACTTTA

                 
       2396 TTTTT
         65 TTTTT

       2401 ACCATTTTAA


Statistics
Matches: 64,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  80   33  0.52
  81   31  0.48

ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53


Consensus pattern (80 bp):   
AGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATCTTTATAATTACTTTAT
TTTTTCAAAATATAG

Found at i:2823 original size:26 final size:26

Alignment explanation


    Indices: 2769--2819  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       2759 ATATATTAGA

                        *             
       2769 ATTTTTAAAATATATTCTCTTACAAT
          1 ATTTTTAAAATAAATTCTCTTACAAT

                                       
       2795 ATTTTTAGAAATAAATT-T-TTACAAT
          1 ATTTTTA-AAATAAATTCTCTTACAAT

       2820 TATTCTACTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  25    7  0.30
  26    8  0.35
  27    8  0.35

ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49


Consensus pattern (26 bp):   
ATTTTTAAAATAAATTCTCTTACAAT
Done.