Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006668.1 Corchorus olitorius cultivar O-4 contig06693, 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, 630

Length: 1050
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44


Found at i:401 original size:124 final size:123

Alignment explanation


    Indices: 208--455  Score: 478
    Period size: 124  Copynumber: 2.0  Consensus size: 123

        198 CATTGTTTAA

                   *                                                         
        208 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT

                                                                       
        273 TTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
         66 TTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT

                                                                             
        332 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT

                                                                      
        397 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
         66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

             
        455 A
          1 A

        456 TTTCTTAAAT


Statistics
Matches: 123,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 123   35  0.28
 124   88  0.72

ACGTcount: A:0.39, C:0.10, G:0.02, T:0.50


Consensus pattern (123 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:477 original size:14 final size:13

Alignment explanation


    Indices: 441--479  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        431 TATATATTAG

                         
        441 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
        454 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
        468 AATTTTTTAAAT
          1 AATTTTTTAAAT

        480 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA

Done.