Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001006.1 Corchorus olitorius cultivar O-4 contig01006, 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, 755

Length: 1259
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29


Found at i:76 original size:45 final size:46

Alignment explanation


    Indices: 6--98  Score: 152
    Period size: 45  Copynumber: 2.0  Consensus size: 46

          1 AGTAC

                       *                    *             
          6 GTAGTGAATATTATTTGAATTAGGGACACGTGTCTTTATGTAATGT
          1 GTAGTGAATATCATTTGAATTAGGGACACGTGCCTTTATGTAATGT

                     *                                    
         52 GTAGTGAATGTCATTT-AATTAGGGACACGTGCCTTTATGTAATGT
          1 GTAGTGAATATCATTTGAATTAGGGACACGTGCCTTTATGTAATGT

              
         97 GT
          1 GT

         99 TGCATGAAAT


Statistics
Matches: 44,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  45   30  0.68
  46   14  0.32

ACGTcount: A:0.27, C:0.09, G:0.25, T:0.40


Consensus pattern (46 bp):   
GTAGTGAATATCATTTGAATTAGGGACACGTGCCTTTATGTAATGT

Found at i:781 original size:13 final size:13

Alignment explanation


    Indices: 756--788  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

        746 ACGGAGTTGT

                         
        756 AATTGGA-AGAAA
          1 AATTGGATAGAAA

                         
        768 AATTGGATAGAAA
          1 AATTGGATAGAAA

                    
        781 AATTGGAT
          1 AATTGGAT

        789 CGAATGGGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    7  0.35
  13   13  0.65

ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24


Consensus pattern (13 bp):   
AATTGGATAGAAA
Done.