Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019595.1 Corchorus olitorius cultivar O-4 contig19628, 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: 3188
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37


Found at i:183 original size:25 final size:24

Alignment explanation


    Indices: 149--195  Score: 76
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        139 ACGTTTGCAC

                                     
        149 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                 *                
        174 AAATATCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        196 TGTAAGTATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    6  0.29
  25   15  0.71

ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:240 original size:39 final size:40

Alignment explanation


    Indices: 186--266  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        176 ATATCTAAGA

                                             *      
        186 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        225 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        265 AT
          1 AT

        267 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.