Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017248.1 Corchorus olitorius cultivar O-4 contig17281, 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: 4493
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38


Found at i:358 original size:39 final size:40

Alignment explanation


    Indices: 304--384  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        294 ATACCTAAGA

                                             *      
        304 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        343 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        383 AT
          1 AT

        385 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

Found at i:619 original size:6 final size:6

Alignment explanation


    Indices: 601--635  Score: 61
    Period size: 6  Copynumber: 5.7  Consensus size: 6

        591 GTTTAGACTT

                                                    
        601 ATATAG TATATAG ATATAG ATATAG ATATAG ATAT
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATAT

        636 TAAACTTAAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   6   22  0.79
   7    6  0.21

ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37


Consensus pattern (6 bp):   
ATATAG

Found at i:3617 original size:6 final size:6

Alignment explanation


    Indices: 3608--3637  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       3598 GATATATCTA

                                              
       3608 TATATC TATATC TATATC TATATAC TATAT
          1 TATATC TATATC TATATC TATAT-C TATAT

       3638 AAGTCTAAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50


Consensus pattern (6 bp):   
TATATC

Done.