Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018267.1 Corchorus olitorius cultivar O-4 contig18300, 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: 5351
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33


Found at i:131 original size:39 final size:40

Alignment explanation


    Indices: 72--152  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

         62 ATACCTAAAA

                           *                 *      
         72 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC

                                 *                  
        111 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC

              
        151 AT
          1 AT

        153 AGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC

Found at i:569 original size:19 final size:20

Alignment explanation


    Indices: 532--574  Score: 63
    Period size: 19  Copynumber: 2.2  Consensus size: 20

        522 TTCTCATAAT

                                
        532 TATTTTTTATTTGTAATTTA
          1 TATTTTTTATTTGTAATTTA

                                 
        552 TATTTATTTA-TT-TAATTTA
          1 TATTT-TTTATTTGTAATTTA

                
        571 TATT
          1 TATT

        575 ACATAAAAAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  19   11  0.50
  20    7  0.32
  21    4  0.18

ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70


Consensus pattern (20 bp):   
TATTTTTTATTTGTAATTTA
Done.