Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024566.1 Corchorus olitorius cultivar O-4 contig24599, 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: 2652
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39


Found at i:350 original size:39 final size:40

Alignment explanation


    Indices: 307--387  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        297 TTACCTAAGA

                                             *      
        307 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        346 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        386 AT
          1 AT

        388 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:2227 original size:58 final size:58

Alignment explanation


    Indices: 2114--2228  Score: 176
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       2104 ATTAATCAAA

                                                          * * *       
       2114 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGATCGAGGCT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCGAGGCT

                *           *            *                           
       2172 TATCGAGTGACATGTTTTTTATTAGATGCCTAAAAAAAGACGTTTTAGAACCGAGGC
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCGAGGC

       2229 ATGATGCTAT


Statistics
Matches: 51,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  58   51  1.00

ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGAACCGAGGCT
Done.