Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018910.1 Corchorus olitorius cultivar O-4 contig18943, 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: 21335
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:620 original size:23 final size:23

Alignment explanation


    Indices: 577--620  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        567 TAAGTTTTTT

                            *      
        577 AATAAAATTAGTAGAATGATAAA
          1 AATAAAATTAGTAGAAGGATAAA

                          *       
        600 AATAAAA-TAGGTATAAGGATA
          1 AATAAAATTA-GTAGAAGGATA

        621 TTAGATTTAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25


Consensus pattern (23 bp):   
AATAAAATTAGTAGAAGGATAAA

Found at i:15859 original size:19 final size:19

Alignment explanation


    Indices: 15839--15875  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      15829 AATTAATTAT

                               
      15839 TTTA-ATATTAAATTTTTA
          1 TTTATATATTAAATTTTTA

                       *       
      15857 TTTATATATTATATTTTTA
          1 TTTATATATTAAATTTTTA

      15876 CTTAAAAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (19 bp):   
TTTATATATTAAATTTTTA

Found at i:20437 original size:2 final size:2

Alignment explanation


    Indices: 20430--20454  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      20420 AGTAGGTTTA

                                                 
      20430 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      20455 CTAGTTAAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.