Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015772.1 Corchorus olitorius cultivar O-4 contig15805, 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: 1698
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Found at i:726 original size:5 final size:5

Alignment explanation


    Indices: 631--722  Score: 132
    Period size: 5  Copynumber: 18.0  Consensus size: 5

        621 CCCAAGCCAG

                                                                    
        631 GAAAA GAAAA -AAAGA GAAAA GAAAA GAAAA GGAAAA GGAAAA GAAAA
          1 GAAAA GAAAA GAAA-A GAAAA GAAAA GAAAA -GAAAA -GAAAA GAAAA

                                                      *     *    
        678 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA TAAAA TAAAA
          1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA

        723 TAAATAAGGA


Statistics
Matches: 83,  Mismatches: 1, Indels: 6
        0.92            0.01        0.07

Matches are distributed among these distances:
   4    3  0.04
   5   66  0.80
   6   14  0.17

ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02


Consensus pattern (5 bp):   
GAAAA

Found at i:763 original size:19 final size:19

Alignment explanation


    Indices: 719--765  Score: 58
    Period size: 19  Copynumber: 2.5  Consensus size: 19

        709 AAAATAAAAT

                *            * 
        719 AAAATAAATAAGGAAATTA
          1 AAAAGAAATAAGGAAATAA

             **                
        738 AGGAGAAATAAGGAAATAA
          1 AAAAGAAATAAGGAAATAA

                     
        757 AAAAGAAAT
          1 AAAAGAAAT

        766 TTTAAAATAT


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15


Consensus pattern (19 bp):   
AAAAGAAATAAGGAAATAA
Done.