Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019397.1 Corchorus olitorius cultivar O-4 contig19430, 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: 40307
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:802 original size:21 final size:20

Alignment explanation


    Indices: 758--807  Score: 61
    Period size: 21  Copynumber: 2.6  Consensus size: 20

        748 GAATTATCCC

                       *        
        758 GAAAGAAAA-ATAAAAAAAG
          1 GAAAGAAAAGAAAAAAAAAG

                                 
        777 G--AGAAAAGAAAAGAAAAAG
          1 GAAAGAAAAGAAAA-AAAAAG

                        
        796 GAAAGAAAAGAA
          1 GAAAGAAAAGAA

        808 TAACGTTGGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17    6  0.23
  18    3  0.12
  19    8  0.31
  21    9  0.35

ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02


Consensus pattern (20 bp):   
GAAAGAAAAGAAAAAAAAAG

Found at i:23802 original size:60 final size:61

Alignment explanation


    Indices: 23685--23840  Score: 187
    Period size: 60  Copynumber: 2.6  Consensus size: 61

      23675 GGCTTATTTC

                                                   *  * *   *            
      23685 AGCATTTTCGCATACGTTA-GATTCCTATTTAACCAAATTAATAGCATGGATCCTAAATTG
          1 AGCATTTTCGCATACGTTAGGATTCCTATTTAACCAAATAAAAAACATAGATCCTAAATTG

                                     *        *           *               
      23745 AGCATTTTCGCATACGTTAGGA-TCTTATTTAACTAAATAAAAAACGTAGA-CCATAAATTG
          1 AGCATTTTCGCATACGTTAGGATTCCTATTTAACCAAATAAAAAACATAGATCC-TAAATTG

                          *                       
      23805 AGCATTTTCGCATATGTTAGGGA--CCTATTTAACCAA
          1 AGCATTTTCGCATACGTTA-GGATTCCTATTTAACCAA

      23841 TTTGCCATGC


Statistics
Matches: 83,  Mismatches: 10, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  59    2  0.02
  60   76  0.92
  61    5  0.06

ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33


Consensus pattern (61 bp):   
AGCATTTTCGCATACGTTAGGATTCCTATTTAACCAAATAAAAAACATAGATCCTAAATTG
Done.