Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007026.1 Corchorus olitorius cultivar O-4 contig07051, 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, 881

Length: 1469
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31


Found at i:692 original size:17 final size:17

Alignment explanation


    Indices: 667--732  Score: 87
    Period size: 17  Copynumber: 3.9  Consensus size: 17

        657 AGGCCAGGCG

                *        * * 
        667 GGCCTAGGCCAGCACGT
          1 GGCCCAGGCCAGCGCAT

                            *
        684 GGCCCAGGCCAGCGCAC
          1 GGCCCAGGCCAGCGCAT

                             
        701 GGCCCAGGCCAGCGCAT
          1 GGCCCAGGCCAGCGCAT

                *          
        718 GGCCTAGGCCAGCGC
          1 GGCCCAGGCCAGCGC

        733 GTGGGCCTCA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   43  1.00

ACGTcount: A:0.17, C:0.41, G:0.36, T:0.06


Consensus pattern (17 bp):   
GGCCCAGGCCAGCGCAT

Found at i:713 original size:34 final size:34

Alignment explanation


    Indices: 667--732  Score: 96
    Period size: 34  Copynumber: 1.9  Consensus size: 34

        657 AGGCCAGGCG

                *          *                  
        667 GGCCTAGGCCAGCACGTGGCCCAGGCCAGCGCAC
          1 GGCCCAGGCCAGCACATGGCCCAGGCCAGCGCAC

                         *       *          
        701 GGCCCAGGCCAGCGCATGGCCTAGGCCAGCGC
          1 GGCCCAGGCCAGCACATGGCCCAGGCCAGCGC

        733 GTGGGCCTCA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   28  1.00

ACGTcount: A:0.17, C:0.41, G:0.36, T:0.06


Consensus pattern (34 bp):   
GGCCCAGGCCAGCACATGGCCCAGGCCAGCGCAC

Found at i:858 original size:5 final size:5

Alignment explanation


    Indices: 850--894  Score: 58
    Period size: 5  Copynumber: 9.0  Consensus size: 5

        840 AGAAAGAAAT

                                                                   
        850 TAAAA TAAAA T--AA TAATAA TAATAA TAAAA TAAAA TAAAA TAAAA
          1 TAAAA TAAAA TAAAA TAA-AA TAA-AA TAAAA TAAAA TAAAA TAAAA

        895 AGAATGAATT


Statistics
Matches: 37,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   3    3  0.08
   5   23  0.62
   6   11  0.30

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (5 bp):   
TAAAA

Found at i:866 original size:3 final size:3

Alignment explanation


    Indices: 853--892  Score: 52
    Period size: 3  Copynumber: 14.7  Consensus size: 3

        843 AAGAAATTAA

                                                                      
        853 AAT AA- AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AA- AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

        893 AAAGAATGAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
   2    8  0.24
   3   25  0.76

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (3 bp):   
AAT

Done.