Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017812.1 Corchorus olitorius cultivar O-4 contig17845, 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: 2072
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:659 original size:18 final size:18

Alignment explanation


    Indices: 599--660  Score: 54
    Period size: 18  Copynumber: 3.3  Consensus size: 18

        589 TGTGCAGGCC

                               
        599 CAGGCACGCGGGCCTAGCG
          1 CAGGCACGCGGGCC-AGCG

                    *   *       
        618 CAGGCCCAGGCGTGCCAG-G
          1 CAGG--CACGCGGGCCAGCG

                  *            
        637 CCAGGCGCGCGGGCCAGCG
          1 -CAGGCACGCGGGCCAGCG

                 
        656 CAGGC
          1 CAGGC

        661 CCAGTGGCCT


Statistics
Matches: 34,  Mismatches: 5, Indels: 9
        0.71            0.10        0.19

Matches are distributed among these distances:
  18   14  0.41
  19    6  0.18
  20    6  0.18
  21    8  0.24

ACGTcount: A:0.15, C:0.39, G:0.44, T:0.03


Consensus pattern (18 bp):   
CAGGCACGCGGGCCAGCG

Found at i:722 original size:10 final size:10

Alignment explanation


    Indices: 707--736  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

        697 CCAACGTTTT

                      
        707 AAAAAAAGAA
          1 AAAAAAAGAA

                      
        717 AAAAAAAGAA
          1 AAAAAAAGAA

               *      
        727 AAAGAAAGAA
          1 AAAAAAAGAA

        737 TTGAGTGGGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (10 bp):   
AAAAAAAGAA

Found at i:803 original size:19 final size:20

Alignment explanation


    Indices: 770--809  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        760 AGAAAAGAAG

                                
        770 AAAGAAATAAAAAGAAATAA
          1 AAAGAAATAAAAAGAAATAA

                                
        790 AAAGAAAT-AAAAGAAATAA
          1 AAAGAAATAAAAAGAAATAA

             
        809 A
          1 A

        810 GAAAATAAGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10


Consensus pattern (20 bp):   
AAAGAAATAAAAAGAAATAA

Found at i:817 original size:9 final size:10

Alignment explanation


    Indices: 770--809  Score: 73
    Period size: 10  Copynumber: 4.1  Consensus size: 10

        760 AGAAAAGAAG

                      
        770 AAAGAAATAA
          1 AAAGAAATAA

                      
        780 AAAGAAATAA
          1 AAAGAAATAA

                      
        790 AAAGAAAT-A
          1 AAAGAAATAA

                      
        799 AAAGAAATAA
          1 AAAGAAATAA

             
        809 A
          1 A

        810 GAAAATAAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   9    9  0.31
  10   20  0.69

ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10


Consensus pattern (10 bp):   
AAAGAAATAA
Done.