Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012112.1 Corchorus capsularis cultivar CVL-1 contig12133, 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: 20993
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:12347 original size:18 final size:18

Alignment explanation


    Indices: 12324--12363  Score: 62
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      12314 ATTTTTTCTA

                              
      12324 AAAAAAAAAATTGCGTCG
          1 AAAAAAAAAATTGCGTCG

                     *   *    
      12342 AAAAAAAAATTTGTGTCG
          1 AAAAAAAAAATTGCGTCG

                
      12360 AAAA
          1 AAAA

      12364 TAAATTTAGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20


Consensus pattern (18 bp):   
AAAAAAAAAATTGCGTCG

Found at i:16923 original size:11 final size:11

Alignment explanation


    Indices: 16907--16938  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

      16897 AAAGTTCGTG

                       
      16907 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
      16918 TTTGAAGATAA
          1 TTTGAAGATTA

                      
      16929 TTTGAAGATT
          1 TTTGAAGATT

      16939 TGAAGACAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:16933 original size:22 final size:22

Alignment explanation


    Indices: 16907--16966  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

      16897 AAAGTTCGTG

                               *  
      16907 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGACAA

                                  
      16929 TTTGAAG---ATTTGAAGACAA
          1 TTTGAAGATTATTTGAAGACAA

                           *    
      16948 -TTGAAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

      16967 AGCAAGAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    6  0.19
  19   11  0.34
  22   15  0.47

ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGACAA

Found at i:16941 original size:19 final size:18

Alignment explanation


    Indices: 16917--16954  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      16907 TTTGAAGATT

                     *         
      16917 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAA-TTGAAG

                              
      16936 ATTTGAAGACAATTGAAG
          1 ATTTGAAGACAATTGAAG

             
      16954 A
          1 A

      16955 ATTATTTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (18 bp):   
ATTTGAAGACAATTGAAG
Done.