Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017804.1 Corchorus olitorius cultivar O-4 contig17837, 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: 5922
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Found at i:834 original size:22 final size:22

Alignment explanation


    Indices: 747--836  Score: 60
    Period size: 22  Copynumber: 4.1  Consensus size: 22

        737 GAAATACTAT

                                  
        747 GACAAACCTTGTAAATA-CTGC
          1 GACAAACCTTGTAAATATCTGC

                *  *           *   
        768 GACATACATCTG-AAATATTTGC
          1 GACAAACCT-TGTAAATATCTGC

                *   * *     * *    
        790 GACATA-CATATAATACAACTGC
          1 GACAAACCTTGTAA-ATATCTGC

                              *   
        812 GACAAACCTTGTAAATATTTGC
          1 GACAAACCTTGTAAATATCTGC

               
        834 GAC
          1 GAC

        837 GGGTTGCGAC


Statistics
Matches: 49,  Mismatches: 15, Indels: 9
        0.67            0.21        0.12

Matches are distributed among these distances:
  20    1  0.02
  21   14  0.29
  22   29  0.59
  23    5  0.10

ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27


Consensus pattern (22 bp):   
GACAAACCTTGTAAATATCTGC

Found at i:2954 original size:26 final size:26

Alignment explanation


    Indices: 2915--2973  Score: 95
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       2905 GTTGTTGTTA

                                  *   
       2915 TTCAC-TT-CTTTAGGTATAAATGAG
          1 TTCACTTTACTTTAGGTATAAAAGAG

                                      
       2939 TTCACTTTACTTTAGGTATAAAAGAG
          1 TTCACTTTACTTTAGGTATAAAAGAG

                     
       2965 TTCACTTTA
          1 TTCACTTTA

       2974 TTGCTCACAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  24    5  0.16
  25    2  0.06
  26   25  0.78

ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42


Consensus pattern (26 bp):   
TTCACTTTACTTTAGGTATAAAAGAG
Done.