Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024376.1 Corchorus olitorius cultivar O-4 contig24409, 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, 672

Length: 1120
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35


Found at i:93 original size:31 final size:31

Alignment explanation


    Indices: 41--241  Score: 276
    Period size: 31  Copynumber: 6.5  Consensus size: 31

         31 TACTTTTGTG

                  * *      *               
         41 CACGTGACATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

               **      **                  
         72 CACACGGCGTGATACATGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                                *     *    
        103 CACGTGGCGTGCCACATGTCGCTTTTCGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

              *    *                       
        134 CAAGTGGTGTGCCACATGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                                *          
        165 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                                *          
        196 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
          1 CACGTGGCGTGCCACATGTCACTTTTTGGTA

                    *      
        227 CACGTGGCATGCCAC
          1 CACGTGGCGTGCCAC

        242 GTCGGACACC


Statistics
Matches: 149,  Mismatches: 21, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31  149  1.00

ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31


Consensus pattern (31 bp):   
CACGTGGCGTGCCACATGTCACTTTTTGGTA

Found at i:886 original size:39 final size:40

Alignment explanation


    Indices: 843--923  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        833 ATACCTAAGA

                           *                 *      
        843 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC

                                 *                  
        882 ATTTAATTAATGTAAATATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC

              
        922 AT
          1 AT

        924 AGAAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Done.