Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015304.1 Corchorus capsularis cultivar CVL-1 contig15325, 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: 8160
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:6230 original size:41 final size:40

Alignment explanation


    Indices: 6135--6271  Score: 152
    Period size: 41  Copynumber: 3.4  Consensus size: 40

       6125 CAAGGTGATA

                    *       *         **   *         
       6135 AGTGTCAACAGTAATTATAATTTACTGGAGTAAC-ACTTCT
          1 AGTGTCAAAAGTAATTTTAATTTAC-CAAGTGACAACTTCT

                     *                             * 
       6175 AGTGTCAAAGGTAATTTTAATTTACCAAAGTGACAACTTTT
          1 AGTGTCAAAAGTAATTTTAATTTACC-AAGTGACAACTTCT

                                                     
       6216 AGTGTCAAAAGTAATTTTAATTTACCAAGATGACAACTTCT
          1 AGTGTCAAAAGTAATTTTAATTTACCAAG-TGACAACTTCT

                      *     
       6257 -GATGTCAAAGGTAAT
          1 AG-TGTCAAAAGTAAT

       6272 CTTCAATATT


Statistics
Matches: 83,  Mismatches: 10, Indels: 7
        0.83            0.10        0.07

Matches are distributed among these distances:
  40   31  0.37
  41   52  0.63

ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34


Consensus pattern (40 bp):   
AGTGTCAAAAGTAATTTTAATTTACCAAGTGACAACTTCT

Found at i:7274 original size:20 final size:21

Alignment explanation


    Indices: 7238--7276  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       7228 CGCGCGTGAG

                                 
       7238 AGGCCATGTTTTAAGCCACAT
          1 AGGCCATGTTTTAAGCCACAT

                        *      
       7259 AGGCCAT-TTTTTAGCCAC
          1 AGGCCATGTTTTAAGCCAC

       7277 GTGTAATTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   10  0.59
  21    7  0.41

ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31


Consensus pattern (21 bp):   
AGGCCATGTTTTAAGCCACAT
Done.