Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005655.1 Corchorus capsularis cultivar CVL-1 contig05673, 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: 2146
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29


Found at i:655 original size:36 final size:36

Alignment explanation


    Indices: 607--797  Score: 233
    Period size: 36  Copynumber: 5.4  Consensus size: 36

        597 CCTACAAGGT

                   *     *                      
        607 TGGCTTAGTTTCAGGGAAATTAGGTAAAGAAAAGAC
          1 TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

                           *      *      *      
        643 TGGCTTAATTTCAAGAAAATTAAGTAAA-CAAAGAC
          1 TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

             *     *     *     *                
        678 TTGCTTAGTTTCACGGAAACTAGGTAAAGAAAAGAC
          1 TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

                                     *    *     
        714 TGGCTTAATTTCAAGGAAATTAGGTGAAGATAAGAC
          1 TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

                                  *        * *  
        750 TGGCTTAATTTCAAGGAAATTAAGTAAA-AAGACAC
          1 TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

            *            
        785 AGGCTTAATTTCA
          1 TGGCTTAATTTCA

        798 GAAAAGGAAA


Statistics
Matches: 130,  Mismatches: 24, Indels: 3
        0.83            0.15        0.02

Matches are distributed among these distances:
  35   44  0.34
  36   86  0.66

ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27


Consensus pattern (36 bp):   
TGGCTTAATTTCAAGGAAATTAGGTAAAGAAAAGAC

Found at i:725 original size:71 final size:72

Alignment explanation


    Indices: 607--802  Score: 254
    Period size: 71  Copynumber: 2.8  Consensus size: 72

        597 CCTACAAGGT

                         *                                                   
        607 TGGCTTAGTTTCAGGGAAATTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAATTAAGTAAAC
          1 TGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAATTAAGTAAAC

                   
        672 A-AAGAC
         66 ATAAGAC

             *           *     *                               *      *  *  *
        678 TTGCTTAGTTTCACGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTGAAG
          1 TGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAATTAAGTAAAC

                   
        743 ATAAGAC
         66 ATAAGAC

                   *              *        * *  *                  
        750 TGGCTTAATTTCAAGGAAATTAAGTAAA-AAGACACAGGCTTAATTTC-AGAAAA
          1 TGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAA

        803 GGAAATTAAG


Statistics
Matches: 108,  Mismatches: 16, Indels: 3
        0.85            0.13        0.02

Matches are distributed among these distances:
  70    5  0.05
  71   75  0.69
  72   28  0.26

ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26


Consensus pattern (72 bp):   
TGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAAGACTGGCTTAATTTCAAGAAAATTAAGTAAAC
ATAAGAC

Found at i:853 original size:36 final size:36

Alignment explanation


    Indices: 801--906  Score: 162
    Period size: 36  Copynumber: 2.9  Consensus size: 36

        791 AATTTCAGAA

                *                               
        801 AAGGAAATTAAGTAGAGTCAATAAAAGACTTAATTC
          1 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC

                                                
        837 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
          1 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC

             *                                  
        873 AGGGTAATTAAGT-GAAGTCAAT-AAAGAACTTAAT
          1 AAGGTAATTAAGTAG-AGTCAATAAAAG-ACTTAAT

        907 CTAAAAAGAG


Statistics
Matches: 66,  Mismatches: 2, Indels: 4
        0.92            0.03        0.06

Matches are distributed among these distances:
  35    5  0.08
  36   61  0.92

ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26


Consensus pattern (36 bp):   
AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
Done.