Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003809.1 Corchorus capsularis cultivar CVL-1 contig03817, 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, 708

Length: 1180
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27


Found at i:776 original size:37 final size:37

Alignment explanation


    Indices: 707--876  Score: 180
    Period size: 37  Copynumber: 4.6  Consensus size: 37

        697 AACAACAAAA

                *   *       *     *            *  
        707 AGAGTCTCAGGCTCAAATCCAAGC-AATCATCAACCAC
          1 AGAGCCTCGGGCTCAAGTCCAAACAAAT-ATCAACAAC

            *                       *        *  *
        744 TGAGCCTCGGGCTCAAGTCCAAACCAATATCAATAAG
          1 AGAGCCTCGGGCTCAAGTCCAAACAAATATCAACAAC

                                       *      *  
        781 AGAGCCTCGGGCTCAAGTCCAAACAAAAATCAACCAC
          1 AGAGCCTCGGGCTCAAGTCCAAACAAATATCAACAAC

            *   *                            *  *
        818 TGAGTCTCGGGCTCAAGTCCAAACAAATATCAATAAG
          1 AGAGCCTCGGGCTCAAGTCCAAACAAATATCAACAAC

                            *     
        855 AGAGCCTCGGGCTCAAATCCAA
          1 AGAGCCTCGGGCTCAAGTCCAA

        877 CGAAATACCA


Statistics
Matches: 109,  Mismatches: 23, Indels: 2
        0.81            0.17        0.01

Matches are distributed among these distances:
  37  106  0.97
  38    3  0.03

ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16


Consensus pattern (37 bp):   
AGAGCCTCGGGCTCAAGTCCAAACAAATATCAACAAC

Found at i:837 original size:74 final size:74

Alignment explanation


    Indices: 707--876  Score: 268
    Period size: 74  Copynumber: 2.3  Consensus size: 74

        697 AACAACAAAA

                *   *             *   **                                 *   
        707 AGAGTCTCAGGCTCAAATCCAAGCAATCATCAACCACTGAGCCTCGGGCTCAAGTCCAAACCAAT
          1 AGAGCCTCGGGCTCAAATCCAAACAAAAATCAACCACTGAGCCTCGGGCTCAAGTCCAAACAAAT

                     
        772 ATCAATAAG
         66 ATCAATAAG

                            *                        *                       
        781 AGAGCCTCGGGCTCAAGTCCAAACAAAAATCAACCACTGAGTCTCGGGCTCAAGTCCAAACAAAT
          1 AGAGCCTCGGGCTCAAATCCAAACAAAAATCAACCACTGAGCCTCGGGCTCAAGTCCAAACAAAT

                     
        846 ATCAATAAG
         66 ATCAATAAG

                                  
        855 AGAGCCTCGGGCTCAAATCCAA
          1 AGAGCCTCGGGCTCAAATCCAA

        877 CGAAATACCA


Statistics
Matches: 87,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  74   87  1.00

ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16


Consensus pattern (74 bp):   
AGAGCCTCGGGCTCAAATCCAAACAAAAATCAACCACTGAGCCTCGGGCTCAAGTCCAAACAAAT
ATCAATAAG

Found at i:883 original size:37 final size:37

Alignment explanation


    Indices: 745--876  Score: 192
    Period size: 37  Copynumber: 3.6  Consensus size: 37

        735 ATCAACCACT

                                   *             
        745 GAGCCTCGGGCTCAAGTCCAAACCAATATCAATAAGA
          1 GAGCCTCGGGCTCAAGTCCAAACAAATATCAATAAGA

                                      *     ** **
        782 GAGCCTCGGGCTCAAGTCCAAACAAAAATCAACCACT
          1 GAGCCTCGGGCTCAAGTCCAAACAAATATCAATAAGA

               *                                 
        819 GAGTCTCGGGCTCAAGTCCAAACAAATATCAATAAGA
          1 GAGCCTCGGGCTCAAGTCCAAACAAATATCAATAAGA

                           *     
        856 GAGCCTCGGGCTCAAATCCAA
          1 GAGCCTCGGGCTCAAGTCCAA

        877 CGAAATACCA


Statistics
Matches: 81,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  37   81  1.00

ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16


Consensus pattern (37 bp):   
GAGCCTCGGGCTCAAGTCCAAACAAATATCAATAAGA
Done.