Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020535.1 Corchorus olitorius cultivar O-4 contig20568, 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: 2127
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Found at i:926 original size:78 final size:77

Alignment explanation


    Indices: 795--1006  Score: 293
    Period size: 78  Copynumber: 2.7  Consensus size: 77

        785 AGGCCACAGG

                           *                           *                     
        795 GCAGAGGCCCGACTGTCGCTGGGCGCCCAGGCAGAACGCCCAAACGCCTAGGCGACAGGCACCCA
          1 GCAGA-GCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCTAGGCGACAGGCACCCA

             *           
        860 GGCCCCAGCCAGA
         65 GACCCCAGCCAGA

                                                            *            *   
        873 GCAGAGACCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCCAGGCGACAGGCATCCA
          1 GCAGAG-CCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCTAGGCGACAGGCACCCA

                     *   
        938 GACCCCAGCTAGA
         65 GACCCCAGCCAGA

               *       *                        *                     
        951 GCAAAGCCCGATTGCCGCTGGGCGCCCAGGC-GAAATGCCTC-AGCGCCTAGGCGACA
          1 GCAGAGCCCGACTGCCGCTGGGCGCCCAGGCAG-AACGCC-CAAGCGCCTAGGCGACA

       1007 AGGCTCAGCG


Statistics
Matches: 121,  Mismatches: 10, Indels: 7
        0.88            0.07        0.05

Matches are distributed among these distances:
  76    1  0.01
  77   44  0.36
  78   76  0.63

ACGTcount: A:0.23, C:0.39, G:0.32, T:0.07


Consensus pattern (77 bp):   
GCAGAGCCCGACTGCCGCTGGGCGCCCAGGCAGAACGCCCAAGCGCCTAGGCGACAGGCACCCAG
ACCCCAGCCAGA

Found at i:996 original size:21 final size:21

Alignment explanation


    Indices: 972--1021  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        962 TTGCCGCTGG

                                  
        972 GCGCCCAGGCGA-AATGCCTCA
          1 GCGCCCAGGCGACAA-GCCTCA

                 *          *    
        993 GCGCCTAGGCGACAAGGCTCA
          1 GCGCCCAGGCGACAAGCCTCA

                    
       1014 GCGCCCAG
          1 GCGCCCAG

       1022 CTCGATCCCT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  21   23  0.92
  22    2  0.08

ACGTcount: A:0.22, C:0.38, G:0.32, T:0.08


Consensus pattern (21 bp):   
GCGCCCAGGCGACAAGCCTCA

Done.