Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003112.1 Corchorus capsularis cultivar CVL-1 contig03120, 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, 756

Length: 1260
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27


Found at i:586 original size:32 final size:32

Alignment explanation


    Indices: 550--637  Score: 124
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        540 CTCAGCCATT

                        * *                  
        550 GCAAGGCCGCACTCTAGGG-GCGGCCTGACGTG
          1 GCAAGGCCG-ACCCCAGGGTGCGGCCTGACGTG

                                       *    
        582 GCAAGGCCGACCCCAGGGTGCGGCCTGCCGTG
          1 GCAAGGCCGACCCCAGGGTGCGGCCTGACGTG

                            *       
        614 GCAAGGCCGACCCCAGTGTGCGGC
          1 GCAAGGCCGACCCCAGGGTGCGGC

        638 TTGCTTGCCA


Statistics
Matches: 51,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  31    7  0.14
  32   44  0.86

ACGTcount: A:0.15, C:0.35, G:0.40, T:0.10


Consensus pattern (32 bp):   
GCAAGGCCGACCCCAGGGTGCGGCCTGACGTG

Found at i:653 original size:31 final size:32

Alignment explanation


    Indices: 569--672  Score: 120
    Period size: 32  Copynumber: 3.3  Consensus size: 32

        559 CACTCTAGGG

                    *    *               *  
        569 GCGGCCTGACGTGGCAAGGCCGACCCCAGGGT
          1 GCGGCCTGCCGTGCCAAGGCCGACCCCAGTGT

                         *                  
        601 GCGGCCTGCCGTGGCAAGGCCGACCCCAGTGT
          1 GCGGCCTGCCGTGCCAAGGCCGACCCCAGTGT

                 *    *           *    *    
        633 GCGGCTTG-CTTGCCAAGGCCGCCCCCTGTGT
          1 GCGGCCTGCCGTGCCAAGGCCGACCCCAGTGT

                *    
        664 GCGGTCTGC
          1 GCGGCCTGC

        673 TGAGGCAAGA


Statistics
Matches: 62,  Mismatches: 9, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  31   25  0.40
  32   37  0.60

ACGTcount: A:0.11, C:0.37, G:0.38, T:0.15


Consensus pattern (32 bp):   
GCGGCCTGCCGTGCCAAGGCCGACCCCAGTGT

Found at i:700 original size:63 final size:63

Alignment explanation


    Indices: 583--701  Score: 141
    Period size: 63  Copynumber: 1.9  Consensus size: 63

        573 CCTGACGTGG

                                         *      *            *             
        583 CAAGGCCGACCCCAGGGTGCGGCCTGCCGTGGCAAGGCCGACCCCAGTGTGCGGCTTGCTTGC
          1 CAAGGCCGACCCCAGGGTGCGGCCTGCCGAGGCAAGACCGACCCCAGTGGGCGGCTTGCTTGC

                    *    * *      *    *              *              
        646 CAAGGCCGCCCCCTGTGTGCGGTCTGCTGAGGCAAGACCG-CGCCAGATGGGCGGCT
          1 CAAGGCCGACCCCAGGGTGCGGCCTGCCGAGGCAAGACCGACCCCAG-TGGGCGGCT

        702 CTGCCTGGCC


Statistics
Matches: 46,  Mismatches: 9, Indels: 2
        0.81            0.16        0.04

Matches are distributed among these distances:
  62    5  0.11
  63   41  0.89

ACGTcount: A:0.13, C:0.35, G:0.37, T:0.14


Consensus pattern (63 bp):   
CAAGGCCGACCCCAGGGTGCGGCCTGCCGAGGCAAGACCGACCCCAGTGGGCGGCTTGCTTGC

Found at i:828 original size:20 final size:20

Alignment explanation


    Indices: 803--842  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        793 CGGCTCAACC

                      *         
        803 CCTAGATCTATTTTTTTACA
          1 CCTAGATCTAATTTTTTACA

                                
        823 CCTAGATCTAATTTTTTACA
          1 CCTAGATCTAATTTTTTACA

        843 TCCATTCCTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47


Consensus pattern (20 bp):   
CCTAGATCTAATTTTTTACA
Done.