Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016342.1 Corchorus capsularis cultivar CVL-1 contig16363, 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: 5772
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:379 original size:33 final size:34

Alignment explanation


    Indices: 342--415  Score: 107
    Period size: 33  Copynumber: 2.2  Consensus size: 34

        332 GCGAGTCGTT

                              *               
        342 TGGCCGGTTG-TAACCGGCCATGTCCATGTCGCG
          1 TGGCCGGTTGATAACCGGACATGTCCATGTCGCG

                        **                    
        375 TGGCCGG-TGATGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTTGATAACCGGACATGTCCATGTCGCG

                    
        408 TGGCCGGT
          1 TGGCCGGT

        416 CTTGTGGCCG


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  32    2  0.06
  33   34  0.94

ACGTcount: A:0.11, C:0.28, G:0.38, T:0.23


Consensus pattern (34 bp):   
TGGCCGGTTGATAACCGGACATGTCCATGTCGCG

Found at i:2244 original size:21 final size:21

Alignment explanation


    Indices: 2206--2246  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2196 CCTTGGCTTA

                         *       
       2206 TGATCTTCAATACTCTTCAAT
          1 TGATCTTCAATACACTTCAAT

                       **       
       2227 TGATCTTCAATGGACTTCAA
          1 TGATCTTCAATACACTTCAA

       2247 GATGAGTTCG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39


Consensus pattern (21 bp):   
TGATCTTCAATACACTTCAAT

Found at i:4396 original size:52 final size:52

Alignment explanation


    Indices: 4266--4396  Score: 203
    Period size: 50  Copynumber: 2.6  Consensus size: 52

       4256 TTTTCAAGTC

                                                                
       4266 TTTTCAAGTCAGAGAGAAGATCAAGCAAACAAAGTAAAATGATGAGCCTACA
          1 TTTTCAAGTCAGAGAGAAGATCAAGCAAACAAAGTAAAATGATGAGCCTACA

                     *    *                *              *   * 
       4318 --TTCAAGTTAGAGGGAAGATCAAGCAAACACAGTAAAATGATGAGTCTAGA
          1 TTTTCAAGTCAGAGAGAAGATCAAGCAAACAAAGTAAAATGATGAGCCTACA

                                         
       4368 TTTTCAAGTCAGAGAGAAGATCAAGCAAA
          1 TTTTCAAGTCAGAGAGAAGATCAAGCAAA

       4397 TACATGCATT


Statistics
Matches: 70,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  50   45  0.64
  52   25  0.36

ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20


Consensus pattern (52 bp):   
TTTTCAAGTCAGAGAGAAGATCAAGCAAACAAAGTAAAATGATGAGCCTACA

Found at i:5481 original size:15 final size:14

Alignment explanation


    Indices: 5458--5488  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       5448 AAACAAAAAA

                 *        
       5458 AAAGGAAAAAAGAG
          1 AAAGGGAAAAAGAG

                          
       5472 AAAGGGAAAAAGAG
          1 AAAGGGAAAAAGAG

               
       5486 AAA
          1 AAA

       5489 AATAAATTTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (14 bp):   
AAAGGGAAAAAGAG
Done.