Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009915.1 Corchorus capsularis cultivar CVL-1 contig09936, 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: 23867
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:11000 original size:74 final size:74

Alignment explanation


    Indices: 10879--11023  Score: 229
    Period size: 74  Copynumber: 2.0  Consensus size: 74

      10869 AACTAAATTT

                                               *                     *       
      10879 AGAAAAGACCAAAACGGGGTAAAAGGTTCTCCCATGTTAAAAGTTGATGGGAGCTATTGGTAATT
          1 AGAAAAGACCAAAACGGGGTAAAAGGTTCTCCCATATTAAAAGTTGATGGGAGCTATCGGTAATT

                     
      10944 TCCAGAGTG
         66 TCCAGAGTG

                    *                                        *               
      10953 AGAAAAGATCAAAA-GGGGTGAAAAGGTTCTCCCATATTAAAAGTTGATTGGAGCTATCGGTAAT
          1 AGAAAAGACCAAAACGGGGT-AAAAGGTTCTCCCATATTAAAAGTTGATGGGAGCTATCGGTAAT

              *    
      11017 TTTCAGA
         65 TTCCAGA

      11024 TGGTATTCAA


Statistics
Matches: 65,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  73    5  0.08
  74   60  0.92

ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26


Consensus pattern (74 bp):   
AGAAAAGACCAAAACGGGGTAAAAGGTTCTCCCATATTAAAAGTTGATGGGAGCTATCGGTAATT
TCCAGAGTG

Found at i:11812 original size:34 final size:34

Alignment explanation


    Indices: 11774--11864  Score: 164
    Period size: 34  Copynumber: 2.7  Consensus size: 34

      11764 CTGGAGTCGT

                       *                      
      11774 TAGGGTCTTAAAGTGTTTGGAGATACTATGTTAA
          1 TAGGGTCTTAAGGTGTTTGGAGATACTATGTTAA

                                              
      11808 TAGGGTCTTAAGGTGTTTGGAGATACTATGTTAA
          1 TAGGGTCTTAAGGTGTTTGGAGATACTATGTTAA

                *                  
      11842 TAGGTTCTTAAGGTGTTTGGAGA
          1 TAGGGTCTTAAGGTGTTTGGAGA

      11865 GCTTAAGAGC


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  34   55  1.00

ACGTcount: A:0.26, C:0.05, G:0.30, T:0.38


Consensus pattern (34 bp):   
TAGGGTCTTAAGGTGTTTGGAGATACTATGTTAA

Found at i:14989 original size:34 final size:35

Alignment explanation


    Indices: 14924--14994  Score: 83
    Period size: 34  Copynumber: 2.1  Consensus size: 35

      14914 AAAATTAGGG

                        **            *     *  
      14924 TTTCCGATTTTTTTTTTAAAAAAATTGTTTTTCTT
          1 TTTCCGATTTTTCCTTTAAAAAAATTATTTTTATT

                                                
      14959 TTTCCG-TTTTTCCTTTAAAAAAGA-TATTTTTATT
          1 TTTCCGATTTTTCCTTTAAAAAA-ATTATTTTTATT

              
      14993 TT
          1 TT

      14995 CTGTTTCTGC


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  34   24  0.77
  35    7  0.23

ACGTcount: A:0.24, C:0.10, G:0.06, T:0.61


Consensus pattern (35 bp):   
TTTCCGATTTTTCCTTTAAAAAAATTATTTTTATT
Done.