Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015725.1 Corchorus capsularis cultivar CVL-1 contig15746, 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: 5809
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:2588 original size:21 final size:21

Alignment explanation


    Indices: 2545--2589  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2535 ATTGGAGATC

                            * *  
       2545 ATGTCTTGGATAAACATGGAG
          1 ATGTCTTGGATAAACAAGAAG

                        **       
       2566 ATGTCTTGGATATTCAAGAAG
          1 ATGTCTTGGATAAACAAGAAG

               
       2587 ATG
          1 ATG

       2590 CCACGGATGA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31


Consensus pattern (21 bp):   
ATGTCTTGGATAAACAAGAAG

Found at i:2689 original size:30 final size:30

Alignment explanation


    Indices: 2655--2743  Score: 84
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       2645 GCCACCATCT

                                          
       2655 CATGGAGCAACCGGCCATGACCGGCCAACG
          1 CATGGAGCAACCGGCCATGACCGGCCAACG

                      *                    
       2685 CATGGAGC-ATC-G-CATG---GAG-CAACG
          1 CATGGAGCAACCGGCCATGACCG-GCCAACG

                 *           **           
       2709 CATGGGGCAACCGGCCACAACCGGCCAACG
          1 CATGGAGCAACCGGCCATGACCGGCCAACG

                 
       2739 CATGG
          1 CATGG

       2744 GACATCGCAC


Statistics
Matches: 46,  Mismatches: 5, Indels: 16
        0.69            0.07        0.24

Matches are distributed among these distances:
  24   13  0.28
  25    3  0.07
  26    1  0.02
  27    6  0.13
  28    1  0.02
  29    3  0.07
  30   19  0.41

ACGTcount: A:0.27, C:0.34, G:0.31, T:0.08


Consensus pattern (30 bp):   
CATGGAGCAACCGGCCATGACCGGCCAACG

Found at i:2700 original size:12 final size:12

Alignment explanation


    Indices: 2680--2719  Score: 62
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       2670 CATGACCGGC

                        
       2680 CAACGCATGGAG
          1 CAACGCATGGAG

              *         
       2692 CATCGCATGGAG
          1 CAACGCATGGAG

                      * 
       2704 CAACGCATGGGG
          1 CAACGCATGGAG

                
       2716 CAAC
          1 CAAC

       2720 CGGCCACAAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.30, C:0.28, G:0.33, T:0.10


Consensus pattern (12 bp):   
CAACGCATGGAG

Found at i:2741 original size:42 final size:42

Alignment explanation


    Indices: 2695--2777  Score: 114
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2685 CATGGAGCAT

                             *   *                     
       2695 CGCAT-GGAGCAACGCATGGGGCAACCGGCCACAACCGGCCAA
          1 CGCATGGGA-CAACGCACGGGCCAACCGGCCACAACCGGCCAA

                       *           *                 
       2737 CGCATGGGACATCGCACGGGCCATCCGGCCACAACCGGCCA
          1 CGCATGGGACAACGCACGGGCCAACCGGCCACAACCGGCCA

       2778 TTCGACCCTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  42   33  0.92
  43    3  0.08

ACGTcount: A:0.25, C:0.39, G:0.30, T:0.06


Consensus pattern (42 bp):   
CGCATGGGACAACGCACGGGCCAACCGGCCACAACCGGCCAA
Done.