Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023320.1 Corchorus olitorius cultivar O-4 contig23353, 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: 2489
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34


Found at i:806 original size:18 final size:17

Alignment explanation


    Indices: 780--821  Score: 57
    Period size: 18  Copynumber: 2.4  Consensus size: 17

        770 TTCTTCTCTT

                *            
        780 TTTCTTTTCTCTTTTCC
          1 TTTCCTTTCTCTTTTCC

                            * 
        797 TCTTCCTTTCTCTTTTTC
          1 T-TTCCTTTCTCTTTTCC

                   
        815 TTTCCTT
          1 TTTCCTT

        822 ATGTCTCTTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17    7  0.32
  18   15  0.68

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (17 bp):   
TTTCCTTTCTCTTTTCC

Found at i:888 original size:12 final size:13

Alignment explanation


    Indices: 863--892  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        853 GCCCACTTTA

                         
        863 TTATTATGTTTTT
          1 TTATTATGTTTTT

                         
        876 TTATTAT-TTTTT
          1 TTATTATGTTTTT

                 
        888 TTATT
          1 TTATT

        893 TGGGCCCAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.59
  13    7  0.41

ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80


Consensus pattern (13 bp):   
TTATTATGTTTTT

Found at i:975 original size:15 final size:16

Alignment explanation


    Indices: 941--1014  Score: 69
    Period size: 16  Copynumber: 4.6  Consensus size: 16

        931 CTGGACCAAG

                *           
        941 GCGCGCCAGGCCCAGC
          1 GCGCACCAGGCCCAGC

                         *  
        957 GCGCACCAGG-CCTGC
          1 GCGCACCAGGCCCAGC

                  * *        
        972 GCGCCAGCTGGCCCAGC
          1 GCG-CACCAGGCCCAGC

                 * *  *     
        989 GCGCAGCTGGTCCAGC
          1 GCGCACCAGGCCCAGC

                      
       1005 GCGCACCAGG
          1 GCGCACCAGG

       1015 GCTGCGCGCG


Statistics
Matches: 48,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  15    7  0.15
  16   34  0.71
  17    7  0.15

ACGTcount: A:0.14, C:0.45, G:0.36, T:0.05


Consensus pattern (16 bp):   
GCGCACCAGGCCCAGC

Found at i:976 original size:48 final size:47

Alignment explanation


    Indices: 923--1023  Score: 123
    Period size: 48  Copynumber: 2.1  Consensus size: 47

        913 TGCTCAGGCC

                  *                                          
        923 CGCGCCTGCTGGACCAAGGCGCGC-CAGGCCCAGCGCGCACCAGGCCTG
          1 CGCGCCAGCTGG-CCAA-GCGCGCACAGGCCCAGCGCGCACCAGGCCTG

                          *          *  *               *   
        971 CGCGCCAGCTGGCCCAGCGCGCAGCTGGTCCAGCGCGCACCAGGGCTG
          1 CGCGCCAGCTGGCCAAGCGCGCA-CAGGCCCAGCGCGCACCAGGCCTG

                 
       1019 CGCGC
          1 CGCGC

       1024 GCCAGGCCTG


Statistics
Matches: 46,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  46    6  0.13
  47    3  0.07
  48   37  0.80

ACGTcount: A:0.13, C:0.44, G:0.37, T:0.07


Consensus pattern (47 bp):   
CGCGCCAGCTGGCCAAGCGCGCACAGGCCCAGCGCGCACCAGGCCTG

Found at i:1023 original size:15 final size:15

Alignment explanation


    Indices: 941--1034  Score: 62
    Period size: 16  Copynumber: 6.0  Consensus size: 15

        931 CTGGACCAAG

                *        *  
        941 GCGCGCCAGGCCCAGC
          1 GCGCACCAGG-CCTGC

                           
        957 GCGCACCAGGCCTGC
          1 GCGCACCAGGCCTGC

                  * *     *  
        972 GCGCCAGCTGGCCCAGC
          1 GCG-CACCAGG-CCTGC

                 * *     *  
        989 GCGCAGCTGGTCCAGC
          1 GCGCACCAGG-CCTGC

                      *    
       1005 GCGCACCAGGGCTGC
          1 GCGCACCAGGCCTGC

                *          
       1020 GCGCGCCAGGCCTGC
          1 GCGCACCAGGCCTGC

       1035 TAGGCAGGCC


Statistics
Matches: 64,  Mismatches: 12, Indels: 5
        0.79            0.15        0.06

Matches are distributed among these distances:
  15   23  0.36
  16   34  0.53
  17    7  0.11

ACGTcount: A:0.12, C:0.45, G:0.37, T:0.06


Consensus pattern (15 bp):   
GCGCACCAGGCCTGC
Done.