Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019939.1 Corchorus olitorius cultivar O-4 contig19972, 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: 4139
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                                         
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         41 GTACCAGTAC


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:784 original size:29 final size:29

Alignment explanation


    Indices: 742--800  Score: 100
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        732 GGCTCTATCA

                            *        *   
        742 CGGTGTCCGACGTGGCGTGCCACATGTAC
          1 CGGTGTCCGACGTGGCATGCCACATATAC

                                         
        771 CGGTGTCCGACGTGGCATGCCACATATAC
          1 CGGTGTCCGACGTGGCATGCCACATATAC

             
        800 C
          1 C

        801 AAAAAGCGAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20


Consensus pattern (29 bp):   
CGGTGTCCGACGTGGCATGCCACATATAC

Found at i:832 original size:31 final size:31

Alignment explanation


    Indices: 797--899  Score: 127
    Period size: 31  Copynumber: 3.3  Consensus size: 31

        787 ATGCCACATA

                                   **      
        797 TACCAAAAAGCGACATGTGACACGTCACGTG
          1 TACCAAAAAGCGACATGTGACACACCACGTG

                               *           
        828 TACCAAAAAGCGACATGTGGCACACCACGTG
          1 TACCAAAAAGCGACATGTGACACACCACGTG

                      *             *   *   
        859 TACCAAAAAGTGACATGT-ATCACTCCATGTG
          1 TACCAAAAAGCGACATGTGA-CACACCACGTG

                *     
        890 TACCCAAAAG
          1 TACCAAAAAG

        900 TAACACTTGG


Statistics
Matches: 63,  Mismatches: 8, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  31   63  1.00

ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17


Consensus pattern (31 bp):   
TACCAAAAAGCGACATGTGACACACCACGTG

Found at i:918 original size:31 final size:31

Alignment explanation


    Indices: 780--947  Score: 77
    Period size: 31  Copynumber: 5.4  Consensus size: 31

        770 CCGGTGTCCG

                         **            **  
        780 ACGTGGCATGCCACATATACCAAAAAGCGAC
          1 ACGTGGCATGCCATGTATACCAAAAAGTAAC

             *   *  * *  *  *          **  
        811 ATGTGACACGTCACGTGTACCAAAAAGCGAC
          1 ACGTGGCATGCCATGTATACCAAAAAGTAAC

             *      **   *  *           *  
        842 ATGTGGCACACCACGTGTACCAAAAAGTGAC
          1 ACGTGGCATGCCATGTATACCAAAAAGTAAC

             *  **           *    *         
        873 ATGTATCACT-CCATGTGTACCCAAAAGTAAC
          1 ACGTGGCA-TGCCATGTATACCAAAAAGTAAC

              *               **        *  
        904 ACTTGGCATGCCATGTATTTCAAAAAGTGAC
          1 ACGTGGCATGCCATGTATACCAAAAAGTAAC

                         
        935 ACGTGGCATGCCA
          1 ACGTGGCATGCCA

        948 CTTGCACAAA


Statistics
Matches: 109,  Mismatches: 26, Indels: 4
        0.78            0.19        0.03

Matches are distributed among these distances:
  30    1  0.01
  31  108  0.99

ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20


Consensus pattern (31 bp):   
ACGTGGCATGCCATGTATACCAAAAAGTAAC
Done.