Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013571.1 Kokia drynarioides strain JFW-HI SEQ_128597, 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, 765

Length: 1276
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34


Found at i:842 original size:23 final size:23

Alignment explanation


    Indices: 816--964  Score: 183
    Period size: 23  Copynumber: 6.3  Consensus size: 23

        806 ACACTAGCGC

                                 * 
        816 GCTCTCTGATTAGCACTGTGTTT
          1 GCTCTCTGATTAGCACTGTGTGT

                    *          *    
        839 GCTCTCTGTTTAGCAC-GTCTCGT
          1 GCTCTCTGATTAGCACTGTGT-GT

                                     
        862 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTG--ATTAGCACTGTGTGT

                             *     
        887 GCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                     *       *     
        910 GCTCTCTGACTAGCACTTTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

             *       *              
        933 AACTCTCTGTTTAGCACTGTGTGT
          1 -GCTCTCTGATTAGCACTGTGTGT

                    
        957 GCTCTCTG
          1 GCTCTCTG

        965 TTGCCCAGCA


Statistics
Matches: 109,  Mismatches: 12, Indels: 10
        0.83            0.09        0.08

Matches are distributed among these distances:
  22    3  0.03
  23   67  0.61
  24   19  0.17
  25   17  0.16
  26    3  0.03

ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTGTGTGT

Found at i:890 original size:48 final size:45

Alignment explanation


    Indices: 816--964  Score: 163
    Period size: 48  Copynumber: 3.2  Consensus size: 45

        806 ACACTAGCGC

                     *           *                        
        816 GCTCTCTGATTAGCACTGTGTTTGCTCTCTGTTTAGCACGTCTCGT
          1 GCTCTCTGACTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-GT

                       *                     *        * *   
        862 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTG--ACTAGCACTGTGTGTGCTCTCTGTTTAGCAC-GTCTGT

                             *      *                  *   
        910 GCTCTCTGACTAGCACTTTGTGTAACTCTCTGTTTAGCACTGTGTGT
          1 GCTCTCTGACTAGCACTGTGTGT-GCTCTCTGTTTAGCAC-GTCTGT

                    
        957 GCTCTCTG
          1 GCTCTCTG

        965 TTGCCCAGCA


Statistics
Matches: 90,  Mismatches: 9, Indels: 7
        0.85            0.08        0.07

Matches are distributed among these distances:
  46   21  0.23
  47   28  0.31
  48   39  0.43
  49    2  0.02

ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42


Consensus pattern (45 bp):   
GCTCTCTGACTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTGT

Found at i:965 original size:23 final size:23

Alignment explanation


    Indices: 816--992  Score: 178
    Period size: 23  Copynumber: 7.5  Consensus size: 23

        806 ACACTAGCGC

                    *            * 
        816 GCTCTCTGATTAGCACTGTGTTT
          1 GCTCTCTGTTTAGCACTGTGTGT

                               *    
        839 GCTCTCTGTTTAGCAC-GTCTCGT
          1 GCTCTCTGTTTAGCACTGTGT-GT

                                     
        862 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTG-T-TTAGCACTGTGTGT

                    *        *     
        887 GCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTGTGT

                    **       *     
        910 GCTCTCTGACTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTGTGT

             *                      
        933 AACTCTCTGTTTAGCACTGTGTGT
          1 -GCTCTCTGTTTAGCACTGTGTGT

                         *        *   
        957 GCTCTCTGTTGCCCAGCACT-TATGT
          1 GCTCTCTGTT---TAGCACTGTGTGT

                       
        982 GCTCTCTGTTT
          1 GCTCTCTGTTT

        993 GTTCCGTATA


Statistics
Matches: 131,  Mismatches: 15, Indels: 17
        0.80            0.09        0.10

Matches are distributed among these distances:
  22    3  0.02
  23   68  0.52
  24   20  0.15
  25   31  0.24
  26    9  0.07

ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42


Consensus pattern (23 bp):   
GCTCTCTGTTTAGCACTGTGTGT
Done.