Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000295.1 Kokia drynarioides strain JFW-HI SEQ_111048, 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: 2998
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37


Found at i:2816 original size:41 final size:40

Alignment explanation


    Indices: 2771--2911  Score: 111
    Period size: 41  Copynumber: 3.3  Consensus size: 40

       2761 CACACGAGTT

                                                  *  
       2771 GGCACACGGGCGTGTGTCAAGGTGTGTGTATACTATTTCGA
          1 GGCACACGGGC-TGTGTCAAGGTGTGTGTATACTATTTGGA

                     *   ***  *                 ** *      
       2812 GGCACACGGACTGACACACGGATGTGTGTCAAGGATTGTGTTTGGA
          1 GGCACACGGGCTGTGTCAAGG-TGTGTGT-----ATACTATTTGGA

                  *            *                     
       2858 GGCACATGGGCTTGTGTCAGGGTGTGTGTATACTATTTGGA
          1 GGCACACGGGC-TGTGTCAAGGTGTGTGTATACTATTTGGA

                         
       2899 GGCACACGGGCTG
          1 GGCACACGGGCTG

       2912 ACACACGAAC


Statistics
Matches: 74,  Mismatches: 19, Indels: 15
        0.69            0.18        0.14

Matches are distributed among these distances:
  40    8  0.11
  41   36  0.49
  46   24  0.32
  47    6  0.08

ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27


Consensus pattern (40 bp):   
GGCACACGGGCTGTGTCAAGGTGTGTGTATACTATTTGGA

Found at i:2852 original size:53 final size:53

Alignment explanation


    Indices: 2739--2845  Score: 153
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       2729 GTCAAGGTGT

                             *            *  *       *           
       2739 GTGTGTGTATACTATTTGGAGGCACACGAGTTGGCACACGGGCGTGTGTCAAG
          1 GTGTGTGTATACTATTTCGAGGCACACGAGCTGACACACGGACGTGTGTCAAG

                                                       *          
       2792 GTGTGTGTATACTATTTCGAGGCACACG-GACTGACACACGGATGTGTGTCAAG
          1 GTGTGTGTATACTATTTCGAGGCACACGAG-CTGACACACGGACGTGTGTCAAG

             
       2845 G
          1 G

       2846 ATTGTGTTTG


Statistics
Matches: 48,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  52    1  0.02
  53   47  0.98

ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26


Consensus pattern (53 bp):   
GTGTGTGTATACTATTTCGAGGCACACGAGCTGACACACGGACGTGTGTCAAG
Done.