Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004146.1 Kokia drynarioides strain JFW-HI SEQ_117349, 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: 6638
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:80 original size:23 final size:23

Alignment explanation


    Indices: 50--103  Score: 90
    Period size: 23  Copynumber: 2.3  Consensus size: 23

         40 ATGCTAGCGC

                               *   
         50 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCATGT

                                   
         73 GCTTACTGTTTCGCACTTCATGT
          1 GCTTACTGTTTCGCACTTCATGT

              *     
         96 GCCTACTG
          1 GCTTACTG

        104 ATTTGCGCTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41


Consensus pattern (23 bp):   
GCTTACTGTTTCGCACTTCATGT

Found at i:163 original size:23 final size:22

Alignment explanation


    Indices: 93--165  Score: 101
    Period size: 23  Copynumber: 3.2  Consensus size: 22

         83 TCGCACTTCA

                             *  *  
         93 TGTGCCTACTGATTTGCGCTATG
          1 TGTGCCTACTGA-TTGCACTGTG

              *                   
        116 TGCGCCTACTGATTGCACTGTG
          1 TGTGCCTACTGATTGCACTGTG

                                   
        138 TGTGCCTACTGGATTGCACTGTG
          1 TGTGCCTACT-GATTGCACTGTG

                 
        161 TGTGC
          1 TGTGC

        166 TTATTGTTTC


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  22   17  0.38
  23   28  0.62

ACGTcount: A:0.12, C:0.23, G:0.29, T:0.36


Consensus pattern (22 bp):   
TGTGCCTACTGATTGCACTGTG

Found at i:1750 original size:16 final size:16

Alignment explanation


    Indices: 1726--1756  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1716 GTCAACAAAA

                            
       1726 TTTTAAAATTATTAAT
          1 TTTTAAAATTATTAAT

                *          
       1742 TTTTTAAATTATTAA
          1 TTTTAAAATTATTAA

       1757 AATTCTTAAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (16 bp):   
TTTTAAAATTATTAAT
Done.