Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001207.1 Kokia drynarioides strain JFW-HI SEQ_112558, 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: 5539
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31


Found at i:250 original size:28 final size:27

Alignment explanation


    Indices: 203--255  Score: 79
    Period size: 28  Copynumber: 1.9  Consensus size: 27

        193 ATAAAATTTA

                                       
        203 AAATTTTTATAAATATTTTAAAATTTA
          1 AAATTTTTATAAATATTTTAAAATTTA

                       *   *          
        230 AAATTTATTATGAATTTTTTAAAATT
          1 AAATTT-TTATAAATATTTTAAAATT

        256 ATTTTGAATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  27    6  0.26
  28   17  0.74

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53


Consensus pattern (27 bp):   
AAATTTTTATAAATATTTTAAAATTTA

Found at i:270 original size:21 final size:21

Alignment explanation


    Indices: 226--269  Score: 72
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        216 TATTTTAAAA

                                 
        226 TTTAAAATTTATTATGAATTT
          1 TTTAAAATTTATTATGAATTT

                         *       
        247 TTTAAAA-TTATTTTGAATTT
          1 TTTAAAATTTATTATGAATTT

               
        267 TTT
          1 TTT

        270 TTTGTAATTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20   15  0.68
  21    7  0.32

ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61


Consensus pattern (21 bp):   
TTTAAAATTTATTATGAATTT

Found at i:2005 original size:2 final size:2

Alignment explanation


    Indices: 1998--2023  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1988 ATACCAAAAC

                                                  
       1998 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       2024 TTATCATGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Done.