Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009540.1 Kokia drynarioides strain JFW-HI SEQ_124252, 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: 2249
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32


Found at i:61 original size:17 final size:18

Alignment explanation


    Indices: 25--101  Score: 88
    Period size: 17  Copynumber: 4.3  Consensus size: 18

         15 TTATAGTAAT

                  *           
         25 TTTAAATTTAAAAATAAA
          1 TTTAAACTTAAAAATAAA

                         *    
         43 TTTAAACTT-AAATTAAA
          1 TTTAAACTTAAAAATAAA

                     *        
         60 TTTAAA-TTCAAAATAAA
          1 TTTAAACTTAAAAATAAA

                                
         77 TTTAAATTCTT-AAAATAAA
          1 TTTAAA--CTTAAAAATAAA

                  
         96 TTTAAA
          1 TTTAAA

        102 GGGAGTTCGG


Statistics
Matches: 52,  Mismatches: 3, Indels: 7
        0.84            0.05        0.11

Matches are distributed among these distances:
  16    2  0.04
  17   26  0.50
  18    8  0.15
  19   14  0.27
  20    2  0.04

ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40


Consensus pattern (18 bp):   
TTTAAACTTAAAAATAAA

Found at i:64 original size:11 final size:11

Alignment explanation


    Indices: 26--84  Score: 57
    Period size: 11  Copynumber: 5.2  Consensus size: 11

         16 TATAGTAATT

                        
         26 TTAAATTTAAAA
          1 TTAAATTT-AAA

            *          
         38 ATAAATTTAAA
          1 TTAAATTTAAA

                        
         49 CTTAAA-TTAAA
          1 -TTAAATTTAAA

                    *   
         60 TTTAAATTCAAA
          1 -TTAAATTTAAA

            *          
         72 ATAAATTTAAA
          1 TTAAATTTAAA

              
         83 TT
          1 TT

         85 CTTAAAATAA


Statistics
Matches: 38,  Mismatches: 7, Indels: 5
        0.76            0.14        0.10

Matches are distributed among these distances:
  11   23  0.61
  12   15  0.39

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (11 bp):   
TTAAATTTAAA

Found at i:101 original size:6 final size:6

Alignment explanation


    Indices: 7--84  Score: 63
    Period size: 6  Copynumber: 13.5  Consensus size: 6

          1 AGCTTT

                        *   *    *              **            *    
          7 ATTTAA ATTTAT A-GTAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA

                             *     *              
         54 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATT
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT

         85 CTTAAAATAA


Statistics
Matches: 54,  Mismatches: 15, Indels: 6
        0.72            0.20        0.08

Matches are distributed among these distances:
   5   10  0.19
   6   44  0.81

ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44


Consensus pattern (6 bp):   
ATTTAA
Done.