Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000175.1 Kokia drynarioides strain JFW-HI SEQ_110847, 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: 12758
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:2592 original size:14 final size:14

Alignment explanation


    Indices: 2573--2603  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       2563 ATAATAGATT

                          
       2573 TTTAATTAAATAAA
          1 TTTAATTAAATAAA

                     *    
       2587 TTTAATTAATTAAA
          1 TTTAATTAAATAAA

               
       2601 TTT
          1 TTT

       2604 TTTAAACCTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (14 bp):   
TTTAATTAAATAAA

Found at i:2872 original size:15 final size:15

Alignment explanation


    Indices: 2848--2883  Score: 54
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       2838 AATCAAAAAG

                          *
       2848 GAAGAAAAAGAAGAT
          1 GAAGAAAAAGAAGAA

                 *         
       2863 GAAGATAAAGAAGAA
          1 GAAGAAAAAGAAGAA

                  
       2878 GAAGAA
          1 GAAGAA

       2884 GAGAGGTGTG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.67, C:0.00, G:0.28, T:0.06


Consensus pattern (15 bp):   
GAAGAAAAAGAAGAA

Found at i:4377 original size:2 final size:2

Alignment explanation


    Indices: 4370--4400  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       4360 AATAGTGTAA

                                                          
       4370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4401 GTTAGTAGTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:12723 original size:28 final size:28

Alignment explanation


    Indices: 12678--12747  Score: 74
    Period size: 26  Copynumber: 2.5  Consensus size: 28

      12668 TGTGATCACT

                           *             
      12678 ATATATAAAA-T-TTCAATAAATAAAA-A
          1 ATATATAAAATTATTAAAT-AATAAAATA

                                *       
      12704 ATATATAAAATTATTAAATATTAAAATA
          1 ATATATAAAATTATTAAATAATAAAATA

                    *       
      12732 ATATAATATAATTATT
          1 ATAT-ATAAAATTATT

      12748 TTTAAATAAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  26   10  0.27
  27    7  0.19
  28   10  0.27
  29   10  0.27

ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39


Consensus pattern (28 bp):   
ATATATAAAATTATTAAATAATAAAATA

Done.