Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007342.1 Kokia drynarioides strain JFW-HI SEQ_121958, 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: 3997
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36


Found at i:3910 original size:17 final size:16

Alignment explanation


    Indices: 3890--3961  Score: 92
    Period size: 17  Copynumber: 4.4  Consensus size: 16

       3880 TTAAATCAAG

                             
       3890 TTTAGAATTATTTTAAA
          1 TTTA-AATTATTTTAAA

                             
       3907 TTTAAATTTATTTTAAA
          1 TTTAAA-TTATTTTAAA

                      *    *
       3924 TTTAAATT-TATTAAG
          1 TTTAAATTATTTTAAA

                             
       3939 TTTAAATTTATTTTAAA
          1 TTTAAA-TTATTTTAAA

                  
       3956 TTTAAA
          1 TTTAAA

       3962 ATTTGAAATA


Statistics
Matches: 48,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
  15   11  0.23
  16    6  0.12
  17   31  0.65

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56


Consensus pattern (16 bp):   
TTTAAATTATTTTAAA

Found at i:3912 original size:6 final size:6

Alignment explanation


    Indices: 3901--3961  Score: 63
    Period size: 6  Copynumber: 10.0  Consensus size: 6

       3891 TTAGAATTAT

                               *                                     *
       3901 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTATTAA GTTTAAA TTT-AT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA -TTTAAA TTTAAA

                         
       3950 TTTAAA TTTAAA
          1 TTTAAA TTTAAA

       3962 ATTTGAAATA


Statistics
Matches: 46,  Mismatches: 4, Indels: 10
        0.77            0.07        0.17

Matches are distributed among these distances:
   5    8  0.17
   6   30  0.65
   7    2  0.04
   8    2  0.04
   9    4  0.09

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56


Consensus pattern (6 bp):   
TTTAAA

Found at i:3921 original size:11 final size:11

Alignment explanation


    Indices: 3907--3959  Score: 56
    Period size: 11  Copynumber: 4.9  Consensus size: 11

       3897 TTATTTTAAA

                       
       3907 TTTAAATTTAT
          1 TTTAAATTTAT

                       *
       3918 TTTAAATTTAAA
          1 TTTAAATTT-AT

                    * *
       3930 TTT--ATTAAG
          1 TTTAAATTTAT

                       
       3939 TTTAAATTTAT
          1 TTTAAATTTAT

                      
       3950 TTTAAATTTA
          1 TTTAAATTTA

       3960 AAATTTGAAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
   9    4  0.12
  10    3  0.09
  11   23  0.68
  12    4  0.12

ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58


Consensus pattern (11 bp):   
TTTAAATTTAT
Done.