Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004380.1 Kokia drynarioides strain JFW-HI SEQ_117753, 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: 11928
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:8888 original size:6 final size:6

Alignment explanation


    Indices: 8856--8913  Score: 50
    Period size: 6  Copynumber: 9.8  Consensus size: 6

       8846 TGAATCTAAT

                                *      *             *              
       8856 TTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
          1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                         
       8902 TTTAAAA TTTAA
          1 TTT-AAA TTTAA

       8914 TTAAATGTCC


Statistics
Matches: 42,  Mismatches: 5, Indels: 9
        0.75            0.09        0.16

Matches are distributed among these distances:
   4    1  0.02
   5    8  0.19
   6   21  0.50
   7   12  0.29

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55


Consensus pattern (6 bp):   
TTTAAA

Found at i:8904 original size:17 final size:17

Alignment explanation


    Indices: 8854--8905  Score: 79
    Period size: 17  Copynumber: 3.1  Consensus size: 17

       8844 ATTGAATCTA

                              
       8854 ATTTTAAATTTTAAA-TT
          1 ATTTTAAA-TTTAAATTT

                   *         
       8871 ATTTTAAGTTTAAATTT
          1 ATTTTAAATTTAAATTT

                             
       8888 ATTTTAAATTTAAATTT
          1 ATTTTAAATTTAAATTT

             
       8905 A
          1 A

       8906 AAATTTAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    6  0.19
  17   26  0.81

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


Consensus pattern (17 bp):   
ATTTTAAATTTAAATTT

Found at i:8915 original size:12 final size:11

Alignment explanation


    Indices: 8873--8919  Score: 51
    Period size: 11  Copynumber: 4.1  Consensus size: 11

       8863 TTTAAATTAT

                        
       8873 TTTAAGTTTAAA
          1 TTTAA-TTTAAA

                *      
       8885 TTTATTTTAAA
          1 TTTAATTTAAA

                         
       8896 TTTAAATTTAAAA
          1 TTT-AATTT-AAA

                       
       8909 TTTAA-TTAAA
          1 TTTAATTTAAA

             
       8919 T
          1 T

       8920 GTCCAAAATT


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  10    4  0.13
  11   11  0.35
  12   10  0.32
  13    6  0.19

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


Consensus pattern (11 bp):   
TTTAATTTAAA
Done.