Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002672.1 Kokia drynarioides strain JFW-HI SEQ_114928, 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: 5459
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:1915 original size:19 final size:19

Alignment explanation


    Indices: 1875--1919  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1865 TTTTATTAGA

                               
       1875 ATTTAATATTTAAGATATT
          1 ATTTAATATTTAAGATATT

                 *          *   
       1894 ATTTATTATTTAA-ATTTGT
          1 ATTTAATATTTAAGATAT-T

                   
       1913 ATTTAAT
          1 ATTTAAT

       1920 TTACATTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18    3  0.14
  19   19  0.86

ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58


Consensus pattern (19 bp):   
ATTTAATATTTAAGATATT

Found at i:3742 original size:16 final size:17

Alignment explanation


    Indices: 3717--3750  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       3707 TTAAAAAATA

                             
       3717 TAAAAATAT-AAATTAT
          1 TAAAAATATAAAATTAT

                 *           
       3733 TAAAATTATAAAATTAT
          1 TAAAAATATAAAATTAT

             
       3750 T
          1 T

       3751 TTTTTACTAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    8  0.50
  17    8  0.50

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (17 bp):   
TAAAAATATAAAATTAT

Found at i:5430 original size:2 final size:2

Alignment explanation


    Indices: 5419--5459  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       5409 TTGATTTGTA

                                                                          
       5419 AT AT -T AT AT AT AT AT 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 AT AT AT AT AT AT AT AT


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Done.