Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007726.1 Kokia drynarioides strain JFW-HI SEQ_122359, 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: 39924
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35

Warning! 20 characters in sequence are not A, C, G, or T


Found at i:84 original size:2 final size:2

Alignment explanation


    Indices: 77--114  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

         67 TGGTTTTTAA

                                                                    
         77 AT 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

        115 TTTTTAATAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:143 original size:18 final size:18

Alignment explanation


    Indices: 111--157  Score: 62
    Period size: 17  Copynumber: 2.7  Consensus size: 18

        101 ATATATATAT

                            * 
        111 ATATTTTTTA-ATATTTA
          1 ATATTTTTTATATATTGA

                       *      
        128 ATATTTTTTATTTATTGA
          1 ATATTTTTTATATATTGA

                         
        146 AT-TTTTTTATAT
          1 ATATTTTTTATAT

        158 TGGTATTTTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  17   19  0.73
  18    7  0.27

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68


Consensus pattern (18 bp):   
ATATTTTTTATATATTGA

Found at i:18857 original size:2 final size:2

Alignment explanation


    Indices: 18852--18893  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      18842 GGAGAAAGAC

                                                                          
      18852 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

             
      18893 A
          1 A

      18894 TTACTGAAGC


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.97

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:22897 original size:14 final size:14

Alignment explanation


    Indices: 22878--22904  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      22868 ATTTTAAACT

                          
      22878 TTTAGAATTTTTAA
          1 TTTAGAATTTTTAA

                         
      22892 TTTAGAATTTTTA
          1 TTTAGAATTTTTA

      22905 TTCTAAAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59


Consensus pattern (14 bp):   
TTTAGAATTTTTAA

Found at i:39899 original size:23 final size:23

Alignment explanation


    Indices: 39869--39922  Score: 90
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      39859 ACGCTAGCGC

                                   
      39869 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

                              *    
      39892 GCTTACTGTTTCGCACTTTGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

              *     
      39915 GCCTACTG
          1 GCTTACTG

      39923 AT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43


Consensus pattern (23 bp):   
GCTTACTGTTTCGCACTTCGTGT
Done.