Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012729.1 Kokia drynarioides strain JFW-HI SEQ_127740, 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: 6013
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32


Found at i:439 original size:40 final size:40

Alignment explanation


    Indices: 356--440  Score: 118
    Period size: 40  Copynumber: 2.1  Consensus size: 40

        346 TTCGACGACT

                *    *                            * 
        356 ATTTGTTTTTCAATATCAAAATTAAGTGATTATTAGTATA
          1 ATTTATTTTCCAATATCAAAATTAAGTGATTATTAGTACA

                                    *                
        396 ATTTATTTTCCAATATCAAAATTATGTGATTATT-GATACA
          1 ATTTATTTTCCAATATCAAAATTAAGTGATTATTAG-TACA

                 
        436 ATTTA
          1 ATTTA

        441 CCCTAAAAGT


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  39    1  0.03
  40   39  0.98

ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47


Consensus pattern (40 bp):   
ATTTATTTTCCAATATCAAAATTAAGTGATTATTAGTACA

Found at i:3060 original size:22 final size:22

Alignment explanation


    Indices: 3000--3075  Score: 109
    Period size: 23  Copynumber: 3.4  Consensus size: 22

       2990 CGGGTCGGGC

                                   
       3000 TTGGGTTTTTATTATAAAAGGGT
          1 TTGGGTTTTTATT-TAAAAGGGT

                               *   
       3023 TTGGGTTTTTATTTTAAAATGGT
          1 TTGGGTTTTTA-TTTAAAAGGGT

                                   
       3046 TTGGGTTTTTATTT-AAAGGGAT
          1 TTGGGTTTTTATTTAAAAGGG-T

                    
       3068 TTGGGTTT
          1 TTGGGTTT

       3076 AAAATAATAT


Statistics
Matches: 49,  Mismatches: 2, Indels: 5
        0.88            0.04        0.09

Matches are distributed among these distances:
  21    5  0.10
  22   12  0.24
  23   30  0.61
  24    2  0.04

ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53


Consensus pattern (22 bp):   
TTGGGTTTTTATTTAAAAGGGT

Found at i:4951 original size:19 final size:21

Alignment explanation


    Indices: 4906--4951  Score: 78
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       4896 TTTGAAATTA

                                 
       4906 TATTTTTACTTAAATTCTCTT
          1 TATTTTTACTTAAATTCTCTT

                                 
       4927 TATTTTTACTTAAATTCT-TT
          1 TATTTTTACTTAAATTCTCTT

                  
       4947 T-TTTT
          1 TATTTT

       4952 CAGACTGTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  19    4  0.16
  20    3  0.12
  21   18  0.72

ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67


Consensus pattern (21 bp):   
TATTTTTACTTAAATTCTCTT
Done.