Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004033.1 Kokia drynarioides strain JFW-HI SEQ_117166, 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: 4709
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:346 original size:17 final size:17

Alignment explanation


    Indices: 318--393  Score: 98
    Period size: 17  Copynumber: 4.4  Consensus size: 17

        308 AACTGGTCCC

                              
        318 TTTATAATTTATTTTAAA
          1 TTTA-AATTTATTTTAAA

                *            
        336 TTTAGATTTATTTTAAA
          1 TTTAAATTTATTTTAAA

                      *     *
        353 TTTAAATTTAATTTAAT
          1 TTTAAATTTATTTTAAA

                             *
        370 TTTAAATTTAATTTTAAT
          1 TTTAAATTT-ATTTTAAA

                  
        388 TTTAAA
          1 TTTAAA

        394 AAGTCCAAAA


Statistics
Matches: 52,  Mismatches: 5, Indels: 2
        0.88            0.08        0.03

Matches are distributed among these distances:
  17   35  0.67
  18   17  0.33

ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA

Found at i:360 original size:23 final size:23

Alignment explanation


    Indices: 330--389  Score: 95
    Period size: 23  Copynumber: 2.6  Consensus size: 23

        320 TATAATTTAT

                                    
        330 TTTAAATTTAGATTT-ATTTTAAA
          1 TTTAAATTTA-ATTTAATTTTAAA

                                   
        353 TTTAAATTTAATTTAATTTTAAA
          1 TTTAAATTTAATTTAATTTTAAA

                 *        
        376 TTTAATTTTAATTT
          1 TTTAAATTTAATTT

        390 TAAAAAGTCC


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  22    4  0.11
  23   31  0.89

ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60


Consensus pattern (23 bp):   
TTTAAATTTAATTTAATTTTAAA

Found at i:390 original size:6 final size:6

Alignment explanation


    Indices: 328--392  Score: 64
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        318 TTTATAATTT

                    *                     *      *                  
        328 ATTTTA AATTTA GA-TTT- ATTTTA AATTTA AATTTA A-TTTA ATTTTA
          1 ATTTTA ATTTTA -ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA

             *                    
        374 AATTTA ATTTTA ATTTTA A
          1 ATTTTA ATTTTA ATTTTA A

        393 AAAGTCCAAA


Statistics
Matches: 51,  Mismatches: 4, Indels: 8
        0.81            0.06        0.13

Matches are distributed among these distances:
   4    1  0.02
   5    8  0.16
   6   41  0.80
   7    1  0.02

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


Consensus pattern (6 bp):   
ATTTTA

Found at i:1680 original size:18 final size:20

Alignment explanation


    Indices: 1645--1688  Score: 65
    Period size: 18  Copynumber: 2.3  Consensus size: 20

       1635 TAAAAAAAAA

                                
       1645 AAATTTCTTCAGAATTTTCT
          1 AAATTTCTTCAGAATTTTCT

                              * 
       1665 AAATTTC-TCA-AATTTTTT
          1 AAATTTCTTCAGAATTTTCT

                  
       1683 AAATTT
          1 AAATTT

       1689 TATATATGTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18   13  0.57
  19    3  0.13
  20    7  0.30

ACGTcount: A:0.34, C:0.11, G:0.02, T:0.52


Consensus pattern (20 bp):   
AAATTTCTTCAGAATTTTCT
Done.