Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001785.1 Kokia drynarioides strain JFW-HI SEQ_113514, 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, 990

Length: 1650
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33


Found at i:424 original size:18 final size:18

Alignment explanation


    Indices: 401--443  Score: 70
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        391 GAATAGATTT

                               
        401 TTAATTAAATAAATTT-AA
          1 TTAATTAAA-AAATTTAAA

                              
        419 TTAATTAAAAAATTTAAA
          1 TTAATTAAAAAATTTAAA

                   
        437 TTAATTA
          1 TTAATTA

        444 CACCTTGAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  17    6  0.25
  18   18  0.75

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (18 bp):   
TTAATTAAAAAATTTAAA

Found at i:634 original size:18 final size:19

Alignment explanation


    Indices: 607--646  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 19

        597 ACTGAATCCA

                             * 
        607 AAAAATTTAAATTTATTTT
          1 AAAAATTTAAATTTATTCT

                      *        
        626 AAAAA-TTAAGTTTATTCT
          1 AAAAATTTAAATTTATTCT

               
        644 AAA
          1 AAA

        647 TTTAAAATTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   14  0.74
  19    5  0.26

ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45


Consensus pattern (19 bp):   
AAAAATTTAAATTTATTCT

Found at i:657 original size:23 final size:23

Alignment explanation


    Indices: 627--681  Score: 83
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        617 ATTTATTTTA

                    *      *       
        627 AAAATTAAGTTTATTCTAAATTT
          1 AAAATTAAATTTATTATAAATTT

                                   
        650 AAAATTAAATTTATTATAAATTT
          1 AAAATTAAATTTATTATAAATTT

               *     
        673 AAATTTAAA
          1 AAAATTAAA

        682 ATTCATTTAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   29  1.00

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (23 bp):   
AAAATTAAATTTATTATAAATTT

Found at i:692 original size:23 final size:23

Alignment explanation


    Indices: 627--693  Score: 73
    Period size: 23  Copynumber: 2.9  Consensus size: 23

        617 ATTTATTTTA

                    *  *   *       
        627 AAAATTAAGTTTATTCTAAATTT
          1 AAAATTAAATTCATTATAAATTT

                       *           
        650 AAAATTAAATTTATTATAAATTT
          1 AAAATTAAATTCATTATAAATTT

               *                  
        673 AAATTTAAAATTCATT-TAAAT
          1 AAAATT-AAATTCATTATAAAT

        694 AATATCCAGT


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  23   31  0.79
  24    8  0.21

ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46


Consensus pattern (23 bp):   
AAAATTAAATTCATTATAAATTT
Done.