Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004011.1 Kokia drynarioides strain JFW-HI SEQ_117130, 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: 5614
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38


Found at i:906 original size:29 final size:29

Alignment explanation


    Indices: 873--932  Score: 86
    Period size: 29  Copynumber: 2.1  Consensus size: 29

        863 ATAATAAGTT

                              *           
        873 TTAAATTTAAA-TATAAATCTAAATTTATA
          1 TTAAATTTAAATTATAAAAC-AAATTTATA

                         *               
        902 TTAAATTTAAATTTTAAAACAAATTTATA
          1 TTAAATTTAAATTATAAAACAAATTTATA

              
        931 TT
          1 TT

        933 CAAAATAAAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29   22  0.79
  30    6  0.21

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (29 bp):   
TTAAATTTAAATTATAAAACAAATTTATA

Found at i:917 original size:18 final size:18

Alignment explanation


    Indices: 872--961  Score: 82
    Period size: 17  Copynumber: 5.2  Consensus size: 18

        862 TATAATAAGT

                              
        872 TTTAAATTTAAATATAAA
          1 TTTAAATTTAAATATAAA

             *        *       
        890 TCTAAATTTATAT-TAAA
          1 TTTAAATTTAAATATAAA

                           *   
        907 TTTAAATTTTAAA-ACAAA
          1 TTTAAA-TTTAAATATAAA

                *   *         
        925 TTTATATTCAAA-ATAAA
          1 TTTAAATTTAAATATAAA

                               
        942 TTTAACA-TTAAA-ATAAA
          1 TTTAA-ATTTAAATATAAA

               
        959 TTT
          1 TTT

        962 TAGAATGAGT


Statistics
Matches: 59,  Mismatches: 10, Indels: 7
        0.78            0.13        0.09

Matches are distributed among these distances:
  17   34  0.58
  18   25  0.42

ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43


Consensus pattern (18 bp):   
TTTAAATTTAAATATAAA

Found at i:919 original size:7 final size:6

Alignment explanation


    Indices: 872--915  Score: 54
    Period size: 6  Copynumber: 7.5  Consensus size: 6

        862 TATAATAAGT

                           *      *         *                   
        872 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT

        916 TAAAACAAAT


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
   5    4  0.12
   6   28  0.88

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (6 bp):   
TTTAAA

Found at i:2391 original size:24 final size:24

Alignment explanation


    Indices: 2350--2402  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       2340 ATTTTATGTT

                                    
       2350 ATTTTAATATTTAATATTTAAT-A
          1 ATTTTAATATTTAATATTTAATAA

                         **      *   
       2373 ATTTTATATATTTTTTATTTATTAA
          1 ATTTTA-ATATTTAATATTTAATAA

                 
       2398 ATTTT
          1 ATTTT

       2403 TTTTATATAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  23    6  0.24
  24   13  0.52
  25    6  0.24

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (24 bp):   
ATTTTAATATTTAATATTTAATAA

Found at i:4032 original size:24 final size:22

Alignment explanation


    Indices: 3983--4029  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3973 CTTTTTTTAA

                                * 
       3983 ATAAAATAAAATTATAAAAACT
          1 ATAAAATAAAATTATAAAAAAT

                                   
       4005 ATAAAATATAAA-TATAAAAAAT
          1 ATAAAATA-AAATTATAAAAAAT

               
       4027 ATA
          1 ATA

       4030 TAAGCGCATG


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

Matches are distributed among these distances:
  22   20  0.87
  23    3  0.13

ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28


Consensus pattern (22 bp):   
ATAAAATAAAATTATAAAAAAT

Found at i:4800 original size:9 final size:9

Alignment explanation


    Indices: 4786--4818  Score: 57
    Period size: 9  Copynumber: 3.7  Consensus size: 9

       4776 ACACCAGAAA

                    *
       4786 TTTTTTTTT
          1 TTTTTTTTC

                     
       4795 TTTTTTTTC
          1 TTTTTTTTC

                     
       4804 TTTTTTTTC
          1 TTTTTTTTC

                  
       4813 TTTTTT
          1 TTTTTT

       4819 GGATTTACTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   9   23  1.00

ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94


Consensus pattern (9 bp):   
TTTTTTTTC
Done.