Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000655.1 Kokia drynarioides strain JFW-HI SEQ_111634, 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: 8634
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34


Found at i:8493 original size:4 final size:4

Alignment explanation


    Indices: 8484--8536  Score: 61
    Period size: 4  Copynumber: 12.8  Consensus size: 4

       8474 AAATAAACGG

                                 *               *      *                
       8484 GAAA GAAA GAAA GAAAA AAAA GAAA GAAA GGAA GAAG GAGAA GAAA GAAA
          1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA

               
       8534 GAA
          1 GAA

       8537 GAAGGAAATA


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
   4   35  0.85
   5    6  0.15

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:8507 original size:17 final size:19

Alignment explanation


    Indices: 8485--8540  Score: 71
    Period size: 17  Copynumber: 2.9  Consensus size: 19

       8475 AATAAACGGG

                               
       8485 AAAGAAAGAAAGAA-AA-A
          1 AAAGAAAGAAAGAAGAAGA

                                 
       8502 AAAGAAAGAAAGGAAGAAGGA
          1 AAAGAAAGAAA-GAAGAA-GA

            *                 
       8523 GAAGAAAGAAAGAAGAAG
          1 AAAGAAAGAAAGAAGAAG

       8541 GAAATATCTC


Statistics
Matches: 34,  Mismatches: 1, Indels: 6
        0.83            0.02        0.15

Matches are distributed among these distances:
  17   11  0.32
  18    3  0.09
  19    3  0.09
  20    6  0.18
  21   11  0.32

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (19 bp):   
AAAGAAAGAAAGAAGAAGA

Found at i:8510 original size:21 final size:21

Alignment explanation


    Indices: 8484--8536  Score: 70
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       8474 AAATAAACGG

                                 
       8484 GAAAGAAAGAAAGAAAAAAAA
          1 GAAAGAAAGAAAGAAAAAAAA

                     *     ** *  
       8505 GAAAGAAAGGAAGAAGGAGAA
          1 GAAAGAAAGAAAGAAAAAAAA

                       
       8526 GAAAGAAAGAA
          1 GAAAGAAAGAA

       8537 GAAGGAAATA


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (21 bp):   
GAAAGAAAGAAAGAAAAAAAA
Done.