Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000580.1 Kokia drynarioides strain JFW-HI SEQ_111506, 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: 20385
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34


Found at i:3430 original size:17 final size:19

Alignment explanation


    Indices: 3395--3431  Score: 60
    Period size: 17  Copynumber: 2.1  Consensus size: 19

       3385 CAAAGTAGTA

                               
       3395 TTATATATTTTATATATGT
          1 TTATATATTTTATATATGT

                               
       3414 TTAT-TATTTTA-ATATGT
          1 TTATATATTTTATATATGT

             
       3431 T
          1 T

       3432 ATAAATTATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17    7  0.39
  18    7  0.39
  19    4  0.22

ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65


Consensus pattern (19 bp):   
TTATATATTTTATATATGT

Found at i:7294 original size:29 final size:31

Alignment explanation


    Indices: 7248--7306  Score: 77
    Period size: 29  Copynumber: 2.0  Consensus size: 31

       7238 AAAAATTAAG

                     *             *       
       7248 TTAAATTATTAGTATTATTAAAATATTTTTA
          1 TTAAATTATAAGTATTATTAAAACATTTTTA

                                *         
       7279 TTAAATT-TAAGT-TTATTATAACATTTTT
          1 TTAAATTATAAGTATTATTAAAACATTTTT

       7307 TTTATTACAT


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

Matches are distributed among these distances:
  29   14  0.56
  30    4  0.16
  31    7  0.28

ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56


Consensus pattern (31 bp):   
TTAAATTATAAGTATTATTAAAACATTTTTA

Found at i:7647 original size:17 final size:17

Alignment explanation


    Indices: 7618--7659  Score: 52
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       7608 TTTAATATTT

                     *       
       7618 TAAAATT-TATAAA-AA
          1 TAAAATTATTTAAATAA

                              
       7633 TATAAATTATTTAAATAA
          1 TA-AAATTATTTAAATAA

                     
       7651 TAAAATTAT
          1 TAAAATTAT

       7660 ATTTTTATTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  15    2  0.09
  16    5  0.22
  17   12  0.52
  18    4  0.17

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (17 bp):   
TAAAATTATTTAAATAA

Found at i:7750 original size:11 final size:11

Alignment explanation


    Indices: 7734--7759  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       7724 TTGGTTTCTC

                       
       7734 AAATTTAACAG
          1 AAATTTAACAG

                       
       7745 AAATTTAACAG
          1 AAATTTAACAG

                
       7756 AAAT
          1 AAAT

       7760 CTAAGGTTGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27


Consensus pattern (11 bp):   
AAATTTAACAG
Done.