Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003122.1 Kokia drynarioides strain JFW-HI SEQ_115695, 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, 847

Length: 1412
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40


Found at i:35 original size:3 final size:3

Alignment explanation


    Indices: 27--52  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

         17 GGCCCAAATT

                                              
         27 ATC ATC ATC ATC ATC ATC ATC ATC AT
          1 ATC ATC ATC ATC ATC ATC ATC ATC AT

         53 TATTATTATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35


Consensus pattern (3 bp):   
ATC

Found at i:57 original size:3 final size:3

Alignment explanation


    Indices: 51--84  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

         41 CATCATCATC

                                                         
         51 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

         85 GGGCCCAAGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:1231 original size:27 final size:25

Alignment explanation


    Indices: 1201--1264  Score: 74
    Period size: 27  Copynumber: 2.4  Consensus size: 25

       1191 CACTTATATA

                                   *   
       1201 ATTTTTATTTATGTTTATTTCATCTTT
          1 ATTTTT-TTTATGTTTATTT-ATATTT

                     *                
       1228 ATTTGTTTTCATGTTTATTTATATTT
          1 ATTT-TTTTTATGTTTATTTATATTT

                       
       1254 ATGTTTTTTTA
          1 AT-TTTTTTTA

       1265 CACATTCCCC


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
  26   12  0.38
  27   18  0.56
  28    2  0.06

ACGTcount: A:0.19, C:0.05, G:0.06, T:0.70


Consensus pattern (25 bp):   
ATTTTTTTTATGTTTATTTATATTT

Found at i:1257 original size:16 final size:16

Alignment explanation


    Indices: 1214--1264  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       1204 TTTATTTATG

                       *    
       1214 TTTA-TTTCATCTTTA
          1 TTTATTTTCATGTTTA

               *            
       1229 TTTGTTTTCATGTTTA
          1 TTTATTTTCATGTTTA

                            *
       1245 TTTATATTT-ATGTTTT
          1 TTTAT-TTTCATGTTTA

                
       1261 TTTA
          1 TTTA

       1265 CACATTCCCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  15    3  0.10
  16   24  0.80
  17    3  0.10

ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71


Consensus pattern (16 bp):   
TTTATTTTCATGTTTA
Done.