Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013909.1 Kokia drynarioides strain JFW-HI SEQ_128938, 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: 22203
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31

Warning! 345 characters in sequence are not A, C, G, or T


Found at i:4515 original size:19 final size:19

Alignment explanation


    Indices: 4491--4538  Score: 96
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       4481 TTTGAGTTTA

                               
       4491 TCTTTTTATTTCTTTATTT
          1 TCTTTTTATTTCTTTATTT

                               
       4510 TCTTTTTATTTCTTTATTT
          1 TCTTTTTATTTCTTTATTT

                      
       4529 TCTTTTTATT
          1 TCTTTTTATT

       4539 CTTCCCTTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   29  1.00

ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79


Consensus pattern (19 bp):   
TCTTTTTATTTCTTTATTT

Found at i:4540 original size:9 final size:9

Alignment explanation


    Indices: 4487--4541  Score: 53
    Period size: 9  Copynumber: 6.0  Consensus size: 9

       4477 TTTTTTTGAG

                     
       4487 TTTA-TCTT
          1 TTTATTCTT

                      
       4495 TTTATTTCTT
          1 TTTA-TTCTT

                      
       4505 TATT-TTCTT
          1 T-TTATTCTT

                      
       4514 TTTATTTCTT
          1 TTTA-TTCTT

                      
       4524 TATT-TTCTT
          1 T-TTATTCTT

                     
       4533 TTTATTCTT
          1 TTTATTCTT

       4542 CCCTTTATTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 13
        0.75            0.00        0.25

Matches are distributed among these distances:
   8    8  0.20
   9   17  0.43
  10   11  0.28
  11    4  0.10

ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78


Consensus pattern (9 bp):   
TTTATTCTT

Found at i:18941 original size:4 final size:4

Alignment explanation


    Indices: 18921--18986  Score: 71
    Period size: 4  Copynumber: 16.2  Consensus size: 4

      18911 AAATAAACGG

                 *                               *      *     *          
      18921 GAAA AAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA

                                 
      18971 -AAA GAAA GAAA GAAA G
          1 GAAA GAAA GAAA GAAA G

      18987 GTAATGTGTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   42  0.79
   5    8  0.15

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (4 bp):   
GAAA

Done.