Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001761.1 Kokia drynarioides strain JFW-HI SEQ_113478, 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: 29202
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:11724 original size:30 final size:30

Alignment explanation


    Indices: 11688--11758  Score: 142
    Period size: 30  Copynumber: 2.4  Consensus size: 30

      11678 GACTAAAGCA

                                          
      11688 AAGTTGGCTAGAGTTCGCAAGTTGTACCAC
          1 AAGTTGGCTAGAGTTCGCAAGTTGTACCAC

                                          
      11718 AAGTTGGCTAGAGTTCGCAAGTTGTACCAC
          1 AAGTTGGCTAGAGTTCGCAAGTTGTACCAC

                       
      11748 AAGTTGGCTAG
          1 AAGTTGGCTAG

      11759 GTTAATTAAT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   41  1.00

ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27


Consensus pattern (30 bp):   
AAGTTGGCTAGAGTTCGCAAGTTGTACCAC

Found at i:13359 original size:18 final size:18

Alignment explanation


    Indices: 13336--13370  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      13326 TAAAATTATA

                              
      13336 AAATAAAATAATTATTTC
          1 AAATAAAATAATTATTTC

                     *       
      13354 AAATAAAATTATTATTT
          1 AAATAAAATAATTATTT

      13371 TTATATGTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43


Consensus pattern (18 bp):   
AAATAAAATAATTATTTC

Found at i:13837 original size:51 final size:51

Alignment explanation


    Indices: 13776--13880  Score: 210
    Period size: 51  Copynumber: 2.1  Consensus size: 51

      13766 ATTCTTTAAA

                                                               
      13776 AAAATTTTAAAACATGAAATAAAAAATATAAACATGAATGAGAGAAGAATT
          1 AAAATTTTAAAACATGAAATAAAAAATATAAACATGAATGAGAGAAGAATT

                                                               
      13827 AAAATTTTAAAACATGAAATAAAAAATATAAACATGAATGAGAGAAGAATT
          1 AAAATTTTAAAACATGAAATAAAAAATATAAACATGAATGAGAGAAGAATT

               
      13878 AAA
          1 AAA

      13881 CCTGAGACTT


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   54  1.00

ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23


Consensus pattern (51 bp):   
AAAATTTTAAAACATGAAATAAAAAATATAAACATGAATGAGAGAAGAATT

Found at i:14507 original size:2 final size:2

Alignment explanation


    Indices: 14500--14535  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      14490 AACTCAGACA

                                                                 
      14500 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

      14536 GGCCACTACA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AG

Done.