Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006685.1 Kokia drynarioides strain JFW-HI SEQ_121279, 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: 25281
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:5910 original size:3 final size:3

Alignment explanation


    Indices: 5902--5934  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       5892 GAAGCCGTGA

                                                       
       5902 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
          1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG

       5935 AGTGAGTGGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33


Consensus pattern (3 bp):   
GTG

Found at i:6212 original size:9 final size:9

Alignment explanation


    Indices: 6194--6223  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       6184 TTGAGCCGAG

                     
       6194 TAATTCAAA
          1 TAATTCAAA

                 *   
       6203 TAATTTAAA
          1 TAATTCAAA

                     
       6212 TAATTCAAA
          1 TAATTCAAA

               
       6221 TAA
          1 TAA

       6224 CATATTGGTG


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   9   19  1.00

ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37


Consensus pattern (9 bp):   
TAATTCAAA

Found at i:9848 original size:21 final size:22

Alignment explanation


    Indices: 9824--9871  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       9814 ATTTTATTGA

                 *                
       9824 ATTTATTA-TTTTACTTTAAAT
          1 ATTTAATATTTTTACTTTAAAT

                          *       
       9845 ATTTAATATTTTTATTTTAAAT
          1 ATTTAATATTTTTACTTTAAAT

            *    
       9867 TTTTA
          1 ATTTA

       9872 GTTCGAAATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  21    7  0.30
  22   16  0.70

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (22 bp):   
ATTTAATATTTTTACTTTAAAT

Found at i:23748 original size:23 final size:24

Alignment explanation


    Indices: 23718--23762  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      23708 AATTAAAAAG

                       *            
      23718 TTATTT-AAATTAATTAAAACACA
          1 TTATTTAAAATAAATTAAAACACA

                                  
      23741 TTATTTAAAATAAATTAAAACA
          1 TTATTTAAAATAAATTAAAACA

      23763 TTAAATATGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23    6  0.30
  24   14  0.70

ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38


Consensus pattern (24 bp):   
TTATTTAAAATAAATTAAAACACA

Done.