Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004988.1 Kokia drynarioides strain JFW-HI SEQ_118738, 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: 5525
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:3205 original size:21 final size:21

Alignment explanation


    Indices: 3179--3221  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3169 TTAATAGATA

                  *  *           
       3179 CCACAGTTTTCTTTTGAAAAT
          1 CCACAGCTTGCTTTTGAAAAT

                                 
       3200 CCACAGCTTGCTTTTGAAAAT
          1 CCACAGCTTGCTTTTGAAAAT

             
       3221 C
          1 C

       3222 TATAGATTGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37


Consensus pattern (21 bp):   
CCACAGCTTGCTTTTGAAAAT

Found at i:4804 original size:22 final size:22

Alignment explanation


    Indices: 4764--4824  Score: 81
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       4754 CGATCTAAGG

                           *      
       4764 AAAAATAAAAG-AAACAGAATT
          1 AAAAATAAAAGAAAATAGAATT

                                  
       4785 AAAAATAAAAGAAAATAGAATT
          1 AAAAATAAAAGAAAATAGAATT

                     *         
       4807 AAAAGA-AATAGAAAATAG
          1 AAAA-ATAAAAGAAAATAG

       4825 GGAAGTCGAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  21   11  0.31
  22   24  0.67
  23    1  0.03

ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15


Consensus pattern (22 bp):   
AAAAATAAAAGAAAATAGAATT

Found at i:4815 original size:15 final size:16

Alignment explanation


    Indices: 4790--4819  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       4780 GAATTAAAAA

                            
       4790 TAAAAGAAAATAGAAT
          1 TAAAAGAAAATAGAAT

                           
       4806 TAAAAG-AAATAGAA
          1 TAAAAGAAAATAGAA

       4820 AATAGGGAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17


Consensus pattern (16 bp):   
TAAAAGAAAATAGAAT
Done.