Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013354.1 Kokia drynarioides strain JFW-HI SEQ_128377, 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: 27298
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34

Warning! 24 characters in sequence are not A, C, G, or T


Found at i:2569 original size:18 final size:18

Alignment explanation


    Indices: 2523--2569  Score: 53
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       2513 AAAATTATTA

                              
       2523 TCAAATATATATAAACAT
          1 TCAAATATATATAAACAT

                 *              
       2541 T-AAAAATTATATAAA-AGT
          1 TCAAATA-TATATAAACA-T

                       
       2559 TCAAATATATA
          1 TCAAATATATA

       2570 ACTAGAAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 6
        0.75            0.06        0.19

Matches are distributed among these distances:
  17    5  0.21
  18   15  0.62
  19    4  0.17

ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34


Consensus pattern (18 bp):   
TCAAATATATATAAACAT

Found at i:22033 original size:30 final size:31

Alignment explanation


    Indices: 21972--22034  Score: 85
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      21962 AAATTGAATC

                     *           *         
      21972 TTTCAATTTTAAATTTTCAATTAATAATAAA
          1 TTTCAATTTAAAATTTTCAATAAATAATAAA

                                            
      22003 TTTCAATTTAAAATTTT-AA-AAATAATTAAA
          1 TTTCAATTTAAAATTTTCAATAAATAA-TAAA

              
      22033 TT
          1 TT

      22035 AGTGTGTCAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29    5  0.17
  30    8  0.28
  31   16  0.55

ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48


Consensus pattern (31 bp):   
TTTCAATTTAAAATTTTCAATAAATAATAAA

Found at i:23886 original size:19 final size:20

Alignment explanation


    Indices: 23862--23901  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      23852 TTCAAATTTG

                      *         
      23862 ATATGGAGCATATT-TAAAT
          1 ATATGGAGCAAATTGTAAAT

                   *            
      23881 ATATGGATCAAATTGTAAAT
          1 ATATGGAGCAAATTGTAAAT

             
      23901 A
          1 A

      23902 GACGTGTAAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  19   12  0.67
  20    6  0.33

ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35


Consensus pattern (20 bp):   
ATATGGAGCAAATTGTAAAT

Done.