Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005551.1 Kokia drynarioides strain JFW-HI SEQ_119656, 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, 780

Length: 1300
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30


Found at i:440 original size:16 final size:16

Alignment explanation


    Indices: 419--451  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        409 GAGGAAATAG

                            
        419 AGGAAGAAAAAAAGGA
          1 AGGAAGAAAAAAAGGA

                      *     
        435 AGGAAGAAAAGAAGGA
          1 AGGAAGAAAAAAAGGA

             
        451 A
          1 A

        452 AAGATGTCGA


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

Matches are distributed among these distances:
  16   16  1.00

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


Consensus pattern (16 bp):   
AGGAAGAAAAAAAGGA

Found at i:920 original size:11 final size:11

Alignment explanation


    Indices: 885--931  Score: 51
    Period size: 11  Copynumber: 4.2  Consensus size: 11

        875 CCTATTTCCT

                       
        885 TTGTCATTGCA
          1 TTGTCATTGCA

              * *       
        896 TTTTAATTGTCA
          1 TTGTCATTG-CA

                        
        908 TTG-CATATGCA
          1 TTGTCAT-TGCA

                       
        919 TTGTCATTGCA
          1 TTGTCATTGCA

              
        930 TT
          1 TT

        932 TCCATTTGTC


Statistics
Matches: 29,  Mismatches: 4, Indels: 6
        0.74            0.10        0.15

Matches are distributed among these distances:
  11   20  0.69
  12    9  0.31

ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49


Consensus pattern (11 bp):   
TTGTCATTGCA

Found at i:937 original size:17 final size:17

Alignment explanation


    Indices: 878--937  Score: 75
    Period size: 17  Copynumber: 3.5  Consensus size: 17

        868 ATTGTCACCT

                  *          
        878 ATTTCCTTTGTCATTGC
          1 ATTTCCATTGTCATTGC

                **           
        895 ATTTTAATTGTCATTGC
          1 ATTTCCATTGTCATTGC

              * *            
        912 ATATGCATTGTCATTGC
          1 ATTTCCATTGTCATTGC

                     
        929 ATTTCCATT
          1 ATTTCCATT

        938 TGTCTTTGTA


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   35  1.00

ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50


Consensus pattern (17 bp):   
ATTTCCATTGTCATTGC
Done.