Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008285.1 Kokia drynarioides strain JFW-HI SEQ_122950, 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: 7707
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:64 original size:27 final size:27

Alignment explanation


    Indices: 10--66  Score: 80
    Period size: 28  Copynumber: 2.1  Consensus size: 27

          1 ATTTTTAAA

                                        
         10 TTCAAAATATTAATAAAAAGTTTAAAAT
          1 TTCAAAATATTAATAAAAAG-TTAAAAT

                                   *    
         38 TTCAAAATATTAATTAAAAA-TTCAAAT
          1 TTCAAAATATTAA-TAAAAAGTTAAAAT

              
         65 TT
          1 TT

         67 TATATTTTTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  27    8  0.30
  28   13  0.48
  29    6  0.22

ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39


Consensus pattern (27 bp):   
TTCAAAATATTAATAAAAAGTTAAAAT

Found at i:95 original size:18 final size:18

Alignment explanation


    Indices: 72--107  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

         62 AATTTTATAT

                              
         72 TTTTTTAAAAAATATAAA
          1 TTTTTTAAAAAATATAAA

                       *      
         90 TTTTTTAAAAATTATAAA
          1 TTTTTTAAAAAATATAAA

        108 AAATATTTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (18 bp):   
TTTTTTAAAAAATATAAA

Found at i:1892 original size:19 final size:20

Alignment explanation


    Indices: 1870--1912  Score: 61
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       1860 TTTTCTAAAA

                  *             
       1870 TTTTAATTATATTTT-ATTT
          1 TTTTAACTATATTTTAATTT

                 *              
       1889 TTTTACCTATATTTTAATTT
          1 TTTTAACTATATTTTAATTT

                
       1909 TTTT
          1 TTTT

       1913 TTAGAATTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   13  0.62
  20    8  0.38

ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72


Consensus pattern (20 bp):   
TTTTAACTATATTTTAATTT

Found at i:4933 original size:18 final size:18

Alignment explanation


    Indices: 4910--4952  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       4900 TAATAGATTT

                               
       4910 TTAATTAAATAAATTT-AA
          1 TTAATTAAA-AAATTTAAA

                  *    *      
       4928 TTAATTGAAAATTTTAAA
          1 TTAATTAAAAAATTTAAA

                   
       4946 TTAATTA
          1 TTAATTA

       4953 CACCCTTGAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  17    5  0.24
  18   16  0.76

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (18 bp):   
TTAATTAAAAAATTTAAA
Done.