Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006516.1 Kokia drynarioides strain JFW-HI SEQ_121100, 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: 11506
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:5499 original size:19 final size:19

Alignment explanation


    Indices: 5477--5514  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       5467 ACATATAAAA

                                
       5477 TTTTAAATATTTTATATATT
          1 TTTTAAA-ATTTTATATATT

                 *            
       5497 TTTTACAATTTTATATAT
          1 TTTTAAAATTTTATATAT

       5515 ATATATATAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   11  0.65
  20    6  0.35

ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63


Consensus pattern (19 bp):   
TTTTAAAATTTTATATATT

Found at i:6178 original size:23 final size:24

Alignment explanation


    Indices: 6142--6215  Score: 89
    Period size: 24  Copynumber: 3.0  Consensus size: 24

       6132 ATCGACTCAA

                                    
       6142 ATTTTAAATAATTAAAAAAAATAT
          1 ATTTTAAATAATTAAAAAAAATAT

                   *                   
       6166 -TTATTATAT-ATTATAAAATAAATAT
          1 ATT-TTAAATAATTA-AAAA-AAATAT

                              *     
       6191 ATTTTAAATAATTAAAAATAATAT
          1 ATTTTAAATAATTAAAAAAAATAT

             
       6215 A
          1 A

       6216 ATATAAGTCA


Statistics
Matches: 42,  Mismatches: 3, Indels: 10
        0.76            0.05        0.18

Matches are distributed among these distances:
  23    6  0.14
  24   15  0.36
  25   15  0.36
  26    6  0.14

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (24 bp):   
ATTTTAAATAATTAAAAAAAATAT

Found at i:6208 original size:25 final size:25

Alignment explanation


    Indices: 6142--6215  Score: 93
    Period size: 25  Copynumber: 3.0  Consensus size: 25

       6132 ATCGACTCAA

                                     
       6142 ATTTTAAATAATTAAAAA-AAATAT
          1 ATTTTAAATAATTAAAAATAAATAT

                   *                   
       6166 -TTATTATAT-ATTATAAAATAAATAT
          1 ATT-TTAAATAATTA-AAAATAAATAT

                                     
       6191 ATTTTAAATAATTAAAAAT-AATAT
          1 ATTTTAAATAATTAAAAATAAATAT

             
       6215 A
          1 A

       6216 ATATAAGTCA


Statistics
Matches: 43,  Mismatches: 2, Indels: 10
        0.78            0.04        0.18

Matches are distributed among these distances:
  23    6  0.14
  24   15  0.35
  25   16  0.37
  26    6  0.14

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (25 bp):   
ATTTTAAATAATTAAAAATAAATAT
Done.