Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007892.1 Kokia drynarioides strain JFW-HI SEQ_122533, 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: 4863
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38


Found at i:1885 original size:18 final size:18

Alignment explanation


    Indices: 1862--1904  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1852 GAATAAATTT

                               
       1862 TTAATTAAATAAGTTT-AA
          1 TTAATTAAA-AAGTTTAAA

                       *      
       1880 TTAATTAAAAATTTTAAA
          1 TTAATTAAAAAGTTTAAA

                   
       1898 TTAATTA
          1 TTAATTA

       1905 CAATTGAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    5  0.22
  18   18  0.78

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


Consensus pattern (18 bp):   
TTAATTAAAAAGTTTAAA

Found at i:3347 original size:8 final size:10

Alignment explanation


    Indices: 3310--3346  Score: 51
    Period size: 9  Copynumber: 3.9  Consensus size: 10

       3300 TTTTAGGAAT

                      
       3310 TATATAAAAA
          1 TATATAAAAA

               *      
       3320 -ATCTAAAAA
          1 TATATAAAAA

                      
       3329 TATATAAAAA
          1 TATATAAAAA

                     
       3339 TA-ATAAAA
          1 TATATAAAA

       3347 TCTATTGAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
   9   14  0.58
  10   10  0.42

ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27


Consensus pattern (10 bp):   
TATATAAAAA

Found at i:3432 original size:19 final size:18

Alignment explanation


    Indices: 3405--3441  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       3395 TTTAATATAA

                         *    
       3405 TTTTTATAATTTCCTATT
          1 TTTTTATAATTTCATATT

                               
       3423 TTTTTAATAATTTCATATT
          1 TTTTT-ATAATTTCATATT

       3442 GTTTAAAAGC


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

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65


Consensus pattern (18 bp):   
TTTTTATAATTTCATATT

Found at i:3913 original size:22 final size:22

Alignment explanation


    Indices: 3887--3939  Score: 65
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       3877 TCATTTAATA

                                   
       3887 TTTACTAATTA-TATATATATCT
          1 TTTACTAATTATTATATATAT-T

                   *              
       3909 TTTAC-ACTTATTATATATATT
          1 TTTACTAATTATTATATATATT

                *     
       3930 TTTATTAATT
          1 TTTACTAATT

       3940 TTTTAAACAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  21    9  0.35
  22   17  0.65

ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58


Consensus pattern (22 bp):   
TTTACTAATTATTATATATATT

Found at i:4670 original size:6 final size:6

Alignment explanation


    Indices: 4663--4703  Score: 73
    Period size: 6  Copynumber: 6.8  Consensus size: 6

       4653 AGTATCCTCT

                 *                                         
       4663 CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
          1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC

       4704 ATTCTTTTGT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37


Consensus pattern (6 bp):   
CTCTCC

Done.