Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003399.1 Kokia drynarioides strain JFW-HI SEQ_116140, 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: 2216
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40


Found at i:690 original size:18 final size:19

Alignment explanation


    Indices: 667--734  Score: 68
    Period size: 18  Copynumber: 3.6  Consensus size: 19

        657 CATTTAAATT

                               
        667 TTAT-TAAAAATTACAAAA
          1 TTATATAAAAATTACAAAA

                      *   *    
        685 TTAT-TAAAAGTTAGAAAA
          1 TTATATAAAAATTACAAAA

                         *  *    
        703 TTATATAGAAAATCATTAAAA
          1 TTATATA-AAAATTA-CAAAA

                       
        724 TTATATAAAAA
          1 TTATATAAAAA

        735 AATATTATAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  18   20  0.48
  19    2  0.05
  20    9  0.21
  21   11  0.26

ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34


Consensus pattern (19 bp):   
TTATATAAAAATTACAAAA

Found at i:1213 original size:20 final size:20

Alignment explanation


    Indices: 1190--1244  Score: 76
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       1180 TATTTTAATG

                                 
       1190 ATTTTTTATAAATATTCTAT-
          1 ATTTTTTATAAAT-TTCTATA

                  *             
       1210 ATTTTTAATAAATTTCTATA
          1 ATTTTTTATAAATTTCTATA

                      *    
       1230 ATTTTTTATATATTT
          1 ATTTTTTATAAATTT

       1245 TTTTAAAAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  19    6  0.19
  20   25  0.81

ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62


Consensus pattern (20 bp):   
ATTTTTTATAAATTTCTATA

Found at i:1807 original size:22 final size:23

Alignment explanation


    Indices: 1767--1818  Score: 79
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       1757 TTAATGTTAC

                     *              
       1767 ATTTATATACTAATTAAAACTAAT
          1 ATTTATATAATAA-TAAAACTAAT

                                   
       1791 ATTTATATAATAA-AAAACTAAT
          1 ATTTATATAATAATAAAACTAAT

                  
       1813 ATTTAT
          1 ATTTAT

       1819 TATTTAATTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22   15  0.56
  24   12  0.44

ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42


Consensus pattern (23 bp):   
ATTTATATAATAATAAAACTAAT
Done.