Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002423.1 Kokia drynarioides strain JFW-HI SEQ_114521, 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: 9084
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Found at i:113 original size:23 final size:23

Alignment explanation


    Indices: 78--151  Score: 80
    Period size: 23  Copynumber: 3.3  Consensus size: 23

         68 TTATTTTTCC

                 *            *    
         78 TTTTTGAAA-TTTAT-AATTATA
          1 TTTTTAAAATTTTATCAAATATA

                                    
         99 TATTTTAAAATTTTATCAAATATA
          1 T-TTTTAAAATTTTATCAAATATA

                    *    * *       
        123 TTTTTAAACTTTTTTTAAATATA
          1 TTTTTAAAATTTTATCAAATATA

                  
        146 TTTTTA
          1 TTTTTA

        152 TGATTTTTTA


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  21    1  0.02
  22    7  0.16
  23   30  0.67
  24    7  0.16

ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58


Consensus pattern (23 bp):   
TTTTTAAAATTTTATCAAATATA

Found at i:1726 original size:30 final size:30

Alignment explanation


    Indices: 1690--1746  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1680 TTTTATAAAT

                             *             
       1690 AATTAATA-TTAATTATTTTAAAATATTCAA
          1 AATTAATATTTAA-TATATTAAAATATTCAA

                       *               
       1720 AATTAATATTTCATATATTAAAATATT
          1 AATTAATATTTAATATATTAAAATATT

       1747 AATAATAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  30   21  0.88
  31    3  0.12

ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47


Consensus pattern (30 bp):   
AATTAATATTTAATATATTAAAATATTCAA

Found at i:1729 original size:23 final size:24

Alignment explanation


    Indices: 1673--1730  Score: 68
    Period size: 23  Copynumber: 2.5  Consensus size: 24

       1663 TATACATTTT

                                    
       1673 AATTAA-ATTTTATAAATAATTAA
          1 AATTAATATTTTATAAATAATTAA

            *                         
       1696 TATTAATTATTTTA-AAAT-ATTCAA
          1 AATTAA-TATTTTATAAATAATT-AA

                       
       1720 AATTAATATTT
          1 AATTAATATTT

       1731 CATATATTAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  23   13  0.43
  24   11  0.37
  25    6  0.20

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (24 bp):   
AATTAATATTTTATAAATAATTAA

Found at i:8561 original size:31 final size:30

Alignment explanation


    Indices: 8526--8610  Score: 84
    Period size: 31  Copynumber: 2.8  Consensus size: 30

       8516 AAGTGTTTAA

                                           
       8526 AGATTAAATTTATAAAATTTATAAATATGAT
          1 AGATTAAATTTATAAAATTTATAAAT-TGAT

                       * **      *      *  
       8557 AGATTAAATTTGTTGAATTATTTAAATTTAT
          1 AGATTAAATTTATAAAATT-TATAAATTGAT

                                     
       8588 -GATTAAATTTATAGAAA-TTATAA
          1 AGATTAAATTTATA-AAATTTATAA

       8611 GTATTGAGAA


Statistics
Matches: 43,  Mismatches: 9, Indels: 6
        0.74            0.16        0.10

Matches are distributed among these distances:
  29    4  0.09
  30   12  0.28
  31   21  0.49
  32    6  0.14

ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45


Consensus pattern (30 bp):   
AGATTAAATTTATAAAATTTATAAATTGAT
Done.