Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010264.1 Kokia drynarioides strain JFW-HI SEQ_125103, 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: 3981
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:749 original size:6 final size:6

Alignment explanation


    Indices: 740--803  Score: 51
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        730 GATTTAAGGA

                               **                                     
        740 AAATTT AAATTT AAAAAGAT AAATTT AAATTT AACA--T AAATTT AAATTT
          1 AAATTT AAATTT --AAATTT AAATTT AAATTT AA-ATTT AAATTT AAATTT

               **            
        789 AAAAAT AAATTT AAA
          1 AAATTT AAATTT AAA

        804 CCAATTTAAA


Statistics
Matches: 45,  Mismatches: 8, Indels: 10
        0.71            0.13        0.16

Matches are distributed among these distances:
   4    1  0.02
   5    3  0.07
   6   36  0.80
   7    1  0.02
   8    4  0.09

ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38


Consensus pattern (6 bp):   
AAATTT

Found at i:766 original size:37 final size:35

Alignment explanation


    Indices: 722--803  Score: 112
    Period size: 37  Copynumber: 2.3  Consensus size: 35

        712 CAAATTTAAT

                    *       *                     
        722 TAAATTTAGATTTAAGGA-AAATTTAAATTTAAAAAGA
          1 TAAATTTAAATTTAA-CATAAATTTAAATTT-AAAA-A

                                               
        759 TAAATTTAAATTTAACATAAATTTAAATTTAAAAA
          1 TAAATTTAAATTTAACATAAATTTAAATTTAAAAA

                      
        794 TAAATTTAAA
          1 TAAATTTAAA

        804 CCAATTTAAA


Statistics
Matches: 42,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  35   11  0.26
  36    5  0.12
  37   26  0.62

ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38


Consensus pattern (35 bp):   
TAAATTTAAATTTAACATAAATTTAAATTTAAAAA

Found at i:780 original size:17 final size:17

Alignment explanation


    Indices: 713--803  Score: 87
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        703 AAATCCATTC

                     *       
        713 AAATTTAA-TTAAATTT
          1 AAATTTAAGATAAATTT

             *                
        729 AGATTTAAGGA-AAATTT
          1 AAATTTAA-GATAAATTT

                                
        746 AAATTTAAAAAGATAAATTT
          1 AAATTT---AAGATAAATTT

                    *        
        766 AAATTTAACATAAATTT
          1 AAATTTAAGATAAATTT

                     *        
        783 AAATTTAAAAATAAATTT
          1 AAATTT-AAGATAAATTT

               
        801 AAA
          1 AAA

        804 CCAATTTAAA


Statistics
Matches: 63,  Mismatches: 5, Indels: 12
        0.79            0.06        0.15

Matches are distributed among these distances:
  16    7  0.11
  17   27  0.43
  18   13  0.21
  19    2  0.03
  20   14  0.22

ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38


Consensus pattern (17 bp):   
AAATTTAAGATAAATTT
Done.