Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010222.1 Kokia drynarioides strain JFW-HI SEQ_125051, 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: 3904
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:671 original size:6 final size:6

Alignment explanation


    Indices: 662--725  Score: 51
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        652 GATTTAAGGC

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

               **            
        711 AAAAAT AAATTT AAA
          1 AAATTT AAATTT AAA

        726 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:688 original size:37 final size:35

Alignment explanation


    Indices: 644--725  Score: 110
    Period size: 37  Copynumber: 2.3  Consensus size: 35

        634 CAAATTTAAT

                    *      **                    
        644 TAAATTTAGATTTAAGGCAAATTTAAATTTAAAAAGA
          1 TAAATTTAAATTTAACACAAATTTAAATTT-AAAA-A

                             *                 
        681 TAAATTTAAATTTAACATAAATTTAAATTTAAAAA
          1 TAAATTTAAATTTAACACAAATTTAAATTTAAAAA

                      
        716 TAAATTTAAA
          1 TAAATTTAAA

        726 CCAATTTAAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  35   11  0.27
  36    4  0.10
  37   26  0.63

ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38


Consensus pattern (35 bp):   
TAAATTTAAATTTAACACAAATTTAAATTTAAAAA

Found at i:702 original size:17 final size:17

Alignment explanation


    Indices: 635--725  Score: 85
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        625 AAATCCATTC

                     *       
        635 AAATTTAA-TTAAATTT
          1 AAATTTAAGATAAATTT

             *       **      
        651 AGATTTAAGGCAAATTT
          1 AAATTTAAGATAAATTT

                                
        668 AAATTTAAAAAGATAAATTT
          1 AAATTT---AAGATAAATTT

                    *        
        688 AAATTTAACATAAATTT
          1 AAATTTAAGATAAATTT

                     *        
        705 AAATTTAAAAATAAATTT
          1 AAATTT-AAGATAAATTT

               
        723 AAA
          1 AAA

        726 CCAATTTAAA


Statistics
Matches: 62,  Mismatches: 8, Indels: 8
        0.79            0.10        0.10

Matches are distributed among these distances:
  16    7  0.11
  17   27  0.44
  18   13  0.21
  20   15  0.24

ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38


Consensus pattern (17 bp):   
AAATTTAAGATAAATTT
Done.