Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001724.1 Kokia drynarioides strain JFW-HI SEQ_113425, 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: 8299
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:49 original size:3 final size:3

Alignment explanation


    Indices: 37--92  Score: 105
    Period size: 3  Copynumber: 19.0  Consensus size: 3

         27 ATTCGACAGC

                                                                           
         37 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                       
         84 ATA ATA ATA
          1 ATA ATA ATA

         93 GAAAAAAACT


Statistics
Matches: 52,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2    2  0.04
   3   50  0.96

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Found at i:3305 original size:22 final size:22

Alignment explanation


    Indices: 3280--3332  Score: 54
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       3270 AAAATGTAAT

                                  
       3280 TTTTATTATAATAAAAATAAAA
          1 TTTTATTATAATAAAAATAAAA

                   * *   *   *     
       3302 TTTT-TAAAAAATTAAATTAAAA
          1 TTTTAT-TATAATAAAAATAAAA

                     
       3324 TTTTATTAT
          1 TTTTATTAT

       3333 TTTTAGAGAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 4
        0.70            0.18        0.12

Matches are distributed among these distances:
  21    1  0.04
  22   21  0.91
  23    1  0.04

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (22 bp):   
TTTTATTATAATAAAAATAAAA

Found at i:3668 original size:29 final size:29

Alignment explanation


    Indices: 3635--3693  Score: 75
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       3625 ATTTTTATAT

                                          
       3635 AATT-AATATAAATCACTTATTAAAATTTA
          1 AATTAAATATAAATCACTTATT-AAATTTA

                      *   *    *         
       3664 AATTAAATATGAATTACTTGTTAAATTTA
          1 AATTAAATATAAATCACTTATTAAATTTA

             
       3693 A
          1 A

       3694 TAATTTTGTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29   12  0.46
  30   14  0.54

ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42


Consensus pattern (29 bp):   
AATTAAATATAAATCACTTATTAAATTTA

Found at i:7843 original size:19 final size:20

Alignment explanation


    Indices: 7798--7851  Score: 65
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       7788 AAATTACAAA

                  *        *    
       7798 AAAAAAATCAAAATACTTTT
          1 AAAAAATTCAAAATAATTTT

                                
       7818 AAAAAATTCAAAATAATTTT
          1 AAAAAATTCAAAATAATTTT

             *      *      
       7838 -TAAAATTTAAAATA
          1 AAAAAATTCAAAATA

       7852 TTTATATTTA


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  19   12  0.40
  20   18  0.60

ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33


Consensus pattern (20 bp):   
AAAAAATTCAAAATAATTTT

Found at i:7883 original size:18 final size:17

Alignment explanation


    Indices: 7819--7917  Score: 76
    Period size: 18  Copynumber: 5.6  Consensus size: 17

       7809 AATACTTTTA

                   *           
       7819 AAAAATTCAAAATAATTTT
          1 AAAAATTTAAAA-AA-TTT

            *           *    
       7838 TAAAATTTAAAATATTT
          1 AAAAATTTAAAAAATTT

               *               
       7855 --ATATTTAAAAAAATTAT
          1 AAAAATTT-AAAAAATT-T

                              
       7872 AAAAATTTAAAAAATTAT
          1 AAAAATTTAAAAAATT-T

                  *       *  
       7890 AAAAATATAAAAAAGTT
          1 AAAAATTTAAAAAATTT

                *      
       7907 AAAATTTTAAA
          1 AAAAATTTAAA

       7918 TATGTTTTAA


Statistics
Matches: 66,  Mismatches: 10, Indels: 10
        0.77            0.12        0.12

Matches are distributed among these distances:
  15    5  0.08
  16    7  0.11
  17   14  0.21
  18   25  0.38
  19   15  0.23

ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36


Consensus pattern (17 bp):   
AAAAATTTAAAAAATTT

Found at i:8264 original size:3 final size:3

Alignment explanation


    Indices: 8252--8299  Score: 89
    Period size: 3  Copynumber: 16.3  Consensus size: 3

       8242 ATTCGACAGC

                                                                           
       8252 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

             
       8299 A
          1 A


Statistics
Matches: 44,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2    2  0.05
   3   42  0.95

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
ATA

Done.