Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007190.1 Kokia drynarioides strain JFW-HI SEQ_121804, 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: 9729
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31


Found at i:5450 original size:23 final size:23

Alignment explanation


    Indices: 5424--5472  Score: 89
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       5414 CTGACGTGAC

                 *                 
       5424 ATCCAGTCAGCAGCTTCTAGAAG
          1 ATCCAATCAGCAGCTTCTAGAAG

                                   
       5447 ATCCAATCAGCAGCTTCTAGAAG
          1 ATCCAATCAGCAGCTTCTAGAAG

               
       5470 ATC
          1 ATC

       5473 TGGACGAGTG


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22


Consensus pattern (23 bp):   
ATCCAATCAGCAGCTTCTAGAAG

Found at i:5644 original size:7 final size:7

Alignment explanation


    Indices: 5632--5663  Score: 64
    Period size: 7  Copynumber: 4.6  Consensus size: 7

       5622 AGCTAGAAGA

                   
       5632 TCATCCC
          1 TCATCCC

                   
       5639 TCATCCC
          1 TCATCCC

                   
       5646 TCATCCC
          1 TCATCCC

                   
       5653 TCATCCC
          1 TCATCCC

                
       5660 TCAT
          1 TCAT

       5664 TACTTTGTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   25  1.00

ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31


Consensus pattern (7 bp):   
TCATCCC

Found at i:9467 original size:6 final size:6

Alignment explanation


    Indices: 9456--9561  Score: 72
    Period size: 6  Copynumber: 17.5  Consensus size: 6

       9446 ACCCATTGTT

                                   *     *        **           *   *
       9456 TTTTTA TTTTTA -TTTTA TTATTA -ATTTA TTTCGA TTATTTA TATTTC
          1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA

             *             *                 *                 * *   
       9503 TATTTA TTTTTA TCTTTA TTTTTA TTTTAAA TTTTTA TTTATTA ATATTA
          1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTT-TTA TTTTTA

                      
       9553 TTTTTA TTT
          1 TTTTTA TTT

       9562 CTTTTTCAGA


Statistics
Matches: 75,  Mismatches: 20, Indels: 10
        0.71            0.19        0.10

Matches are distributed among these distances:
   5    8  0.11
   6   55  0.73
   7   12  0.16

ACGTcount: A:0.25, C:0.03, G:0.01, T:0.72


Consensus pattern (6 bp):   
TTTTTA

Found at i:9536 original size:13 final size:11

Alignment explanation


    Indices: 9457--9542  Score: 75
    Period size: 11  Copynumber: 7.3  Consensus size: 11

       9447 CCCATTGTTT

                       
       9457 TTTTATTTTTA
          1 TTTTATTTTTA

                   *   
       9468 TTTTATTATTA
          1 TTTTATTTTTA

            *             
       9479 ATTTATTTCGATTA
          1 TTTTATTT---TTA

                     *  
       9493 TTTATATTTCTA
          1 TTT-TATTTTTA

                       
       9505 -TTTATTTTTA
          1 TTTTATTTTTA

                        
       9515 TCTTTATTTTTA
          1 T-TTTATTTTTA

                         
       9527 TTTTAAATTTTTA
          1 TTTT--ATTTTTA

               
       9540 TTT
          1 TTT

       9543 ATTAATATTA


Statistics
Matches: 61,  Mismatches: 6, Indels: 14
        0.75            0.07        0.17

Matches are distributed among these distances:
  10    7  0.11
  11   21  0.34
  12   13  0.21
  13   10  0.16
  14    5  0.08
  15    5  0.08

ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72


Consensus pattern (11 bp):   
TTTTATTTTTA
Done.