Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010733.1 Kokia drynarioides strain JFW-HI SEQ_125686, 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: 31199
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:5596 original size:20 final size:19

Alignment explanation


    Indices: 5573--5624  Score: 63
    Period size: 18  Copynumber: 2.8  Consensus size: 19

       5563 TTTCTCCCAA

                           **   
       5573 TAATGTAGAGCTATTTTAAG
          1 TAATGTAGAG-TATTACAAG

                               
       5593 TAATGTA-AGTATTACAAG
          1 TAATGTAGAGTATTACAAG

                           
       5611 TAATG-AGAGTATTA
          1 TAATGTAGAGTATTA

       5625 TCAGTTTTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  17    1  0.03
  18   19  0.66
  19    2  0.07
  20    7  0.24

ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37


Consensus pattern (19 bp):   
TAATGTAGAGTATTACAAG

Found at i:7726 original size:19 final size:18

Alignment explanation


    Indices: 7694--7732  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       7684 TTTAAAAAAT

                               
       7694 TAAAAATTAAAAATATTTA
          1 TAAAAATTAAAAAT-TTTA

                    **        
       7713 TAAAAATTTCAAATTTTA
          1 TAAAAATTAAAAATTTTA

              
       7731 TA
          1 TA

       7733 TTTTTTTAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18    6  0.33
  19   12  0.67

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (18 bp):   
TAAAAATTAAAAATTTTA

Found at i:7774 original size:20 final size:20

Alignment explanation


    Indices: 7737--7784  Score: 55
    Period size: 18  Copynumber: 2.5  Consensus size: 20

       7727 TTTATATTTT

                                
       7737 TTTAAAAAAACTATAAAAAA
          1 TTTAAAAAAACTATAAAAAA

                 *      *       
       7757 TTTAATAAAA-TCT-AAAAA
          1 TTTAAAAAAACTATAAAAAA

             *        
       7775 TATAAAAAAA
          1 TTTAAAAAAA

       7785 AATTAAAATT


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  18   13  0.54
  19    2  0.08
  20    9  0.38

ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27


Consensus pattern (20 bp):   
TTTAAAAAAACTATAAAAAA

Found at i:11704 original size:6 final size:6

Alignment explanation


    Indices: 11685--11766  Score: 65
    Period size: 6  Copynumber: 13.2  Consensus size: 6

      11675 CAGATGAAGT

                      *            *                 * *        **    
      11685 AAAAGA AAAGGA AAAAGA AACAGAA ACAGAAGA AAAGGT AAAAGA TGAAGA
          1 AAAAGA AAAAGA AAAAGA AAAAG-A A-A-AAGA AAAAGA AAAAGA AAAAGA

                 *        *                     
      11736 AAAAGG AAAAGA TAAAGA AAAAGA AAAAGA A
          1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A

      11767 GAGATTGCCG


Statistics
Matches: 57,  Mismatches: 16, Indels: 6
        0.72            0.20        0.08

Matches are distributed among these distances:
   6   49  0.86
   7    3  0.05
   8    3  0.05
   9    2  0.04

ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04


Consensus pattern (6 bp):   
AAAAGA

Done.