Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007666.1 Kokia drynarioides strain JFW-HI SEQ_122297, 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: 16806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:3728 original size:9 final size:9

Alignment explanation


    Indices: 3714--3757  Score: 54
    Period size: 9  Copynumber: 4.9  Consensus size: 9

       3704 ACTGTCACTT

                     
       3714 CTATTATTA
          1 CTATTATTA

                     
       3723 CTATTATTA
          1 CTATTATTA

            *        
       3732 TTATTATTA
          1 CTATTATTA

            *         
       3741 TTATTATTTA
          1 CTATTA-TTA

                    
       3751 C-ATTATT
          1 CTATTATT

       3758 GAAATAGGTG


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
   8    2  0.06
   9   27  0.84
  10    3  0.09

ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61


Consensus pattern (9 bp):   
CTATTATTA

Found at i:3730 original size:3 final size:3

Alignment explanation


    Indices: 3715--3748  Score: 59
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       3705 CTGTCACTTC

                      *                                  
       3715 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T

       3749 TACATTATTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:11529 original size:14 final size:14

Alignment explanation


    Indices: 11510--11536  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      11500 CTAATTAGGA

                          
      11510 TTATATTTTATTTC
          1 TTATATTTTATTTC

                         
      11524 TTATATTTTATTT
          1 TTATATTTTATTT

      11537 AAATAAATAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74


Consensus pattern (14 bp):   
TTATATTTTATTTC

Found at i:14378 original size:21 final size:21

Alignment explanation


    Indices: 14351--14414  Score: 92
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      14341 AGTTGCATGC

                                 
      14351 ATATGCGAACTCTTTTATATG
          1 ATATGCGAACTCTTTTATATG

            *                *   
      14372 TTATGCGAACTCTTTTACATG
          1 ATATGCGAACTCTTTTATATG

              *             *    
      14393 ATGTGCGAACTCTTTTGTATG
          1 ATATGCGAACTCTTTTATATG

             
      14414 A
          1 A

      14415 ATCTGTTTGT


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   37  1.00

ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42


Consensus pattern (21 bp):   
ATATGCGAACTCTTTTATATG

Found at i:16660 original size:18 final size:18

Alignment explanation


    Indices: 16637--16684  Score: 69
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      16627 GTTGGTGAAA

                  *           
      16637 ATTAGGGATTTAGAAATG
          1 ATTAGGAATTTAGAAATG

                              
      16655 ATTAGGAATTTAGAAATG
          1 ATTAGGAATTTAGAAATG

               *        
      16673 AATGAGGAATTT
          1 -ATTAGGAATTT

      16685 TTGAATCAGC


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  18   17  0.63
  19   10  0.37

ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33


Consensus pattern (18 bp):   
ATTAGGAATTTAGAAATG

Done.