Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014181.1 Kokia drynarioides strain JFW-HI SEQ_129214, 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: 27441
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34

Warning! 14 characters in sequence are not A, C, G, or T


Found at i:811 original size:23 final size:23

Alignment explanation


    Indices: 685--809  Score: 144
    Period size: 23  Copynumber: 5.4  Consensus size: 23

        675 GAACACTAGC

                      *            *
        685 GTGCTCTCTGTTTAGCACGTTT-C
          1 GTGCTCTCTGATTAGCAC-TTTGT

                *       *          
        708 GTGCCCTCTGATCAGCACTTTGT
          1 GTGCTCTCTGATTAGCACTTTGT

                                   
        731 GTGCTCTCTGATTAGCACTTTGT
          1 GTGCTCTCTGATTAGCACTTTGT

               *     *     *       
        754 GTGTTCTCTAATTAGTACTTTGT
          1 GTGCTCTCTGATTAGCACTTTGT

              *       *        *   
        777 GTACTCTCTGTTTAGCACTGTGT
          1 GTGCTCTCTGATTAGCACTTTGT

                      
        800 GTGCTCTCTG
          1 GTGCTCTCTG

        810 TTGCCCAGCA


Statistics
Matches: 85,  Mismatches: 16, Indels: 2
        0.83            0.16        0.02

Matches are distributed among these distances:
  22    3  0.04
  23   82  0.96

ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43


Consensus pattern (23 bp):   
GTGCTCTCTGATTAGCACTTTGT

Found at i:4119 original size:16 final size:16

Alignment explanation


    Indices: 4095--4126  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       4085 TCCTTACAAA

                *           
       4095 TTTATTCCTTTAACAT
          1 TTTAGTCCTTTAACAT

                            
       4111 TTTAGTCCTTTAACAT
          1 TTTAGTCCTTTAACAT

       4127 AAAAATCATC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53


Consensus pattern (16 bp):   
TTTAGTCCTTTAACAT

Found at i:13629 original size:15 final size:13

Alignment explanation


    Indices: 13601--13639  Score: 53
    Period size: 15  Copynumber: 2.9  Consensus size: 13

      13591 AAAAAGAAAT

                         
      13601 TATTTATTAAAAG
          1 TATTTATTAAAAG

                           
      13614 TATTTATGTAAAAAG
          1 TATTTAT-T-AAAAG

                        
      13629 TATTT-TTAAAA
          1 TATTTATTAAAA

      13640 AAATATATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  12    4  0.17
  13    8  0.33
  14    2  0.08
  15   10  0.42

ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46


Consensus pattern (13 bp):   
TATTTATTAAAAG

Found at i:14481 original size:2 final size:2

Alignment explanation


    Indices: 14474--14507  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      14464 CTTCCAACTT

                                                              
      14474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      14508 ATAAACTTTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:14574 original size:62 final size:63

Alignment explanation


    Indices: 14498--14626  Score: 233
    Period size: 62  Copynumber: 2.1  Consensus size: 63

      14488 TATATATATA

                    *                        *                             
      14498 TATATATATAATAAACTTTATAAACTCTTACACTAAAA-CCACTCACATATTATTTAATACCT
          1 TATATATAAAATAAACTTTATAAACTCTTACACCAAAACCCACTCACATATTATTTAATACCT

                                                                           
      14560 TATATATAAAATAAACTTTATAAACTCTTACACCAAAACCCACTCACATATTATTTAATACCT
          1 TATATATAAAATAAACTTTATAAACTCTTACACCAAAACCCACTCACATATTATTTAATACCT

                
      14623 TATA
          1 TATA

      14627 CTAATTATCA


Statistics
Matches: 64,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  62   36  0.56
  63   28  0.44

ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36


Consensus pattern (63 bp):   
TATATATAAAATAAACTTTATAAACTCTTACACCAAAACCCACTCACATATTATTTAATACCT

Found at i:20859 original size:15 final size:16

Alignment explanation


    Indices: 20839--20868  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      20829 CTTTCCTATT

                            
      20839 TTCTA-TTTCTTTTAA
          1 TTCTATTTTCTTTTAA

                           
      20854 TTCTATTTTCTTTTA
          1 TTCTATTTTCTTTTA

      20869 TTTTTAATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70


Consensus pattern (16 bp):   
TTCTATTTTCTTTTAA

Found at i:20862 original size:22 final size:22

Alignment explanation


    Indices: 20834--20894  Score: 65
    Period size: 21  Copynumber: 2.8  Consensus size: 22

      20824 TTCGACTTTC

                                   
      20834 CTATTTTCTATTT-CTTTTAATT
          1 CTATTTTCT-TTTACTTTTAATT

                         *        
      20856 CTATTTTCTTTTATTTTTAATT
          1 CTATTTTCTTTTACTTTTAATT

                          *    
      20878 -T-TGTTTCTTTTATTTTT
          1 CTAT-TTTCTTTTACTTTT

      20895 CCTTAGAACG


Statistics
Matches: 36,  Mismatches: 1, Indels: 5
        0.86            0.02        0.12

Matches are distributed among these distances:
  20    1  0.03
  21   18  0.50
  22   17  0.47

ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74


Consensus pattern (22 bp):   
CTATTTTCTTTTACTTTTAATT

Done.