Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013597.1 Kokia drynarioides strain JFW-HI SEQ_128624, 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: 17654
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35

Warning! 107 characters in sequence are not A, C, G, or T


Found at i:994 original size:30 final size:31

Alignment explanation


    Indices: 960--1031  Score: 103
    Period size: 30  Copynumber: 2.4  Consensus size: 31

        950 GTTACATTTA

                                            
        960 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
          1 ACAAAACAGTCACTCAACTTATCGAAAA-GTG

                          *  *             
        990 ACAAAACAGTCACTTAAGTTATCGAAAAGTG
          1 ACAAAACAGTCACTCAACTTATCGAAAAGTG

                       
       1021 ACAAAACAGTC
          1 ACAAAACAGTC

       1032 CTCTTGGCTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  30   18  0.47
  31   15  0.39
  32    5  0.13

ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21


Consensus pattern (31 bp):   
ACAAAACAGTCACTCAACTTATCGAAAAGTG

Found at i:2150 original size:16 final size:17

Alignment explanation


    Indices: 2118--2150  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       2108 TCTCAAATTT

                      *      
       2118 TTAATATTGTTGAAGAA
          1 TTAATATTGTAGAAGAA

                             
       2135 TTAATA-TGTAGAAGAA
          1 TTAATATTGTAGAAGAA

       2151 ACAAAGAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    9  0.60
  17    6  0.40

ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36


Consensus pattern (17 bp):   
TTAATATTGTAGAAGAA

Found at i:5412 original size:34 final size:34

Alignment explanation


    Indices: 5359--5456  Score: 171
    Period size: 34  Copynumber: 2.9  Consensus size: 34

       5349 GTGTCATTTT

                                              
       5359 TACATACTAA-TTCTTGAGTTTGAAAACTTAAAA
          1 TACATACTAATTTCTTGAGTTTGAAAACTTAAAA

                                           *  
       5392 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
          1 TACATACTAATTTCTTGAGTTTGAAAACTTAAAA

                    *                      
       5426 TACATACTGATTTCTTGAGTTTGAAAACTTA
          1 TACATACTAATTTCTTGAGTTTGAAAACTTA

       5457 CAAAGTTAGT


Statistics
Matches: 62,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  33   10  0.16
  34   52  0.84

ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39


Consensus pattern (34 bp):   
TACATACTAATTTCTTGAGTTTGAAAACTTAAAA

Found at i:9445 original size:15 final size:16

Alignment explanation


    Indices: 9415--9465  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       9405 TAAAAGGTTT

                            
       9415 AAATTATATTTATTTG
          1 AAATTATATTTATTTG

                       *    
       9431 AAATTA-ATTTTTTTG
          1 AAATTATATTTATTTG

                  *          
       9446 -AATGTTTATTTATTTG
          1 AAAT-TATATTTATTTG

                
       9462 AAAT
          1 AAAT

       9466 ATTCCATTTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  14    3  0.10
  15    9  0.31
  16   14  0.48
  17    3  0.10

ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57


Consensus pattern (16 bp):   
AAATTATATTTATTTG

Found at i:10557 original size:75 final size:75

Alignment explanation


    Indices: 10434--10586  Score: 288
    Period size: 75  Copynumber: 2.0  Consensus size: 75

      10424 ACTTAAGTAG

                                                                 *           
      10434 ACCGTTGACTTGTCAAAGTTAACACATTGTCCTGAACTCTCTTCATATTCCTTGAAAATATTCAT
          1 ACCGTTGACTTGTCAAAGTTAACACATTGTCCTGAACTCTCTTCATATTCCTTCAAAATATTCAT

                      
      10499 TAAAACCGCA
         66 TAAAACCGCA

                           *                                                 
      10509 ACCGTTGACTTGTCATAGTTAACACATTGTCCTGAACTCTCTTCATATTCCTTCAAAATATTCAT
          1 ACCGTTGACTTGTCAAAGTTAACACATTGTCCTGAACTCTCTTCATATTCCTTCAAAATATTCAT

                      
      10574 TAAAACCGCA
         66 TAAAACCGCA

               
      10584 ACC
          1 ACC

      10587 CCTTTTGTAA


Statistics
Matches: 76,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  75   76  1.00

ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33


Consensus pattern (75 bp):   
ACCGTTGACTTGTCAAAGTTAACACATTGTCCTGAACTCTCTTCATATTCCTTCAAAATATTCAT
TAAAACCGCA
Done.