Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008451.1 Kokia drynarioides strain JFW-HI SEQ_123125, 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: 19109
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:601 original size:21 final size:21

Alignment explanation


    Indices: 564--608  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        554 CATTCCCCCG

                        *        
        564 AACCATTGACTCTTAAATCCA
          1 AACCATTGACTCCTAAATCCA

                                * 
        585 AACCATTGAAC-CCTAAATCTA
          1 AACCATTG-ACTCCTAAATCCA

               
        606 AAC
          1 AAC

        609 TCAAACCTTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   19  0.90
  22    2  0.10

ACGTcount: A:0.42, C:0.29, G:0.04, T:0.24


Consensus pattern (21 bp):   
AACCATTGACTCCTAAATCCA

Found at i:1014 original size:74 final size:73

Alignment explanation


    Indices: 894--1043  Score: 273
    Period size: 74  Copynumber: 2.0  Consensus size: 73

        884 ATATAGATAG

                                                                             
        894 AAGTGCTCATGGGTTGGGCCGATCGGGTTCGAGCCAGATCTAAGCATGATATTAATATGTTTTGT
          1 AAGTGCTCATGGGTTGGGCCGATCGGGTTCGAGCCAGATCTAAGCATGATATTAATATGTTTTGT

                    
        959 ACTTACCC
         66 ACTTACCC

                                                    *                        
        967 AAGTGCTCATGGGTTGGGCCTGATCGGGTTCGAGCCAGATGTAAGCATGATATTAATATGTTTTG
          1 AAGTGCTCATGGGTTGGGCC-GATCGGGTTCGAGCCAGATCTAAGCATGATATTAATATGTTTTG

                  *  
       1032 TACTTATCC
         65 TACTTACCC

               
       1041 AAG
          1 AAG

       1044 CTTGGCCTGA


Statistics
Matches: 74,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  73   20  0.27
  74   54  0.73

ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32


Consensus pattern (73 bp):   
AAGTGCTCATGGGTTGGGCCGATCGGGTTCGAGCCAGATCTAAGCATGATATTAATATGTTTTGT
ACTTACCC

Found at i:1991 original size:17 final size:16

Alignment explanation


    Indices: 1957--2013  Score: 60
    Period size: 17  Copynumber: 3.3  Consensus size: 16

       1947 TTAAATTGGT

                              
       1957 TTTAAATTTATTTTTAAA
          1 TTTAAATTTA--TTTAAA

                             
       1975 TTTAAATTTACTTTAAA
          1 TTTAAATTTA-TTTAAA

               *    *        
       1992 TTTGAATTGATTTAAAA
          1 TTTAAATTTATTT-AAA

                 
       2009 TTTAA
          1 TTTAA

       2014 TATTAAATTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  16    3  0.09
  17   21  0.62
  18   10  0.29

ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54


Consensus pattern (16 bp):   
TTTAAATTTATTTAAA

Found at i:9254 original size:18 final size:18

Alignment explanation


    Indices: 9211--9257  Score: 62
    Period size: 19  Copynumber: 2.6  Consensus size: 18

       9201 CTTTTTTTTC

                              
       9211 AATA-AAAATACATATAA
          1 AATATAAAATACATATAA

                                
       9228 AATTATAAAATACAT-TCAA
          1 AA-TATAAAATACATAT-AA

                       
       9247 AATATAAAATA
          1 AATATAAAATA

       9258 TTTATAAATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  17    2  0.07
  18   12  0.44
  19   13  0.48

ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28


Consensus pattern (18 bp):   
AATATAAAATACATATAA

Found at i:12277 original size:14 final size:14

Alignment explanation


    Indices: 12254--12287  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      12244 ACACCCCATT

                          
      12254 TTCTTCAATTCTTC
          1 TTCTTCAATTCTTC

                 *        
      12268 TTCTTTAATTCTTC
          1 TTCTTCAATTCTTC

             *    
      12282 TCCTTC
          1 TTCTTC

      12288 TTTGCAGTTT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59


Consensus pattern (14 bp):   
TTCTTCAATTCTTC

Found at i:15177 original size:25 final size:26

Alignment explanation


    Indices: 15144--15194  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

      15134 AATTTAAATT

                                  *    
      15144 TTATAAAAA-TATTA-AAAAATTAAAA
          1 TTATAAAAAGT-TTATAAAAATAAAAA

                                      
      15169 TTATAAAAAGTTTATAAAAATAAAAA
          1 TTATAAAAAGTTTATAAAAATAAAAA

      15195 AGAACATAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  25   12  0.52
  26   11  0.48

ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31


Consensus pattern (26 bp):   
TTATAAAAAGTTTATAAAAATAAAAA
Done.