Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013766.1 Kokia drynarioides strain JFW-HI SEQ_128794, 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: 4914
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:59 original size:39 final size:39

Alignment explanation


    Indices: 5--95  Score: 155
    Period size: 39  Copynumber: 2.3  Consensus size: 39

          1 ACTT

                  *                                
          5 AGACACCTTAAAAACAACTATTAAATATGTATCAAAATA
          1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA

                                                *  
         44 AGACACATTAAAAACAACTATTAAATATGTATCAAACTA
          1 AGACACATTAAAAACAACTATTAAATATGTATCAAAATA

              *          
         83 AGTCACATTAAAA
          1 AGACACATTAAAA

         96 CCCTATTTAA


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  39   49  1.00

ACGTcount: A:0.54, C:0.15, G:0.05, T:0.25


Consensus pattern (39 bp):   
AGACACATTAAAAACAACTATTAAATATGTATCAAAATA

Found at i:2169 original size:23 final size:24

Alignment explanation


    Indices: 2143--2194  Score: 72
    Period size: 23  Copynumber: 2.2  Consensus size: 24

       2133 AAAAGTGATA

                                     
       2143 AAAAAGTA-GAGAAAAA-AAAAAAG
          1 AAAAA-TACGAGAAAAAGAAAAAAG

                                   *
       2166 AAAAATACGAGAAAAAGAAAAAAT
          1 AAAAATACGAGAAAAAGAAAAAAG

                 
       2190 AAAAA
          1 AAAAA

       2195 AATATTTCGT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  22    2  0.08
  23   13  0.50
  24   11  0.42

ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06


Consensus pattern (24 bp):   
AAAAATACGAGAAAAAGAAAAAAG

Found at i:4653 original size:26 final size:25

Alignment explanation


    Indices: 4615--4663  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 25

       4605 AAACAACTTC

                                      
       4615 TAAAAAAAAACTC-AAGAGCAATTCT
          1 TAAAAAAAAACTCAAAGAG-AATTCT

                                    
       4640 TAAAGAAAAAACTCAAAGAGAATT
          1 TAAA-AAAAAACTCAAAGAGAATT

       4664 ATTATTAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  25    4  0.18
  26   13  0.59
  27    5  0.23

ACGTcount: A:0.59, C:0.12, G:0.10, T:0.18


Consensus pattern (25 bp):   
TAAAAAAAAACTCAAAGAGAATTCT

Done.