Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002603.1 Kokia drynarioides strain JFW-HI SEQ_114816, 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: 3383
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33


Found at i:809 original size:28 final size:28

Alignment explanation


    Indices: 778--831  Score: 81
    Period size: 28  Copynumber: 1.9  Consensus size: 28

        768 GGTTGTTCTA

                                        
        778 TTATGTGGAAGCCTTTATGACTATTTGT
          1 TTATGTGGAAGCCTTTATGACTATTTGT

                        *   *  *      
        806 TTATGTGGAAGCTTTTGTGGCTATTT
          1 TTATGTGGAAGCCTTTATGACTATTT

        832 CCATTACCAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  28   23  1.00

ACGTcount: A:0.19, C:0.09, G:0.24, T:0.48


Consensus pattern (28 bp):   
TTATGTGGAAGCCTTTATGACTATTTGT

Found at i:1043 original size:25 final size:25

Alignment explanation


    Indices: 973--1034  Score: 106
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        963 TACACGTAAG

                                      
        973 CCTTCGTGGCAACTCTGTGATAAGGC
          1 CCTT-GTGGCAACTCTGTGATAAGGC

                                  *  
        999 CCTTGTGGCAACTCTGTGATAATGC
          1 CCTTGTGGCAACTCTGTGATAAGGC

                       
       1024 CCTTGTGGCAA
          1 CCTTGTGGCAA

       1035 TGCTATGATG


Statistics
Matches: 35,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  25   31  0.89
  26    4  0.11

ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29


Consensus pattern (25 bp):   
CCTTGTGGCAACTCTGTGATAAGGC

Found at i:1123 original size:26 final size:26

Alignment explanation


    Indices: 1094--1146  Score: 106
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1084 TCATGACTAA

                                      
       1094 TTCTGTTTGAATGCAGGTGAATGTCT
          1 TTCTGTTTGAATGCAGGTGAATGTCT

                                      
       1120 TTCTGTTTGAATGCAGGTGAATGTCT
          1 TTCTGTTTGAATGCAGGTGAATGTCT

             
       1146 T
          1 T

       1147 CATGGCTATC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43


Consensus pattern (26 bp):   
TTCTGTTTGAATGCAGGTGAATGTCT

Found at i:1756 original size:3 final size:3

Alignment explanation


    Indices: 1748--1779  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       1738 GAGAGTTGCT

                                                      
       1748 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG

       1780 TAAAAGTACA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34


Consensus pattern (3 bp):   
TGA

Found at i:1882 original size:110 final size:110

Alignment explanation


    Indices: 1762--1984  Score: 437
    Period size: 110  Copynumber: 2.0  Consensus size: 110

       1752 GATGATGATG

                                                                             
       1762 ATGATGATGATGATGATGTAAAAGTACATAAGAGAAGCCTTAGGGCGAAGTTAAGTATGCACACA
          1 ATGATGATGATGATGATGTAAAAGTACATAAGAGAAGCCTTAGGGCGAAGTTAAGTATGCACACA

                                                         
       1827 TGTAATACTCTGATAACGATAGGAAGTGAGGCAAGAACACTAGTT
         66 TGTAATACTCTGATAACGATAGGAAGTGAGGCAAGAACACTAGTT

                                                             *               
       1872 ATGATGATGATGATGATGTAAAAGTACATAAGAGAAGCCTTAGGGCGAATTTAAGTATGCACACA
          1 ATGATGATGATGATGATGTAAAAGTACATAAGAGAAGCCTTAGGGCGAAGTTAAGTATGCACACA

                                                         
       1937 TGTAATACTCTGATAACGATAGGAAGTGAGGCAAGAACACTAGTT
         66 TGTAATACTCTGATAACGATAGGAAGTGAGGCAAGAACACTAGTT

               
       1982 ATG
          1 ATG

       1985 TTATTTCAAT


Statistics
Matches: 112,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 110  112  1.00

ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24


Consensus pattern (110 bp):   
ATGATGATGATGATGATGTAAAAGTACATAAGAGAAGCCTTAGGGCGAAGTTAAGTATGCACACA
TGTAATACTCTGATAACGATAGGAAGTGAGGCAAGAACACTAGTT
Done.