Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014925.1 Kokia drynarioides strain JFW-HI SEQ_129968, 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: 43586
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1807 original size:21 final size:22

Alignment explanation


    Indices: 1780--1835  Score: 71
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       1770 AGAGTTTTTA

                                  
       1780 GTATCGGTAGAAGTA-AAACTT
          1 GTATCGGTAGAAGTAGAAACTT

              *             **    
       1801 GTTTCGGTAGAAG-AGTCACTT
          1 GTATCGGTAGAAGTAGAAACTT

                          
       1822 GTATCGGTAGAAGT
          1 GTATCGGTAGAAGT

       1836 TAGCACTATT


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  20    1  0.03
  21   28  0.97

ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30


Consensus pattern (22 bp):   
GTATCGGTAGAAGTAGAAACTT

Found at i:4266 original size:59 final size:59

Alignment explanation


    Indices: 4174--4292  Score: 211
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       4164 TTTGAGTGAA

                     *                                   *             
       4174 TACTCTCAAGAATTCAATTAATCAATGAAGTGATTTACAATGAGGTGGAGATGCCTCTT
          1 TACTCTCAAAAATTCAATTAATCAATGAAGTGATTTACAATGAGGGGGAGATGCCTCTT

                                *                                      
       4233 TACTCTCAAAAATTCAATTACTCAATGAAGTGATTTACAATGAGGGGGAGATGCCTCTT
          1 TACTCTCAAAAATTCAATTAATCAATGAAGTGATTTACAATGAGGGGGAGATGCCTCTT

             
       4292 T
          1 T

       4293 TTATAGTTGA


Statistics
Matches: 57,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  59   57  1.00

ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Consensus pattern (59 bp):   
TACTCTCAAAAATTCAATTAATCAATGAAGTGATTTACAATGAGGGGGAGATGCCTCTT

Found at i:39025 original size:18 final size:17

Alignment explanation


    Indices: 38989--39023  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      38979 GGGCAGCTGC

                        *    
      38989 TAAATTTTTTTTCATTT
          1 TAAATTTTTTTTAATTT

                             
      39006 TAAATTTTTTTTAATTT
          1 TAAATTTTTTTTAATTT

             
      39023 T
          1 T

      39024 TAGGCTTTGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71


Consensus pattern (17 bp):   
TAAATTTTTTTTAATTT

Found at i:39105 original size:13 final size:16

Alignment explanation


    Indices: 39087--39122  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      39077 ATATCAAGAA

                            
      39087 TATTATT-TT-AAA-T
          1 TATTATTGTTAAAATT

                            
      39100 TATTATTGTTAAAATT
          1 TATTATTGTTAAAATT

                   
      39116 TATTATT
          1 TATTATT

      39123 AACACAATGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  13    7  0.35
  14    2  0.10
  15    3  0.15
  16    8  0.40

ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61


Consensus pattern (16 bp):   
TATTATTGTTAAAATT
Done.