Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005687.1 Kokia drynarioides strain JFW-HI SEQ_119883, 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: 3424
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34


Found at i:2077 original size:18 final size:18

Alignment explanation


    Indices: 2054--2138  Score: 80
    Period size: 18  Copynumber: 4.7  Consensus size: 18

       2044 CGAAAGAATT

                  *           
       2054 AGCATATTGGCTCGTTAA
          1 AGCATACTGGCTCGTTAA

                     *  *   * 
       2072 AGCATACTGACTTGTTTA
          1 AGCATACTGGCTCGTTAA

                    **      **
       2090 AGCATACTATCTCGTTTG
          1 AGCATACTGGCTCGTTAA

                             *
       2108 AGCATACTGGCTCGTTAG
          1 AGCATACTGGCTCGTTAA

                 *       
       2126 AGCATGCTGGCTC
          1 AGCATACTGGCTC

       2139 ATAAGAGCAT


Statistics
Matches: 55,  Mismatches: 12, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  18   55  1.00

ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33


Consensus pattern (18 bp):   
AGCATACTGGCTCGTTAA

Found at i:2145 original size:18 final size:18

Alignment explanation


    Indices: 2107--2148  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       2097 TATCTCGTTT

                          * * 
       2107 GAGCATACTGGCTCGTTA
          1 GAGCATACTGGCTCATAA

                  *           
       2125 GAGCATGCTGGCTCATAA
          1 GAGCATACTGGCTCATAA

                  
       2143 GAGCAT
          1 GAGCAT

       2149 TATTGGATTG


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24


Consensus pattern (18 bp):   
GAGCATACTGGCTCATAA

Found at i:2871 original size:21 final size:21

Alignment explanation


    Indices: 2847--2916  Score: 65
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       2837 TATAGTATTT

                                 
       2847 GTAGAAGCATATCAAGTATCA
          1 GTAGAAGCATATCAAGTATCA

                    *       *      
       2868 GTAGAAG-GTA-CACTTGTATCA
          1 GTAGAAGCATATCA--AGTATCA

                  *               
       2889 GTAGAACCAT-TACAAGTATCA
          1 GTAGAAGCATAT-CAAGTATCA

                   
       2910 GTAGAAG
          1 GTAGAAG

       2917 TTTGTTACTG


Statistics
Matches: 38,  Mismatches: 6, Indels: 10
        0.70            0.11        0.19

Matches are distributed among these distances:
  19    2  0.05
  20    2  0.05
  21   31  0.82
  22    1  0.03
  23    2  0.05

ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24


Consensus pattern (21 bp):   
GTAGAAGCATATCAAGTATCA
Done.