Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010509.1 Kokia drynarioides strain JFW-HI SEQ_125421, 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: 2292
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.34

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


Found at i:2011 original size:6 final size:6

Alignment explanation


    Indices: 2002--2079  Score: 54
    Period size: 6  Copynumber: 13.5  Consensus size: 6

       1992 TTAATAATTT

                          **            *                       *  
       2002 TTTAAA TTTAAA AATAAA TTTAAA CTTAAA -TTAAA TTTAAA -TTCAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

            ***                   *       *       
       2048 GGCAAA TTTAAA TTTAAA -ATAAA TTCAAA TTT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT

       2080 TTAAACAAAT


Statistics
Matches: 53,  Mismatches: 16, Indels: 6
        0.71            0.21        0.08

Matches are distributed among these distances:
   5   13  0.25
   6   40  0.75

ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40


Consensus pattern (6 bp):   
TTTAAA

Found at i:2076 original size:23 final size:23

Alignment explanation


    Indices: 2032--2079  Score: 60
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       2022 TAAACTTAAA

                       * *         
       2032 TTAAATTTAAATTCAAGGCAAAT
          1 TTAAATTTAAAATAAAGGCAAAT

                            **     
       2055 TTAAATTTAAAATAAATTCAAAT
          1 TTAAATTTAAAATAAAGGCAAAT

              
       2078 TT
          1 TT

       2080 TTAAACAAAT


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40


Consensus pattern (23 bp):   
TTAAATTTAAAATAAAGGCAAAT

Found at i:2077 original size:17 final size:17

Alignment explanation


    Indices: 2002--2094  Score: 87
    Period size: 17  Copynumber: 5.4  Consensus size: 17

       1992 TTAATAATTT

                              
       2002 TTTAAATTTAAAAATAAA
          1 TTTAAATTT-AAAATAAA

                  *     *    
       2020 TTTAAACTTAAATTAAA
          1 TTTAAATTTAAAATAAA

                    *  ***   
       2037 TTTAAATTCAAGGCAAA
          1 TTTAAATTTAAAATAAA

                             
       2054 TTTAAATTTAAAATAAA
          1 TTTAAATTTAAAATAAA

              *       *   *   
       2071 TTCAAATTTTTAAACAAA
          1 TTTAAA-TTTAAAATAAA

                  
       2089 TTTAAA
          1 TTTAAA

       2095 AGGGAGTGTG


Statistics
Matches: 59,  Mismatches: 15, Indels: 2
        0.78            0.20        0.03

Matches are distributed among these distances:
  17   37  0.63
  18   22  0.37

ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39


Consensus pattern (17 bp):   
TTTAAATTTAAAATAAA
Done.