Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010893.1 Kokia drynarioides strain JFW-HI SEQ_125861, 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: 11109
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33


Found at i:10469 original size:59 final size:58

Alignment explanation


    Indices: 10405--10841  Score: 431
    Period size: 59  Copynumber: 7.5  Consensus size: 58

      10395 AATTCGGGGT

                              *                  *        **      *    
      10405 TAAAAATAGGG-TTTTTGAAAGTTTAGGGGTAAAAATAGAATTTTTAAAAGTTTCGAGG
          1 TAAAAAT-GGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG

                                    **                                   
      10463 TAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GAGATTTTTGGAAG-TTTGAGGG
          1 T-AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGA-ATTTTTGGAAGTTTTGA-GG

                  * *                                              * *  
      10522 T-AAAACGAGATTTTTGGAAGTTT-GAGGGT-AAAAT-GAGATTTTTGGAAGTTTGGGGG
          1 TAAAAATGGGATTTTTGGAAGTTTAG-GGGTAAAAATGGA-ATTTTTGGAAGTTTTGAGG

                                     * *   *              *  *         
      10578 TAAAAATGGGATTTTTTGGAAGTTTTGAGGTTAAAATGGAATTTTTAGAGGTTTTGAGG
          1 TAAAAATGGGA-TTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG

             *              *       *              *       *       *   
      10637 TTAAAATGGGATTTTTTGAAGTTTCGGGGTCAAAAATGGGATTTTTGAAAG-TTTAAGG
          1 TAAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTTGAGG

                      *               *             *                *  
      10695 ATAAAAATGGAATTTTTGGAAGTTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGG
          1 -TAAAAATGGGATTTTTGGAAGTTT-AGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG

                    *        **       *              *              *  
      10755 TCAAAAATAGGATTTTTTAAAGTTTAAGGGTAAAAATGGAAGTTTTGGAAGTTTTGGGG
          1 T-AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG

                                        
      10814 TAAAAATGGGATTTTTGGAAGTTTAGGG
          1 TAAAAATGGGATTTTTGGAAGTTTAGGG

      10842 ACCTTCGAGG


Statistics
Matches: 316,  Mismatches: 47, Indels: 32
        0.80            0.12        0.08

Matches are distributed among these distances:
  56   23  0.07
  57   33  0.10
  58   71  0.22
  59  158  0.50
  60   31  0.10

ACGTcount: A:0.33, C:0.02, G:0.30, T:0.36


Consensus pattern (58 bp):   
TAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG

Found at i:10478 original size:30 final size:29

Alignment explanation


    Indices: 10397--10837  Score: 426
    Period size: 29  Copynumber: 15.1  Consensus size: 29

      10387 TTTAGGATAA

                                      *    
      10397 TTCGGGGTTAAAAATAGGG-TTTTTGAAAGT
          1 TTCGGGG-TAAAAAT-GGGATTTTTGGAAGT

              *           * *      **    
      10427 TTAGGGGTAAAAATAGAATTTTTAAAAGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

                *                         
      10456 TTCGAGGTAAAAAATGGGATTTTTGGAAG-
          1 TTCGGGGT-AAAAATGGGATTTTTGGAAGT

                            *             
      10485 TTCGGGGGTAAAAATGAGATTTTTGGAAGT
          1 TTC-GGGGTAAAAATGGGATTTTTGGAAGT

                          * *             
      10515 TT-GAGGGT-AAAACGAGATTTTTGGAAGT
          1 TTCG-GGGTAAAAATGGGATTTTTGGAAGT

                            *             
      10543 TT-GAGGGT-AAAATGAGATTTTTGGAAGT
          1 TTCG-GGGTAAAAATGGGATTTTTGGAAGT

              *                           
      10571 TTGGGGGTAAAAATGGGATTTTTTGGAAGT
          1 TTCGGGGTAAAAATGGGA-TTTTTGGAAGT

              * *   *       *      *  *  
      10601 TTTGAGGTTAAAATGGAATTTTTAGAGGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

              * *   *              *     
      10630 TTTGAGGTTAAAATGGGATTTTTTGAAGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

                                     *    
      10659 TTCGGGGTCAAAAATGGGATTTTTGAAAGT
          1 TTCGGGGT-AAAAATGGGATTTTTGGAAGT

              **  *         *            
      10689 TTAAGGATAAAAATGGAATTTTTGGAAGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

                                          
      10718 TTCGGGGGTAAAAATGGGATTTTTGGAAGT
          1 TTC-GGGGTAAAAATGGGATTTTTGGAAGT

              *            *        **    
      10748 TTTGGGGTCAAAAATAGGATTTTTTAAAGT
          1 TTCGGGGT-AAAAATGGGATTTTTGGAAGT

              **            * *          
      10778 TTAAGGGTAAAAATGGAAGTTTTGGAAGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

              *                          
      10807 TTTGGGGTAAAAATGGGATTTTTGGAAGT
          1 TTCGGGGTAAAAATGGGATTTTTGGAAGT

              
      10836 TT
          1 TT

      10838 AGGGACCTTC


Statistics
Matches: 347,  Mismatches: 53, Indels: 23
        0.82            0.13        0.05

Matches are distributed among these distances:
  28   54  0.16
  29  168  0.48
  30  125  0.36

ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36


Consensus pattern (29 bp):   
TTCGGGGTAAAAATGGGATTTTTGGAAGT
Done.