Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014164.1 Kokia drynarioides strain JFW-HI SEQ_129197, 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: 1933
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32


Found at i:387 original size:59 final size:59

Alignment explanation


    Indices: 325--624  Score: 297
    Period size: 60  Copynumber: 5.1  Consensus size: 59

        315 ATCCGTGAAT

                                                                        
        325 AAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA
          1 AAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA

                           *        *          *    **                    
        385 AAAAT-GAAGTTTTTAGAAGTTT-TAGGGTCAAAATTGGATTTTTTTGGAAGTTTGGGGGTA
          1 AAAATGGAA-TTTTTGGAAGTTTCGA-GGTCAAAAAT-GAAATTTTTGGAAGTTTGGGGGTA

                 *            *   * *             *                *  *  
        445 AAAATAGAATTTTTGG-ATTTTTGGGTGTCAAAAATGAGATTTTTGGAAGTTTTGAGGTTA
          1 AAAATGGAATTTTTGGAAGTTTCGAG-GTCAAAAATGAAATTTTTGGAAG-TTTGGGGGTA

                   *      *          *          *        *       *      
        505 AAAATGGGATTTTTTGAAG-TTCGGGGGT-AAAAATTAAATTTTTAGAAGTTTTGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA

                                    *           **             *       
        563 AAAATGGAATTTTTGGAAGTTT-GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA

                
        621 AAAA
          1 AAAA

        625 CAAAATTTTC


Statistics
Matches: 196,  Mismatches: 33, Indels: 24
        0.77            0.13        0.09

Matches are distributed among these distances:
  57    5  0.03
  58   55  0.28
  59   58  0.30
  60   71  0.36
  61    7  0.04

ACGTcount: A:0.32, C:0.02, G:0.28, T:0.37


Consensus pattern (59 bp):   
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA

Found at i:633 original size:29 final size:29

Alignment explanation


    Indices: 325--624  Score: 291
    Period size: 29  Copynumber: 10.1  Consensus size: 29

        315 ATCCGTGAAT

                                   * *     
        325 AAAATGGTAATTTTTGGAAGTTTCGAGGTCA
          1 AAAATGG-AATTTTTGGAAGTTTGGGGGT-A

                  *                      
        356 AAAATGAAATTTTTGGAAGTTTGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGTA

                           *       **      
        385 AAAAT-GAAGTTTTTAGAAGTTTTAGGGTCA
          1 AAAATGGAA-TTTTTGGAAGTTTGGGGGT-A

               *     *                    
        415 AAATTGGATTTTTTTGGAAGTTTGGGGGTA
          1 AAAATGGA-ATTTTTGGAAGTTTGGGGGTA

                 *           **      *    
        445 AAAATAGAATTTTTGGATTTTTGGGTGTCA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGT-A

                                     *  *  
        475 AAAAT-GAGATTTTTGGAAGTTTTGAGGTTA
          1 AAAATGGA-ATTTTTGGAAG-TTTGGGGGTA

                   *      *      *       
        505 AAAATGGGATTTTTTGAAGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGTA

                 **       *       *      
        534 AAAATTAAATTTTTAGAAGTTTTGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGTA

                                          
        563 AAAATGGAATTTTTGGAAGTTT-GGGGTCA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGT-A

                   *             *       
        592 AAAATGGGATTTTTGGAAGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTGGGGGTA

                
        621 AAAA
          1 AAAA

        625 CAAAATTTTC


Statistics
Matches: 220,  Mismatches: 39, Indels: 22
        0.78            0.14        0.08

Matches are distributed among these distances:
  28    7  0.03
  29  115  0.52
  30   67  0.30
  31   31  0.14

ACGTcount: A:0.32, C:0.02, G:0.28, T:0.37


Consensus pattern (29 bp):   
AAAATGGAATTTTTGGAAGTTTGGGGGTA

Found at i:647 original size:58 final size:58

Alignment explanation


    Indices: 325--648  Score: 321
    Period size: 58  Copynumber: 5.5  Consensus size: 58

        315 ATCCGTGAAT

                                     *            *                     
        325 AAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTA
          1 AAAATGG-AATTTTTGGAAG-TTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTA

                           *       **         *                           
        385 AAAAT-GAAGTTTTTAGAAGTTTTAGGGTCAAAATTG-GATTTTTTTGGAAGTTTGGGGGTA
          1 AAAATGGAA-TTTTTGGAAG-TTCGGGGTCAAAAATGAGA--TTTTTGGAAGTTTGGGGGTA

                 *           **  *                                *  *  
        445 AAAATAGAATTTTTGGATTTTTGGGTGTCAAAAATGAGATTTTTGGAAGTTTTGAGGTTA
          1 AAAATGGAATTTTTGGAAGTTCGGG-GTCAAAAATGAGATTTTTGGAAG-TTTGGGGGTA

                   *      *                    * *      *       *      
        505 AAAATGGGATTTTTTGAAGTTCGGGGGT-AAAAATTAAATTTTTAGAAGTTTTGGGGTA
          1 AAAATGGAATTTTTGGAAGTTC-GGGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTA

                                 *             *              *       
        563 AAAATGGAATTTTTGGAAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTA

                ***      *              
        621 AAAACAAAATTTTCGGAAGTTCGGGGTC
          1 AAAATGGAATTTTTGGAAGTTCGGGGTC

        649 GTCTAGGGCA


Statistics
Matches: 216,  Mismatches: 39, Indels: 20
        0.79            0.14        0.07

Matches are distributed among these distances:
  57    5  0.02
  58   76  0.35
  59   55  0.25
  60   72  0.33
  61    8  0.04

ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36


Consensus pattern (58 bp):   
AAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTA
Done.