Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012390.1 Kokia drynarioides strain JFW-HI SEQ_127394, 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: 4355
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32


Found at i:3422 original size:29 final size:29

Alignment explanation


    Indices: 3386--3877  Score: 329
    Period size: 29  Copynumber: 16.8  Consensus size: 29

       3376 GGATGCACGA

                          *              
       3386 GGGT-AAAATGGTAGTTTTGGAAGGTTCG
          1 GGGTCAAAATGGTATTTTTGGAAGGTTCG

             *                           * 
       3414 GAGTCAAAAATGAG-ATTTTTGGAA-GTTTG
          1 GGGTC-AAAATG-GTATTTTTGGAAGGTTCG

                                 **        
       3443 AGGGT-AAAATGGTAATTTTTAAAAGGTTCG
          1 -GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

                         * *              
       3473 GGGTCAAAAATGGAACTTTTGGAA-GTTCG
          1 GGGTC-AAAATGGTATTTTTGGAAGGTTCG

             *                    *      **
       3502 ATGGT-AAAATGGTAATTTTTGAAAGGTTAA
          1 -GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

                      *  *              * 
       3532 GGGTCAAAAAAGGGATTTTTGGAA-GTTTG
          1 GGGTC-AAAATGGTATTTTTGGAAGGTTCG

                        *                
       3561 GGGTCAAAATGGGATTTTTGGAA-GTTCG
          1 GGGTCAAAATGGTATTTTTGGAAGGTTCG

                 *                           
       3589 GGGTTAAAAATGAG-ATTTTTAGG-A-GTTCAG
          1 GGG-TCAAAATG-GTATTTTT-GGAAGGTTC-G

                                *     *  *
       3619 GGGT-AAAATGGTAATTTTTAGAAGGCTCA
          1 GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

                                  *  *  * 
       3648 GGGTCAAAAATGGTATTTTTGGGAGTTTAG
          1 GGGTC-AAAATGGTATTTTTGGAAGGTTCG

                                *         
       3678 GGGT-AAAATGGTAATTTTTAGAAGGTTCG
          1 GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

             *           *                 
       3707 GTGTCAAAAGTGGGATTTTTGGAA-GTTCGG
          1 GGGTCAAAA-TGGTATTTTTGGAAGGTTC-G

                                *         
       3737 GGGT-AAAATGGTAATTTTTAGAAGGTTCG
          1 GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

            *                     *        
       3766 TGGTCAAAAATGGTATTTTTGGGA-GTTCGG
          1 GGGTC-AAAATGGTATTTTTGGAAGGTTC-G

                            *   *       * 
       3796 GGGT-AAAATGGTAATGTTTAGAAGGTTTG
          1 GGGTCAAAATGGT-ATTTTTGGAAGGTTCG

            *            *          *     
       3825 AGGTCAAAAGTGGGATTTTT-GAAAGTTCG
          1 GGGTCAAAA-TGGTATTTTTGGAAGGTTCG

                                     
       3854 AGGGT-AAAATGGTAATTTTTGGAA
          1 -GGGTCAAAATGGT-ATTTTTGGAA

       3878 AGTTTAGGGA


Statistics
Matches: 364,  Mismatches: 60, Indels: 78
        0.73            0.12        0.16

Matches are distributed among these distances:
  27    2  0.01
  28   69  0.19
  29  138  0.38
  30  119  0.33
  31   36  0.10

ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33


Consensus pattern (29 bp):   
GGGTCAAAATGGTATTTTTGGAAGGTTCG

Found at i:3479 original size:59 final size:58

Alignment explanation


    Indices: 3383--3873  Score: 548
    Period size: 59  Copynumber: 8.4  Consensus size: 58

       3373 TTCGGATGCA

                             *    *          *                         
       3383 CGAGGGTAAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG-GATTTTTGGAAGTT

            *                      *                       *           
       3441 TGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTCAAAAATGGAACTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGG-ATTTTTGGAAGTT

               *                           **           *               
       3500 CGATGGTAAAATGGTAATTTTT-GAAAGGTTAAGGGTCAAAAAAGGGATTTTTGGAAGTT
          1 CGAGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGTC-AAAAATGGATTTTTGGAAGTT

            *               *      *             *                       
       3559 TG-GGGTCAAAATGG-GATTTTTGGAA-GTTCGGGGTTAAAAATGAGATTTTTAGG-AGTT
          1 CGAGGGT-AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATG-GATTTTT-GGAAGTT

                                         *  *                      *    
       3616 C-AGGGGTAAAATGGTAATTTTTAGAAGGCTCAGGGTCAAAAATGGTATTTTTGGGAGTT
          1 CGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGG-ATTTTTGGAAGTT

             *                                *       *                 
       3675 -TAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGTGTCAAAAGTGGGATTTTTGGAAGTT
          1 CGA-GGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT-GGATTTTTGGAAGTT

              *                             *                     *    
       3734 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGTGGTCAAAAATGGTATTTTTGGGAGTT
          1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGG-ATTTTTGGAAGTT

              *               *           * *        *           *     
       3793 CGGGGGTAAAATGGTAATGTTTAGAAGGTTTGAGGTCAAAAGTGGGATTTTTGAAAGTT
          1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT-GGATTTTTGGAAGTT

                                  
       3852 CGAGGGTAAAATGGTAATTTTT
          1 CGAGGGTAAAATGGTAATTTTT

       3874 GGAAAGTTTA


Statistics
Matches: 369,  Mismatches: 45, Indels: 37
        0.82            0.10        0.08

Matches are distributed among these distances:
  56    6  0.02
  57   25  0.07
  58   46  0.12
  59  281  0.76
  60   11  0.03

ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33


Consensus pattern (58 bp):   
CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGATTTTTGGAAGTT

Done.