Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013363.1 Kokia drynarioides strain JFW-HI SEQ_128386, 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: 8652
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34


Found at i:8430 original size:29 final size:29

Alignment explanation


    Indices: 8372--8652  Score: 216
    Period size: 30  Copynumber: 9.6  Consensus size: 29

       8362 TGGATGCACG

                         * *       *  *  
       8372 GGGGT-AAAATGGTAGTTTTGGAGGGATC
          1 GGGGTAAAAATGGGATTTTTGGAAGGTTC

              *                           
       8400 GGAGTCAAAAATGGGATTTTTGGAA-GTTC
          1 GGGGT-AAAAATGGGATTTTTGGAAGGTTC

                           *      *       *
       8429 GGGGGT-AAAATGGTAATTTTTAGAAGGTTT
          1 -GGGGTAAAAATGG-GATTTTTGGAAGGTTC

                         *            *  *
       8459 GGGGTCAAAAATGAGATTTTTGGAAGTTTA
          1 GGGGT-AAAAATGGGATTTTTGGAAGGTTC

                          *       *       
       8489 GGGGT-AAAATGGTAATTTTTGAAAGGTTC
          1 GGGGTAAAAATGG-GATTTTTGGAAGGTTC

             *  *                *    *  *
       8518 AAGGTTAAAAATGGGATTTTTTGAAGTTTA
          1 -GGGGTAAAAATGGGATTTTTGGAAGGTTC

                          *      *        
       8548 GGGGT-AAAATGGTAATTTTTAGAAGGTTC
          1 GGGGTAAAAATGG-GATTTTTGGAAGGTTC

                                          
       8577 GGGGTCAAAAATGGGATTTTTGGAA-GTTC
          1 GGGGT-AAAAATGGGATTTTTGGAAGGTTC

                           *               
       8606 GAGGGT-AAAATGGTAATTTTTGGAAGGTTC
          1 G-GGGTAAAAATGG-GATTTTTGGAAGGTTC

             *               
       8636 GAGGTCAAAAATGGGAT
          1 GGGGT-AAAAATGGGAT


Statistics
Matches: 198,  Mismatches: 37, Indels: 34
        0.74            0.14        0.13

Matches are distributed among these distances:
  28   31  0.16
  29   67  0.34
  30   73  0.37
  31   27  0.14

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


Consensus pattern (29 bp):   
GGGGTAAAAATGGGATTTTTGGAAGGTTC

Found at i:8481 original size:59 final size:59

Alignment explanation


    Indices: 8370--8652  Score: 381
    Period size: 59  Copynumber: 4.8  Consensus size: 59

       8360 TTTGGATGCA

                             *    *  *  *    *                         
       8370 CGGGGGTAAAATGGT-AGTTTTGGAGGGATCGGAGTCAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT

                                          *             *              
       8428 CGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATGAGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT

            **                              **   *               *      
       8487 TAGGGGTAAAATGGTAATTTTT-GAAAGGTTCAAGGTTAAAAATGGGATTTTTTGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT

            **                                                         
       8546 TAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT

              *                   *         *               
       8605 CGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGAT
          1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGAT


Statistics
Matches: 198,  Mismatches: 24, Indels: 5
        0.87            0.11        0.02

Matches are distributed among these distances:
  58   16  0.08
  59  181  0.91
  60    1  0.01

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


Consensus pattern (59 bp):   
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT

Done.