Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004822.1 Kokia drynarioides strain JFW-HI SEQ_118460, 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, 905

Length: 1509
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31


Found at i:348 original size:29 final size:29

Alignment explanation


    Indices: 311--576  Score: 259
    Period size: 29  Copynumber: 9.1  Consensus size: 29

        301 TTAGACATCC

                *                       *
        311 GGGGGAAAAATGGAATTTTTGGAAGTTTG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTA

                                          
        340 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTTA

                           *             *
        370 -GGGTCAAAAATGGATTTTTTGGAAG-TTC
          1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA

               *                 *        
        398 GAGTGTAAAAATGGAATTTTTTGAAGTTTA
          1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA

             *                          *
        428 GAGGTAAAAATGGAA-TTTTGGAAGTTTC
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTA

             *           *       *      * 
        456 GAGGTAAAAAATGAAATTTTTTGAAGTTCA
          1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA

                               ***        
        486 GGGGTAAAAATGGAATTTTCAAAAGTTTTA
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTTA

               *            *          * 
        516 GGGTTAAAAATGGAATATTTGGAAGTTCA
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTA

            *          **      *          
        545 AGGGTAAAAATTAAATTTTCGGACAGTTTA
          1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA

              
        575 GG
          1 GG

        577 AACCTCCAGG


Statistics
Matches: 192,  Mismatches: 36, Indels: 17
        0.78            0.15        0.07

Matches are distributed among these distances:
  28   18  0.09
  29  103  0.54
  30   71  0.37

ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34


Consensus pattern (29 bp):   
GGGGTAAAAATGGAATTTTTGGAAGTTTA

Found at i:575 original size:59 final size:58

Alignment explanation


    Indices: 316--576  Score: 258
    Period size: 59  Copynumber: 4.4  Consensus size: 58

        306 CATCCGGGGG

                          *        *   *                       **     
        316 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT
          1 AAAAATGGAATTTTCGGAAGTTTAGGGTTAAAAATGGAATTTTTGGAAGTTCAAGGGT

                      *    *        * *                   *       *      
        374 CAAAAATGGATTTTTTGGAAG-TTCGAGTGTAAAAATGGAATTTTTTGAAGTT-TAGAGGT
          1 -AAAAATGGAATTTTCGGAAGTTTAGGGT-TAAAAATGGAATTTTTGGAAGTTCAAG-GGT

                                   *     *       *       *        *    
        433 AAAAATGGAATTTT-GGAAGTTTCGAGGTAAAAAATGAAATTTTTTGAAGTTCAGGGGT
          1 AAAAATGGAATTTTCGGAAGTTTAG-GGTTAAAAATGGAATTTTTGGAAGTTCAAGGGT

                           **                        *                 
        491 AAAAATGGAATTTTCAAAAGTTTTAGGGTTAAAAATGGAATATTTGGAAGTTCAAGGGT
          1 AAAAATGGAATTTTCGGAAG-TTTAGGGTTAAAAATGGAATTTTTGGAAGTTCAAGGGT

                  **                   
        550 AAAAATTAAATTTTCGGACAGTTTAGG
          1 AAAAATGGAATTTTCGGA-AGTTTAGG

        577 AACCTCCAGG


Statistics
Matches: 171,  Mismatches: 23, Indels: 16
        0.81            0.11        0.08

Matches are distributed among these distances:
  57    5  0.03
  58   62  0.36
  59   98  0.57
  60    6  0.04

ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34


Consensus pattern (58 bp):   
AAAAATGGAATTTTCGGAAGTTTAGGGTTAAAAATGGAATTTTTGGAAGTTCAAGGGT

Found at i:1445 original size:10 final size:10

Alignment explanation


    Indices: 1430--1454  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1420 TTCTATTTTT

                      
       1430 TTATTTATTA
          1 TTATTTATTA

                      
       1440 TTATTTATTA
          1 TTATTTATTA

                 
       1450 TTATT
          1 TTATT

       1455 AATAAACTCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (10 bp):   
TTATTTATTA
Done.