Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004792.1 Kokia drynarioides strain JFW-HI SEQ_118417, 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: 268
    Period size: 29  Copynumber: 9.1  Consensus size: 29

        301 TTAGACATCC

                *                       *
        311 GGGGGAAAAATGGAATTTTTGGAAGTTTG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTA

                                          
        340 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTTA

                                         *
        370 -GGGTCAAAAATGGAATTTTTGGAAG-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: 194,  Mismatches: 34, Indels: 17
        0.79            0.14        0.07

Matches are distributed among these distances:
  28   18  0.09
  29  104  0.54
  30   72  0.37

ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33


Consensus pattern (29 bp):   
GGGGTAAAAATGGAATTTTTGGAAGTTTA

Found at i:457 original size:58 final size:57

Alignment explanation


    Indices: 316--573  Score: 270
    Period size: 59  Copynumber: 4.4  Consensus size: 57

        306 CATCCGGGGG

                                   * *                  *             
        316 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT
          1 AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAG-TTTAGGGT

                                                                        
        374 CAAAAATGGAATTTTTGGAAG-TTCGAGTGTAAAAATGGAATTTTTTGAAGTTTAGAGGT
          1 -AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAATGGAATTTTTTGAAGTTTAG-GGT

                                                 *              *      
        433 AAAAATGGAA-TTTTGGAAGTTTCGAGGTAAAAAATGAAATTTTTTGAAGTTCAGGGGT
          1 AAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTTGAAGTTTA-GGGT

                          ***       *                 *   *       *     
        491 AAAAATGGAATTTTCAAAAGTTT-TAGGGTTAAAAATGGAATATTTGGAAGTTCAAGGGT
          1 AAAAATGGAATTTTTGGAAGTTTCGA-GG-TAAAAATGGAATTTTTTGAAGTT-TAGGGT

                  **      *         
        550 AAAAATTAAATTTTCGGACAGTTT
          1 AAAAATGGAATTTTTGGA-AGTTT

        574 AGGAACCTCC


Statistics
Matches: 172,  Mismatches: 17, Indels: 19
        0.83            0.08        0.09

Matches are distributed among these distances:
  57   11  0.06
  58   61  0.35
  59   93  0.54
  60    7  0.04

ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34


Consensus pattern (57 bp):   
AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAGTTTAGGGT

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.