Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010678.1 Kokia drynarioides strain JFW-HI SEQ_125624, 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: 6700
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33


Found at i:6024 original size:59 final size:59

Alignment explanation


    Indices: 5948--6274  Score: 408
    Period size: 59  Copynumber: 5.6  Consensus size: 59

       5938 CGAATACCAT

                                *    **    *           *        *       
       5948 GGGGT-AAAATGGTAATTTTGGGAAAATTCGAGGTCAAAAATGAGATTTTCGGAAGTTCG
          1 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

                                *                *                     
       6007 GGGGTAAAAATGGAATTTTTTGAAGTTTCGGGGTCAAGAATGGGATTTTCGAAAGTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

            * *                               *  *                     
       6066 AGAGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAGAATGGGATTTTCGAAAGTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

            * *                         *      *             *         
       6125 AGAGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCTAAAATGGGATTTTTGAAAGTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

                       *                   *                 * *       
       6184 GGGGTAAAAATAGAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

                      **                      
       6243 GGGG-AAAAACAGAATTTTTGGACAGTTT-GGGG
          1 GGGGTAAAAATGGAATTTTTGGA-AGTTTCGGGG

       6275 ACCTCTGGGG


Statistics
Matches: 240,  Mismatches: 26, Indels: 5
        0.89            0.10        0.02

Matches are distributed among these distances:
  58   20  0.08
  59  213  0.89
  60    7  0.03

ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31


Consensus pattern (59 bp):   
GGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCG

Found at i:6039 original size:30 final size:29

Alignment explanation


    Indices: 5948--6274  Score: 252
    Period size: 29  Copynumber: 11.1  Consensus size: 29

       5938 CGAATACCAT

                                *     *    
       5948 GGGGT-AAAATGGTAATTTTGGGAAAATTC-
          1 GGGGTAAAAATGG-AATTTTTGG-AAGTTCG

             *                   *         
       5977 GAGGTCAAAAAT-GAGATTTTCGGAAGTTCG
          1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTCG

                                *         
       6007 GGGGTAAAAATGGAATTTTTTGAAGTTTC-
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTCG

                    *     *     * *       
       6036 GGGGTCAAGAATGGGATTTTCGAAAGTTCG
          1 GGGGT-AAAAATGGAATTTTTGGAAGTTCG

            * *                           
       6066 AGAGTAAAAATGGAATTTTTGGAAGTTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTCG

               *   *     *     * *       
       6096 GGGTTAAGAATGGGATTTTCGAAAGTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTCG

            * *                        **
       6125 AGAGTAAAAATGGAATTTTTGGAAGTTTT
          1 GGGGTAAAAATGGAATTTTTGGAAGTTCG

                  *       *       *       
       6154 GGGGTCTAAAATGGGATTTTTGAAAGTTCG
          1 GGGGT-AAAAATGGAATTTTTGGAAGTTCG

                       *                  
       6184 GGGGTAAAAATAGAATTTTTGGAAGTTTC-
          1 GGGGTAAAAATGGAATTTTTGGAAG-TTCG

              *           *               
       6213 GGAGTCAAAAATGGGATTTTTGGAAGTTCG
          1 GGGGT-AAAAATGGAATTTTTGGAAGTTCG

                      **                * 
       6243 GGGG-AAAAACAGAATTTTTGGACAGTTTG
          1 GGGGTAAAAATGGAATTTTTGGA-AGTTCG

               
       6272 GGG
          1 GGG

       6275 ACCTCTGGGG


Statistics
Matches: 232,  Mismatches: 52, Indels: 28
        0.74            0.17        0.09

Matches are distributed among these distances:
  28   15  0.06
  29  107  0.46
  30  105  0.45
  31    5  0.02

ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31


Consensus pattern (29 bp):   
GGGGTAAAAATGGAATTTTTGGAAGTTCG

Done.