Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001026.1 Kokia drynarioides strain JFW-HI SEQ_112245, 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: 3662
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:768 original size:30 final size:28

Alignment explanation


    Indices: 732--910  Score: 164
    Period size: 30  Copynumber: 6.1  Consensus size: 28

        722 AAATGGATTT

                                          
        732 TTTGGGGGTTAAAAATGACATTTTTGGAAG
          1 TTTGGGGG-TAAAAATGA-ATTTTTGGAAG

                                         
        762 TTTGGGGGT-AAAATGGAATTTTTGGAAG
          1 TTTGGGGGTAAAAAT-GAATTTTTGGAAG

               *                          
        790 TTTCGGGGTAAAAAATGAGATTTTTGGAAG
          1 TTTGGGGGT-AAAAATGA-ATTTTTGGAAG

               **                        
        820 TTTAAGGGTAAAACA-GAATTTTTGGAAG
          1 TTTGGGGGTAAAA-ATGAATTTTTGGAAG

               * *          * *           
        848 TTTCGAGGTCAAAAACGGGATTTTTGGAAG
          1 TTTGGGGGT-AAAAA-TGAATTTTTGGAAG

              * *         *               
        878 TTCGAGGGTAAAAACGAAATTTTTGGACAG
          1 TTTGGGGGTAAAAATG-AATTTTTGGA-AG

               
        908 TTT
          1 TTT

        911 AGGGACCTCC


Statistics
Matches: 125,  Mismatches: 14, Indels: 20
        0.79            0.09        0.13

Matches are distributed among these distances:
  28   43  0.34
  29   29  0.23
  30   53  0.42

ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34


Consensus pattern (28 bp):   
TTTGGGGGTAAAAATGAATTTTTGGAAG

Found at i:829 original size:58 final size:58

Alignment explanation


    Indices: 736--910  Score: 224
    Period size: 58  Copynumber: 3.0  Consensus size: 58

        726 GGATTTTTTG

                 *        *               *        *                  
        736 GGGGTTAAAAATGACATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTTGGAAGTTTC
          1 GGGGTAAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAACGGAATTTTTGGAAGTTTC

                                         *          *                 
        794 GGGGTAAAAAATGAGATTTTTGGAAGTTTAAGGGTAAAACAGAATTTTTGGAAGTTTC
          1 GGGGTAAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAACGGAATTTTTGGAAGTTTC

             *   *     * *              *             *                
        852 GAGGTCAAAAACGGGATTTTTGGAAGTTCGAGGGTAAAAACGAAATTTTTGGACAGTTT
          1 GGGGTAAAAAATGAGATTTTTGGAAGTTTGAGGGT-AAAACGGAATTTTTGGA-AGTTT

        911 AGGGACCTCC


Statistics
Matches: 101,  Mismatches: 14, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  58   81  0.80
  59   15  0.15
  60    5  0.05

ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33


Consensus pattern (58 bp):   
GGGGTAAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAACGGAATTTTTGGAAGTTTC

Done.