Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009673.1 Kokia drynarioides strain JFW-HI SEQ_124391, 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: 10824
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24


Found at i:8954 original size:43 final size:43

Alignment explanation


    Indices: 8874--8958  Score: 118
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       8864 AATACTTCGC

                   *            *                       
       8874 CTAAAAATAAAAGGGGCATTGAGATGAAAACCCGTAAAGGGCGT
          1 CTAAAAAAAAAAGGGG-ATTCAGATGAAAACCCGTAAAGGGCGT

                                           *          
       8918 CTAAAAAAAAAAGGGG-TTCAGGATGAAAACTCGTAAAGGGC
          1 CTAAAAAAAAAAGGGGATTCA-GATGAAAACCCGTAAAGGGC

       8959 ATCCTGGAAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  42    3  0.08
  43   19  0.51
  44   15  0.41

ACGTcount: A:0.45, C:0.13, G:0.27, T:0.15


Consensus pattern (43 bp):   
CTAAAAAAAAAAGGGGATTCAGATGAAAACCCGTAAAGGGCGT

Found at i:10091 original size:206 final size:206

Alignment explanation


    Indices: 9737--10415  Score: 1187
    Period size: 206  Copynumber: 3.3  Consensus size: 206

       9727 CGCGATATCC

                                                                             
       9737 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
          1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA

                         *        *                                          
       9802 AGCGAGCAAAATCACTGAACCCTAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
         66 AGCGAGCAAAATCTCTGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA

                                      **              *                      
       9867 CGGTTAGCTTCCTGATAAGATACTGAAAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGA
        131 CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA

                       
       9932 AGCGGATTGAA
        196 AGCGGATTGAA

                                            *                     *   *      
       9943 ACAAACGACGCGGTCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAAACCATGCTCAA
          1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA

                        *                           *       *                
      10008 AGCGAGCAAAATGTCTGAACCCCAGCTTCCTGATGAGACATCGAGAAGTAGGTCGAAGCAATAAA
         66 AGCGAGCAAAATCTCTGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA

                                                                         *   
      10073 CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACATAGA
        131 CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA

                 *     
      10138 AGCGGTTTGAA
        196 AGCGGATTGAA

                      * *                                                    
      10149 ACAAACGACGTGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
          1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA

                                                                             
      10214 AGCGAGCAAAATCTCTGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
         66 AGCGAGCAAAATCTCTGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA

                                                                             
      10279 CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
        131 CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA

                       
      10344 AGCGGATTGAA
        196 AGCGGATTGAA

                     * *                         *       *               
      10355 ACAAACGACACAGTCATCTTCCTGATGAGATACTGAGGAGAAGACTAAATCAAACCCACGC
          1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC

      10416 GCGATGAACG


Statistics
Matches: 444,  Mismatches: 29, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 206  444  1.00

ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19


Consensus pattern (206 bp):   
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
AGCGAGCAAAATCTCTGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAA
CGGTTAGCTTCCTGATAAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
AGCGGATTGAA

Found at i:10783 original size:17 final size:17

Alignment explanation


    Indices: 10755--10817  Score: 83
    Period size: 17  Copynumber: 3.7  Consensus size: 17

      10745 GGCCTATTGG

                 *           
      10755 AAATTGAATTTATTTTA
          1 AAATTAAATTTATTTTA

                   *         
      10772 AAATTAAGTTTATTTTA
          1 AAATTAAATTTATTTTA

              *              
      10789 AATTTAAATTTA-TTTA
          1 AAATTAAATTTATTTTA

                         
      10805 AAATTTAAATTTA
          1 AAA-TTAAATTTA

      10818 AAATGTC


Statistics
Matches: 40,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  16    6  0.15
  17   34  0.85

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52


Consensus pattern (17 bp):   
AAATTAAATTTATTTTA

Found at i:10794 original size:23 final size:23

Alignment explanation


    Indices: 10768--10821  Score: 58
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      10758 TTGAATTTAT

                             *      
      10768 TTTAAAATTAAGTTT-ATTTTAAA
          1 TTTAAAATTAA-TTTAAATTTAAA

                     *              
      10791 TTT-AAATTTATTTAAAATTTAAA
          1 TTTAAAATTAATTT-AAATTTAAA

                    
      10814 TTTAAAAT
          1 TTTAAAAT

      10822 GTC


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  21    3  0.12
  22    6  0.23
  23   13  0.50
  24    4  0.15

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (23 bp):   
TTTAAAATTAATTTAAATTTAAA
Done.