Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010419.1 Kokia drynarioides strain JFW-HI SEQ_125305, 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: 1708
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28


Found at i:491 original size:216 final size:216

Alignment explanation


    Indices: 1--1701  Score: 1773
    Period size: 216  Copynumber: 8.0  Consensus size: 216

                                      *             *            * *       * 
          1 GTTGTTTACAAAATGACAGATTATTTAGACCAAATGATGCAATTTCCCAAGAACGAAATGTTCGA
          1 GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA

                                    *                   **                   
         66 AAAATTGTTCGAAGAAAT-GAATCATCTTGAATACTTTAAGGAAAAAAAGTTATAAAAGAACTCG
         66 AAAATTGTTCGAAGAAATCG-ATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG

                                 *    *   *       *   *    *      *  *       
        130 AAAAAGTTT-ACAAAG-T--AGGTTCTGCCTAGAACCACGAGTGAAATAATTCTTA-TGTAAATA
        130 AAAAAGTTTGA-AAAGTTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATA

                             * *   
        190 AGTTTTTAATTCAAAGATCGAAA
        194 AGTTTTTAATTCAAAGACCAAAA

               *   *     *                         **        *     *         
        213 GTTTTTTGCAAAAGGACTA-ATTATTTGGACCAAATGATATGATTTCCCGAGAATAGAATGTTCA
          1 GTTGTTTACAAAATGAC-AGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCA

                    *      *                              *   *        *     
        277 AAAAATTGATCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAGATATAAAAGTACTCG
         65 AAAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG

             *                        *              *                       
        342 ATAAAGTTTGAAAAGTTCGGAAGTTCAGCCAAGAACCAAGAAAGAAACAATTCTCACAG-AAATA
        130 AAAAAGTTTGAAAAGTT-GGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATA

             *          *           
        406 AATTTTTAA-TCCAAGAACCAAAA
        194 AGTTTTTAATTCAAAG-ACCAAAA

                            *                      *      * *     **       * 
        429 GTTGTTTACAAAATGATAGATTATTTGGACCAAATGATGTGATTTCTCGAGAATTTAATGTTCGA
          1 GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA

                        *     *                                              
        494 AAAATTGTTCGACGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGA
         66 AAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGA

                     *                  *           *  * *    *              
        559 AAAAGTTTGCAAAG-T-----TT-GGCCTAGAACCAAGAGTGAGATAATTATCAC-GTAAATAAG
        131 AAAAGTTTGAAAAGTTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATAAG

                                 
        616 TTTTTAATTCAAAGACCAAAA
        196 TTTTTAATTCAAAGACCAAAA

               *         *   *                      *        *               
        637 GTTTTTTACAAAAGGATTA-ATTATTTGGACCAAATGATGTGATTTCTCGAA-AATGGAATGTTC
          1 GTTGTTTACAAAATGA-CAGATTATTTGGACCAAATGATGCGATTTC-CCAAGAATGGAATGTTC

            *        *      *   *    *                     *            *    
        700 GAAAAATTGCTCGAAGGAATTGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGTACTC
         64 AAAAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC

                        *                                         *          
        765 GAAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACC-A-AGAGAAACAATTCCCACA-TAAAT
        129 GAAAAAGTTTGAAAAGTT-GGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAAT

              *   *                  
        827 AAATTTATAA-TCAAAAGACCAAAA
        193 AAGTTTTTAATTC-AAAGACCAAAA

              *                       *             *    *         *       * 
        851 GTAGTTTACAAAATGACAGATTATTTAGACCAAATGATGCAATTTTCCAAGAATGAAATGTTCGA
          1 GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA

                              *    *                   **                    
        916 AAAATTGTTCGAAGAAATGGATCATCTTGAATACTTTAAGGAAAAAAAGTTATAAAAGAACTCGA
         66 AAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGA

                                    **   *            *    *      *          
        981 AAAAGTTT-ACAAAG-T--AAGTTTTGCCTAGAA-CAACGAGTGAAATAATTCTTAC-GTAAATA
        131 AAAAGTTTGA-AAAGTTGGAAGTTCGGCCAAGAACCAA-GAGAGAAACAATTCTCACAGTAAATA

                             * *   
       1040 AGTTTTTAATTCAAAGATCGAAA
        194 AGTTTTTAATTCAAAGACCAAAA

               *   *     *                                         *         
       1063 GTTTTTTGCAAAAGGACTA-ATTATTTGGACCAAATGATGCGATTTCCCAAGAATAGAATGTTCA
          1 GTTGTTTACAAAATGAC-AGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCA

                    *      *    *             *           *   *        *     
       1127 AAAAATTGATCGAAGGAATCAATCGTCTTGAATATTTTAAGGAACCGAAGATATAAAAGTACTCG
         65 AAAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG

             *           *            **             *                       
       1192 ACAAAGTTTGAAATGTTCGGAAGTTCAACCAAGAACCAAGAAAGAAACAATTCTCACAG-AAATT
        130 AAAAAGTTTGAAAAGTT-GGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAA-T

               *       *      *     
       1256 AA-ATTTTAATCCAAAGAGCAAAA
        193 AAGTTTTTAATTCAAAGACCAAAA

                                       *                                *   *
       1279 GTTGTTTACAAAATGACAGATTATTTGAACCAAATGATGCGATTTCCCAAGAATGGAATGCTCAG
          1 GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA

                   *      *       *   *        *         *   *            *  
       1344 AAAATTGCTCGAAGGAATCGATTGTCATGAATACTCTAAGGAACCGAAGCTATAAAAGAACTTGA
         66 AAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGA

                      **             *         *            *                
       1409 AAAAGTTTGACTAGTTTGGAAGTTCTGCCAAGAACAAAGAGAGAAACATTTCTCACA-TAAATAA
        131 AAAAGTTTGAAAAG-TTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATAA

            *        *       *    
       1473 TTTTTTAATCCAAAGACAAAAA
        195 GTTTTTAATTCAAAGACCAAAA

                               *           *        *     * *    *           
       1495 GTTGTTTA-AAAATGACAGCTTATTTGGACCTAATGATGCAATTTCTCGAGAACGGAATGTTCAA
          1 GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA

                               *                                        *    
       1559 AAAATTGTTCGAA-AAATTAGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAGCTCG
         66 AAAATTGTTCGAAGAAA-TCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG

               *      *              *    *                *      *          
       1623 AAACAGTTTGCAAAGTTTGGAAGTTTGGCCTAGAACCAAGAGAGAAATAATTCTTAC-GTAAATA
        130 AAAAAGTTTGAAAAG-TTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATA

                           
       1687 AGTTTTTAATTCAAA
        194 AGTTTTTAATTCAAA

       1702 AACCGAA


Statistics
Matches: 1233,  Mismatches: 209, Indels: 91
        0.80            0.14        0.06

Matches are distributed among these distances:
 207    1  0.00
 208  167  0.14
 209   12  0.01
 210   13  0.01
 212  269  0.22
 213   17  0.01
 214  156  0.13
 215  177  0.14
 216  411  0.33
 217   10  0.01

ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28


Consensus pattern (216 bp):   
GTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGTTCAA
AAAATTGTTCGAAGAAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGA
AAAAGTTTGAAAAGTTGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAGTAAATAAG
TTTTTAATTCAAAGACCAAAA
Done.