Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012678.1 Kokia drynarioides strain JFW-HI SEQ_127689, 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, 862

Length: 1437
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.26

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:699 original size:215 final size:216

Alignment explanation


    Indices: 1--1437  Score: 1494
    Period size: 215  Copynumber: 6.6  Consensus size: 216

                            *                    *   *                       
          1 GGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCGTGACTACTTTAAGGAACCAAAGTTATA
          1 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATA

                                       * *                     *           * 
         66 AAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAAAGAAACAATCTGA
         66 AAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTCA

             *            *    *                                             
        131 CGTAAATAAGTTTTAAATTTAAAGACCAAAAAGTTGTTTACAAAATGACAAGAC-ATTTGGACCA
        131 CTTAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATGACAA-ACTATTTGGACCA

                           *      
        195 AATGATGCGATTTCCTGAGCAT
        195 AATGATGCGATTTCCCGAGCAT

                            *                    *         *                 
        217 GGAATGTTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTGAAGGAA-CAAATGTTAT
          1 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAA-GTTAT

                *    **                 * *                                  
        281 AAAATAACTAATAAAAGTTTGACAAGTTTGGAAGTTCGTCC-A-AACCAAAAGAGAAACAATTCT
         65 AAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAA-TCT

            *    *            *                                              
        344 TA-TGCAAATAAGTTTTTTATTCAAAGACCAAAAAGTTGTTTACAAAATGACAAACTATTTTGGA
        129 CACT-TAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATGACAAACTA-TTTGGA

                 *           *       
        408 CCAAAAGATGCGATTTCTCGAGCAT
        192 CCAAATGATGCGATTTCCCGAGCAT

                  *               *            * *                 * *   * * 
        433 GGAATGCTCGGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAGGAATCGAAGCTGT
          1 GGAATGTTC-GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAT

                     *    * *         *          *                           
        498 AAAAGAACTTGTAACATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCT
         65 AAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAA-TCT

                                 *   *            *                          
        563 CACTTAAATAAGTTTTTAATTTAAAAACC-AAAAGTTGCTTAC-AAATGACAAACTATTTGGACC
        129 CACTTAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATGACAAACTATTTGGACC

                             *     
        626 AAATGATGCGATTTCCCAAGCAT
        194 AAATGATGCGATTTCCCGAGCAT

                             *                *                              
        649 GGAATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATA
          1 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATA

                    *          *        *                         ***********
        714 AAAGAACTTGTAAAAGTTTCACAAGTTCATAAGTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         66 AAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTC------------------GTCCAAGAACC

            *********************            *    *                          
        779 NNNNNNNNNNNNNNNNNNNNNAAATAAGTTTTTTATTCGAAGACCAAAAAGTTGTTTACAAAATG
        113 AAAAGAGAAACAATCTCACTTAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATG

                                            *       
        844 ACAAACTATTTTGGACCAAATGATGCGATTTCTCGAGCAT
        178 ACAAACTA-TTTGGACCAAATGATGCGATTTCCCGAGCAT

                  *               *              *                 *         
        884 GGAATGCTCGGAAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCAAAGTTAT
          1 GGAATGTTC-GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAT

                          * *         * *        *                           
        949 AAAAGAACTCGTAACATTTTGACAAGCTAGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCT
         65 AAAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAA-TCT

              *                       *            *                         
       1014 CATTTAAATAAGTTTTTAA-TCTAAAAACC-AAAAGTTGCTTAC-AAATGACAAACTATTTGGAC
        129 CACTTAAATAAGTTTTTAATTC-AAAGACCAAAAAGTTGTTTACAAAATGACAAACTATTTGGAC

                              *     
       1076 CAAATGATGCGATTTCCCAAGCAT
        193 CAAATGATGCGATTTCCCGAGCAT

                             *                *     *                        
       1100 GGAATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGTATACTTTAAGGAACCAAAGTTATA
          1 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATA

                    *          *        *                      *           * 
       1165 AAAGAACTTGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAACCAAAACAGAAACAATCTGA
         66 AAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTCA

             *            *                          *                       
       1230 CGTAAATAAGTTTTAAATTCAAAGACC-AAAAGTTGTTTACGAAATGACAAAGC-ATTTGGACCA
        131 CTTAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATGACAAA-CTATTTGGACCA

                  *               
       1293 AATGATACGATTTCCCGAGCAT
        195 AATGATGCGATTTCCCGAGCAT

                            *       *        *   *   *                       
       1315 GGAATGTTCGAAAAATGGCTCGAACGAATGGATTGTCGTGACTACTTTAAGGAACCAAAGTTATA
          1 GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATA

                                       * *                     *      
       1380 AAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAAAGAAAC
         66 AAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAAC


Statistics
Matches: 998,  Mismatches: 186, Indels: 75
        0.79            0.15        0.06

Matches are distributed among these distances:
 214   54  0.05
 215  387  0.39
 216  204  0.20
 217  100  0.10
 218   30  0.03
 219   60  0.06
 220    1  0.00
 232   20  0.02
 233   12  0.01
 234   13  0.01
 235   37  0.04
 236   80  0.08

ACGTcount: A:0.39, C:0.14, G:0.17, T:0.26


Consensus pattern (216 bp):   
GGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATA
AAAGAACTCGTAAAAGTTTGACAAGTTCGTAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTCA
CTTAAATAAGTTTTTAATTCAAAGACCAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAA
ATGATGCGATTTCCCGAGCAT
Done.