Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003992.1 Kokia drynarioides strain JFW-HI SEQ_117102, 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: 1811
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.27

Warning! 82 characters in sequence are not A, C, G, or T


Found at i:524 original size:216 final size:215

Alignment explanation


    Indices: 2--1246  Score: 1392
    Period size: 216  Copynumber: 5.8  Consensus size: 215

          1 G

                 *         *   *                 *        *      *           
          2 ATTCTGACTTAATAAATTTATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                              *    *                *  *   *        *      * 
         67 ACCAAATGATGCGATTTCACGAGAATGGAATGTTCGAAAAGTTGCTCAAAGGAATGTATCGTCCT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTT

                        **    *     *                       *                
        132 GAATA-TTTAGAATAACCGAAGTTGTAAAAGAACTCGTAAAAGTTTGAGAAGTT----AG-T--A
        131 GAATACTTTA-AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGA

             *                   
        189 CAAAT-ACCAAGAGAGAAACA
        195 CCAATAACCAAGAGAGAAACA

                    *   *             *     * *          *                   
        209 ATTCTCACGTAAAAAGTTTTTAATTCGAAGACTACAAGTTGTTTAGAAAATGACAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                                      **                *               *    
        274 ACCAAATGATGCGATTTCCCGAGCATTAAATGTTCGAAAAATTATTCGAAGGAATGGATCTTCTT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTT

                      *                        *   *                  *      
        339 GAATACTTTAGGGAACCAAAGTTATAAAAGAACTCATAATAGTTTGACAAGTTC-AGACGTTCGA
        131 GAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCGA

                    *            
        403 CCAATAACAAAGAGAGAAACA
        195 CCAATAACCAAGAGAGAAACA

              *         *             *                        *   *        *
        424 ATACTCACATTAGTAAGTTTTTAATTTAAAGACCAAAAGTCT-TTTACAAATTGATAAACTATTG
          1 ATTCTCAC-TTAATAAGTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGACAAACTATTT

              *          *     **   *    *       *       *  *                
        488 AGGCCAAATGATGTGATTTTTCGATCATGTAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTC
         64 AGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTC

                   *          *    *                                        *
        553 TTGAATATTTTAAGGAACGAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTT
        129 TTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG-TTC

                 **              **
        618 G-CCAGGAACCAAGAGAGAAATG
        193 GACCAATAACCAAGAGAGAAACA

                                                                     *       
        640 ATTCTCACTTAATAAGTTTTTAATTCGAAAGACCAAAAGTTGTTTACAAAATGACAACCTATTTA
          1 ATTCTCACTTAATAAGTTTTTAATTC-AAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA

             *                                           **                 *
        705 GCCCAAATGATGCGATTTCCC-ATGCATGGAATGTTCGAAAAATTGTTCGATA-GAATGGA-CAA
         65 GACCAAATGATGCGATTTCCCGA-GCATGGAATGTTCGAAAAATTACTCGA-AGGAATGGATC-G

                      *                                                      
        767 TCTTGAATACCTTAAGGAACCGAAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
        127 TCTTGAATACTTTAAGGAACC-AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT

             *                     * 
        831 TTGACCAATAACCAAGAGAGAAATA
        191 TCGACCAATAACCAAGAGAGAAACA

              *  *    *               *                                      
        856 ATACTGACGTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA
          1 ATTCTCAC-TTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA

             *       *        ** * *            *                            
        921 GGCCAAATGGTGCGATTTTTCAATCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATCGTCT
         65 GACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCT

                  *       *                     *              *            *
        986 TGAATATTTTAAGGTACCAAAGTTATAAAAGAACTCTTAAAAGTTTGACAAATTCGAAAGTTCGG
        130 TGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGA

                *          *    *
       1051 CCAAGAACCAAGAGATAAACG
        195 CCAATAACCAAGAGAGAAACA

                   *                                             *           
       1072 ATTCTCATTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                *                  *                        *       *    *   
       1137 ACCAGATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGATT-CTCAAAGGAATTGATCATCT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAA-ATTACTCGAAGGAATGGATCGTCT

                         **    *     *                     
       1201 TGAATAC-TTAGAATAACCGAAGTTGTAAAAGAACTCGTAAAAGTTT
        130 TGAATACTTTA-AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTT

       1247 AAGAAGTTAT


Statistics
Matches: 866,  Mismatches: 145, Indels: 46
        0.82            0.14        0.04

Matches are distributed among these distances:
 207  147  0.17
 208    4  0.00
 211    1  0.00
 212    1  0.00
 214    8  0.01
 215  185  0.21
 216  493  0.57
 217   27  0.03

ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29


Consensus pattern (215 bp):   
ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG
ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTT
GAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGAC
CAATAACCAAGAGAGAAACA

Found at i:1191 original size:215 final size:214

Alignment explanation


    Indices: 2--1810  Score: 1366
    Period size: 216  Copynumber: 8.5  Consensus size: 214

          1 G

                 *         *   *                 *        *      *           
          2 ATTCTGACTTAATAAATTTATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                              *    *                *               *      * 
         67 ACCAAATGATGCGATTTCACGAGAATGGAATGTTCGAAAAGTTGCTCAAAGGAATGTATCGTCCT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTT

                       **    *     *                       *                 
        132 GAATATTTAGAATAACCGAAGTTGTAAAAGAACTCGTAAAAGTTTGAGAAGTT----AG-T--A-
        131 GAATATTTA-AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGAC

                                 
        189 CAA-ATACCAAGAGAGAAACA
        195 CAAGA-ACCAAGAGAGAAACA

                    *   *             *     * *          *                   
        209 ATTCTCACGTAAAAAGTTTTTAATTCGAAGACTACAAGTTGTTTAGAAAATGACAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                                      **               **  *            *    
        274 ACCAAATGATGCGATTTCCCGAGCATTAAATGTTCGAAAAATTATTCGAAGGAATGGATCTTCTT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTT

                      *                        *   *                  *      
        339 GAATACTTTAGGGAACCAAAGTTATAAAAGAACTCATAATAGTTTGACAAGTTC-AGACGTTCGA
        131 GAATA-TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCGA

                *   *            
        403 CCAATAACAAAGAGAGAAACA
        194 CCAAGAACCAAGAGAGAAACA

              *         *             *                        *   *        *
        424 ATACTCACATTAGTAAGTTTTTAATTTAAAGACCAAAAGTCT-TTTACAAATTGATAAACTATTG
          1 ATTCTCAC-TTAATAAGTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGACAAACTATTT

              *          *     **   *    *       *          **               
        488 AGGCCAAATGATGTGATTTTTCGATCATGTAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTC
         64 AGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTC

                              *    *                                        *
        553 TTGAATATTTTAAGGAACGAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTT
        129 TTGAATA-TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG-TTC

                 *               **
        618 G-CCAGGAACCAAGAGAGAAATG
        192 GACCAAGAACCAAGAGAGAAACA

                                                                     *       
        640 ATTCTCACTTAATAAGTTTTTAATTCGAAAGACCAAAAGTTGTTTACAAAATGACAACCTATTTA
          1 ATTCTCACTTAATAAGTTTTTAATTC-AAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA

             *                                            *    *            *
        705 GCCCAAATGATGCGATTTCCC-ATGCATGGAATGTTCGAAAAATTGTTCGATA-GAATGGA-CAA
         65 GACCAAATGATGCGATTTCCCGA-GCATGGAATGTTCGAAAAATTGCTC-AAAGGAATGGATC-G

                      *                                                      
        767 TCTTGAATACCTTAAGGAACCGAAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
        127 TCTTGAATA-TTTAAGGAACC-AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT

             *      *              * 
        831 TTGACCAATAACCAAGAGAGAAATA
        190 TCGACCAAGAACCAAGAGAGAAACA

              *  *    *               *                                      
        856 ATACTGACGTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA
          1 ATTCTCAC-TTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA

             *       *        ** * *            *       *   *                
        921 GGCCAAATGGTGCGATTTTTCAATCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATCGTCT
         65 GACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCT

                          *                     *              *            *
        986 TGAATATTTTAAGGTACCAAAGTTATAAAAGAACTCTTAAAAGTTTGACAAATTCGAAAGTTCGG
        130 TGAATA-TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGA

                           *    *
       1051 CCAAGAACCAAGAGATAAACG
        194 CCAAGAACCAAGAGAGAAACA

                   *                                             *           
       1072 ATTCTCATTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTATTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                *                  *                                *    *   
       1137 ACCAGATGATGCGATTTCCCGAGAATGGAATGTTCGAAAAGATT-CTCAAAGGAATTGATCATCT
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAA-ATTGCTCAAAGGAATGGATCGTCT

                  *     **    *     *                     * *                
       1201 TGAATACTTAGAATAACCGAAGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGTT----A--T-GA
        130 TGAATATTTA-AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGA

             *                   
       1259 CAAAG-ACCAAGAGAGAAACA
        194 CCAAGAACCAAGAGAGAAACA

                      *  *      *        ************************************
       1279 ATTCTCACGTAAAAAAGTTTCTAATTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          1 ATTCTCAC-TTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTA

            **********************************************  *           *    
       1344 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCGAAGGAATGGATAGTCT
         65 GACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCT

                              *                                     *        
       1409 TGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGA
        130 TGAATA-TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGA

             *  *                
       1474 CTAATAACCAAGAGAGAAACA
        194 CCAAGAACCAAGAGAGAAACA

              *                        *                                 *   
       1495 ATACTCA-TGTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACTGTTT
          1 ATTCTCACT-T-AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTT

              * *   * *  *     **   *            *                           
       1559 AGGCTAAAGGGTGTGATTTTTCGATCATGGAATGTTCAAAAAATTGCTCAAAGGAATGGATCGTC
         64 AGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTC

                                                      *                      
       1624 TTGAATATTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAGGTTTGACAAGTTCGAAAGTTCG
        129 TTGAATA-TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCG

            *                *   *
       1689 GCCAAGAACCAAGAGAGTAACT
        193 ACCAAGAACCAAGAGAGAAACA

                    *                                                  *     
       1711 ATTCTCACATAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTTTAG
          1 ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG

                      *                        
       1776 ACCAAATGATTCGATTTCCCGAGCATGGAATGTTC
         66 ACCAAATGATGCGATTTCCCGAGCATGGAATGTTC

       1811 A


Statistics
Matches: 1197,  Mismatches: 363, Indels: 76
        0.73            0.22        0.05

Matches are distributed among these distances:
 207  167  0.14
 208   85  0.07
 209    4  0.00
 211    2  0.00
 212    2  0.00
 214    6  0.01
 215  277  0.23
 216  627  0.52
 217   27  0.02

ACGTcount: A:0.39, C:0.13, G:0.17, T:0.27


Consensus pattern (214 bp):   
ATTCTCACTTAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAG
ACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTT
GAATATTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGACC
AAGAACCAAGAGAGAAACA
Done.