Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000542.1 Kokia drynarioides strain JFW-HI SEQ_111446, 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, 890

Length: 1484
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39


Found at i:385 original size:216 final size:216

Alignment explanation


    Indices: 1--1484  Score: 1432
    Period size: 216  Copynumber: 6.9  Consensus size: 216

                    *                 *                 *       **         * 
          1 GGGAAATCGCATCATTTTGTCTAAATTGTTTGTCATTTTCTAAAAAACTTTTTATCTTTGAATTA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

                 *      ***    *   **          *         *        *          
         66 AAAACCTATTTATACGAGATTTCCCTT-TCTCTTGCTTCTTAGA-TATAC-TTCCAAGCTTGACA
         66 AAAACTTATTTACGTGAGAGTT-GTTTCTCTCTTGGTTCTTAGACGA-ACTTTCGAA-CTTGACA

                 *            *       **   *              *   *           ** 
        128 AACTTGTACGAGTTCTTCAATAACTTTGGTTTC-TCAAAGTATTCAGGACAATCCATTCCTTAAA
        128 AACTTTTACGAGTTCTTCTATAACTTCAGTTCCAT-AAAGTATTCATGACGATCCATTCCTTCGA

                      *               
        192 GCAATTTGT-TGAACATTCCATGCTT
        192 GCAATTT-TCCGAACATTCCATGCTT

                             *         *                 *                   
        217 GGGAAATCACATCATTTGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTGAATGA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

                      *                 *                            * *     
        282 AAAACTTATTCACGTGAGAGTTGTTTCTATCTTGGTTCTTAGACGAACTTTCGAACTCGGCAAAC
         66 AAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTAGACGAACTTTCGAACTTGACAAAC

                          *                               *                  
        347 TTTTACGAGTTCTTTTATAACTTCAGTTCCATAAAGTATTCATGACCATCCATTCCTTCGAGCAA
        131 TTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCATTCCTTCGAGCAA

                         *       
        412 TTTTCCGAACATTTCATGCTT
        196 TTTTCCGAACATTCCATGCTT

                    *         *                    **                        
        433 GGGAAATCGCATCATTTTTTCTAAACTA-TTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATG
          1 GGGAAATCACATCATTTTGTCTAAA-TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATG

                          *     *     *         * *  *  *         *          
        497 AAAAACTTATTTACATGAGAATTGTTCCTCTCTTGGATATTGGATGAAC-TTCTAAACTTGACAA
         65 AAAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTAGACGAACTTTC-GAACTTGACAA

                 *                      *  **                               *
        561 ACTTTGACGAGTTCTTCTATAACTTCAGCTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGA
        129 ACTTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCATTCCTTCGAGC

                  **               
        626 AATTTTTTGAACATTCCATGCTT
        194 AATTTTCCGAACATTCCATGCTT

                              *                *  **  *             *      * 
        649 GGGAAATCACATCATTTTCTCTAAATAGTTTGTCACTTGGTATACAACTTTTGGTCATTGAATTA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

                               *       *        *  * *   *     *       *   * 
        714 AAAACTTATTTACGTGAGAATT-TATTATCTCTTGGATCATGGACAAACTTCCGAACTTTACAGA
         66 AAAACTTATTTACGTGAGAGTTGT-TTCTCTCTTGGTTCTTAGACGAACTTTCGAACTTGACAAA

              *    *    *    *      **                           *           
        778 CTGTTACCAGTTGTTCTCTAACTTTGGTT-CATTAAAGTATTCATGACGATCCTTTCCTTCGAGC
        130 CTTTTACGAGTTCTTCTATAACTTCAGTTCCA-TAAAGTATTCATGACGATCCATTCCTTCGAGC

                            * *  **
        842 AATTTTCCGAACATTCAAAGCAC
        194 AATTTTCCGAACATTCCATGCTT

               *  * *       *  *           *   *                 *   ***   * 
        865 GGGGAACCGCATCATTCTGCCTAAATAGTTTTTCACTTTCTAAACAACTTTTGTTCTACAAATTA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

              * *             *                *     *         *          *  
        930 AACAGTTATTTACGTGAGTGTTGTTTCTCTCATT-ATTCTTGGACGAACTTCCGAACTTGACGAA
         66 AAAACTTATTTACGTGAGAGTTGTTTCTCTC-TTGGTTCTTAGACGAACTTTCGAACTTGACAAA

            *                 *            *    *    *          *       *    
        994 GTTTTACGAGTTCTTCTAAAACTTCAGTTCCTTAAATTATTTATGACGATCCGTTCCTTCTAGCA
        130 CTTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCATTCCTTCGAGCA

                       *        **
       1059 ATTTTCCGAACTTTCCATGCAC
        195 ATTTTCCGAACATTCCATGCTT

                    *                 *                 *       **         * 
       1081 GGGAAATCGCATCATTTTGTCTAAATTGTTTGTCATTTTCTAAAAAACTTTTTATCTTTGAATTA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

                 *        *         *          *        *        *           
       1146 AAAACCTATTTACGCGAGAGTTGCCTT-TCTCTTGCTTCTTAGATGAAC-TTCCAAGCTTGACAA
         66 AAAACTTATTTACGTGAGAGTTG-TTTCTCTCTTGGTTCTTAGACGAACTTTCGAA-CTTGACAA

                                      **   *              *   *           *  
       1209 ACTTTTACGAGTTCTT-TAATAACTTTGGTTTC-TCAAAGTATTCAGGACAATCCATTCCTTAGA
        129 ACTTTTACGAGTTCTTCT-ATAACTTCAGTTCCAT-AAAGTATTCATGACGATCCATTCCTTCGA

                      *       *       
       1272 GCAATTTGT-TGAACATTTCATGCTT
        192 GCAATTT-TCCGAACATTCCATGCTT

                             *         *                 *                   
       1297 GGGAAATCACATCATTTGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTGGTCTTTGAATGA
          1 GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA

                     **    *            *     *   *                  * *     
       1362 AAAACTTATCGACGTTAGAGTTGTTTCTATCTTGATTCGTAGACGAACTTTCGAACTCGGCAAAC
         66 AAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTAGACGAACTTTCGAACTTGACAAAC

                          *                               *           
       1427 TTTTACGAGTTCTTTTATAACTTCAGTTCCATAAAGTATTCATGACCATCCATTCCTT
        131 TTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCATTCCTT


Statistics
Matches: 1034,  Mismatches: 210, Indels: 48
        0.80            0.16        0.04

Matches are distributed among these distances:
 215   19  0.02
 216  990  0.96
 217   25  0.02

ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39


Consensus pattern (216 bp):   
GGGAAATCACATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATGA
AAAACTTATTTACGTGAGAGTTGTTTCTCTCTTGGTTCTTAGACGAACTTTCGAACTTGACAAAC
TTTTACGAGTTCTTCTATAACTTCAGTTCCATAAAGTATTCATGACGATCCATTCCTTCGAGCAA
TTTTCCGAACATTCCATGCTT

Done.