Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003706.1 Kokia drynarioides strain JFW-HI SEQ_116647, 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, 706

Length: 1178
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42

Warning! 9 characters in sequence are not A, C, G, or T


Found at i:377 original size:216 final size:216

Alignment explanation


    Indices: 1--1178  Score: 1612
    Period size: 216  Copynumber: 5.5  Consensus size: 216

                                                     *                       
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGGACGAACTTTCGAACTTGTCAAAC

                        *      *   **                        *               
         66 TTTTACGAGTTACTTTTTATCTTTTGTTCCCTAAAGTATTCAACAAGATTCATTCCTTTGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCAA

                                                   *                         
        131 TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAGTTTGTCATTTTGTAAA
        131 TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA

                                 
        196 CAAGTTTTTGTCTTTGAATTA
        196 CAAGTTTTTGTCTTTGAATTA

                        *    *     *   *                                     
        217 AAAACTTATTTATGTGAAAATTGCTTCCCTCTTTGT-TCTTGGACGAACTTTCGAACTTGTCAAA
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCT-TTGGACGAACTTTCGAACTTGTCAAA

              * *                            *    *                          
        281 CTGTCACGAGTTATTTTTTAACTTCAGTTCCCTTAAGTTTTCAACAAGATCCATTCCTTTGAGCA
         65 CTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCA

                   *  **      *  *  *       *                                
        346 ATTTTTCAAATTTTCCATACTTGGAAAATCGCTTCATTTGGTCTAAATAGTTTGTCATTTTGTAA
        130 ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAA

                                  
        411 ACAAGTTTTTGTCTTTGAATTA
        195 ACAAGTTTTTGTCTTTGAATTA

                *                    *               *     *                 
        433 AAAATTTATTTACGTGAGAATTGTTCCTCTCTTTGTCTTTGTACGAAGTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGGACGAACTTTCGAACTTGTCAAAC

                  *                 *      *********                  *      
        498 TTTTACAAGTTATTTTTTAACTTCGGTTCCCNNNNNNNNNCAACAAGATCCATTCCTTAGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCAA

                *                                  *     *  *  *         *   
        563 TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGTTCTAAGTAATTCGTCATTTTGCAAA
        131 TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA

                    * *          
        628 CAAGTTTTAGACTTTGAATTA
        196 CAAGTTTTTGTCTTTGAATTA

                       **         *                  *                 *     
        649 AAAACTTATTTTTGTGAGAATTATTTCTCTCTTTGT-TCTTCGACGAACTTTCGAACTTTTCAAA
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCT-TTGGACGAACTTTCGAACTTGTCAAA

                      *    *                    *                        *   
        713 CTTTTACGAGATATTCTTTAACTTCAGTTCCCTAAACTATTCAACAAGATCCATTCCTTTGTGCA
         65 CTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCA

                      **      ** *                                           
        778 ATTTTTCGAATTTTCCATAATTGGGAAATCGCATCATTTGGT-TAAAATAGTTTGTCATTTTGTA
        130 ATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCT-AAATAGTTTGTCATTTTGTA

                                   
        842 AACAAGTTTTTGTCTTTGAATTA
        194 AACAAGTTTTTGTCTTTGAATTA

                                                     *  *                    
        865 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACTAACTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGGACGAACTTTCGAACTTGTCAAAC

                   *                *                                 *      
        930 TTTTACGGGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTCGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCAA

                *                       * *              *  *                
        995 TTTTCCGAACATTCCATGCTCGGGAAATTGTATCATTTGGTCTAATTAATTTGTCATTTTGTAAA
        131 TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA

                       *          
       1060 CAAG-TTTTGCACTTTGAATTA
        196 CAAGTTTTTG-TCTTTGAATTA

                         *                               *                   
       1081 AAAACTTATTTACATGAGAATTGTTTCTCTCTTTGT-TCTTGG-CAAACTTTCGAACTTGTCAAA
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCT-TTGGACGAACTTTCGAACTTGTCAAA

                                               
       1144 CTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAA
         65 CTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAA


Statistics
Matches: 828,  Mismatches: 126, Indels: 17
        0.85            0.13        0.02

Matches are distributed among these distances:
 215   62  0.07
 216  763  0.92
 217    3  0.00

ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42


Consensus pattern (216 bp):   
AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGGACGAACTTTCGAACTTGTCAAAC
TTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAAGTATTCAACAAGATCCATTCCTTTGAGCAA
TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA
CAAGTTTTTGTCTTTGAATTA

Found at i:809 original size:432 final size:430

Alignment explanation


    Indices: 1--1178  Score: 1800
    Period size: 432  Copynumber: 2.7  Consensus size: 430

                                                                             
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC

                        *      *   **                        *        *      
         66 TTTTACGAGTTACTTTTTATCTTTTGTTCCCTAAAGTATTCAACAAGATTCATTCCTTTGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGAGCAA

                *                                           *                
        131 TTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAGTTTGTCATTTTGTAAA
        131 TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAATTTGTCATTTTGTAAA

                      *                           *     *   *                
        196 CAAGTTTTTGTCTTTGAATTAAAAACTTATTTATGTGAAAATTGCTTCCCTCTTTGTTCTTGGAC
        196 CAAG-TTTTGACTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTT-GAC

                                  * *                            *  * *      
        261 GAACTTTCGAACTTGTCAAACTGTCACGAGTTATTTTTTAACTTCAGTTCCCTTAAGTTTTCAAC
        259 GAACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAACTATTCAAC

                                                   *            *            
        326 AAGATCCATTCCTTTGAGCAATTTTTCAAATTTTCCATACTTGGAAAATCGCTTCATTTGGTCT-
        324 AAGATCCATTCCTTTGAGCAATTTTTCAAATTTTCCATAATTGGAAAATCGCATCATTTGGT-TA

                                                       
        390 AAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTA
        388 AAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTA

                *                    *                     *                 
        433 AAAATTTATTTACGTGAGAATTGTTCCTCTCTTTGTCTTTGTACGAAGTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC

                  *                        *********                         
        498 TTTTACAAGTTATTTTTTAACTTCGGTTCCCNNNNNNNNNCAACAAGATCCATTCCTTAGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGAGCAA

                                                   *     *     *         *   
        563 TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGTTCTAAGTAATTCGTCATTTTGCAAA
        131 TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAATTTGTCATTTTGTAAA

                                            *          *                     
        628 CAAGTTTTAGACTTTGAATTAAAAACTTATTTTTGTGAGAATTATTTCTCTCTTTGTTCTTCGAC
        196 CAAGTTTT-GACTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTT-GAC

                          *               *    *                             
        693 GAACTTTCGAACTTTTCAAACTTTTACGAGATATTCTTTAACTTCAGTTCCCTAAACTATTCAAC
        259 GAACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAACTATTCAAC

                            *          *                *                    
        758 AAGATCCATTCCTTTGTGCAATTTTTCGAATTTTCCATAATTGGGAAATCGCATCATTTGGTTAA
        324 AAGATCCATTCCTTTGAGCAATTTTTCAAATTTTCCATAATTGGAAAATCGCATCATTTGGTTAA

                                                      
        823 AATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTA
        389 AATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTA

                                                        *                    
        865 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACTAACTTTCGAACTTGTCAAAC
          1 AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC

                   *                                                  *      
        930 TTTTACGGGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTCGAGCAA
         66 TTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGAGCAA

                                        * *        *     *                   
        995 TTTTCCGAACATTCCATGCTCGGGAAATTGTATCATTTGGTCTAATTAATTTGTCATTTTGTAAA
        131 TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAATTTGTCATTTTGTAAA

                                             **                           * *
       1060 CAAGTTTTGCACTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTCTTTGTTCTTGGCA
        196 CAAGTTTTG-ACTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTTGACG

                                                                  
       1125 AACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAA
        260 AACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAA


Statistics
Matches: 667,  Mismatches: 76, Indels: 7
        0.89            0.10        0.01

Matches are distributed among these distances:
 431   59  0.09
 432  608  0.91

ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42


Consensus pattern (430 bp):   
AAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTCTTTGTACGAACTTTCGAACTTGTCAAAC
TTTTACGAGTTATTTTTTAACTTCGGTTCCCTAAAGTATTCAACAAGATCCATTCCTTAGAGCAA
TTTTCCGAACATTCCATGCTCGGGAAATCGCATCATTTGCTCTAAATAATTTGTCATTTTGTAAA
CAAGTTTTGACTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTTGTTCTTGACGA
ACTTTCGAACTTGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTAAACTATTCAACAA
GATCCATTCCTTTGAGCAATTTTTCAAATTTTCCATAATTGGAAAATCGCATCATTTGGTTAAAA
TAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTTGAATTA
Done.