Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013257.1 Kokia drynarioides strain JFW-HI SEQ_128277, 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, 843

Length: 1405
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.25

Warning! 53 characters in sequence are not A, C, G, or T


Found at i:397 original size:215 final size:214

Alignment explanation


    Indices: 7--453  Score: 615
    Period size: 215  Copynumber: 2.1  Consensus size: 214

          1 TTAAAA

                       *               *     *          *      *             
          7 ACCAAAAGTTGCTTACAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAAT
          1 ACCAAAAGTTGTTTACAAATGACAAATCATTTGAACCAAATGATACGATTTACCAAGCATGGAAT

                     * *       *            *                 *            * 
         72 GTTCGAAAATTTACTCGAATGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGA
         66 GTTCGAAAAATGACTCGAAGGAATGGATCATCGTGAATACTTTAAGGAACAAAAGTTATAAAACA

               *            *       *  *       * *        *  *               
        137 ACTTGTAAAACTTTCAGAAGTTCATAAGTTCATCCCAGAACCAAAAGAGGAACAATCTGACGTAA
        131 ACTCGTAAAACTTTCACAAGTTCAGAAATTCATCCAACAACCAAAAAAGAAACAATCTGACGTAA

                               
        202 ATAAGTTTTAAATTCAAAG
        196 ATAAGTTTTAAATTCAAAG

                                                                   *         
        221 ACCAAAAGTTGTTTACGAAATGACAAATCATTTGAACCAAATGATACGATTTACCGAGCATGGAA
          1 ACCAAAAGTTGTTTAC-AAATGACAAATCATTTGAACCAAATGATACGATTTACCAAGCATGGAA

                         *                *      *                           
        286 TGTTCGAAAAATGGCTCGAAGGAATGGATCGTCGTGACTACTTTAAGGAACAAAAGTTATAAAAC
         65 TGTTCGAAAAATGACTCGAAGGAATGGATCATCGTGAATACTTTAAGGAACAAAAGTTATAAAAC

                       *   *       **              *                         
        351 AACTCGTAAAAGTTTGACAAGTTTGGAAATTCATCCAACTACCAAAAAAGAAACAATCTGACGTA
        130 AACTCGTAAAACTTTCACAAGTTCAGAAATTCATCCAACAACCAAAAAAGAAACAATCTGACGTA

                           *    
        416 AATAAGTTTTAAATTTAAAG
        195 AATAAGTTTTAAATTCAAAG

                              
        436 ACCAAAAAGTTGTTTACA
          1 ACC-AAAAGTTGTTTACA

        454 NNNNNNNNNN


Statistics
Matches: 202,  Mismatches: 29, Indels: 3
        0.86            0.12        0.01

Matches are distributed among these distances:
 214   15  0.07
 215  174  0.86
 216   13  0.06

ACGTcount: A:0.42, C:0.15, G:0.16, T:0.26


Consensus pattern (214 bp):   
ACCAAAAGTTGTTTACAAATGACAAATCATTTGAACCAAATGATACGATTTACCAAGCATGGAAT
GTTCGAAAAATGACTCGAAGGAATGGATCATCGTGAATACTTTAAGGAACAAAAGTTATAAAACA
ACTCGTAAAACTTTCACAAGTTCAGAAATTCATCCAACAACCAAAAAAGAAACAATCTGACGTAA
ATAAGTTTTAAATTCAAAG

Found at i:1030 original size:215 final size:216

Alignment explanation


    Indices: 507--1405  Score: 1162
    Period size: 215  Copynumber: 4.2  Consensus size: 216

        497 NNNNNNNNNN

                                                *                            
        507 AATGACAAACCATTTGGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAAATGGCTCA
          1 AATGACAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCA

                           *         *          *         *    * *           
        572 AAGGAATGGATCATCATGAATACTTGAAGGAACCAAGGTTATAAAATAACTTGGAAAAGTTTGAC
         66 AAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC

                 *                           *      *     * *           *    
        637 AAGTTTGGAAGTTCGTCC-A-AACCAAAAGAGAGACAATTTTGACGCAGATAAGCTTTT-TATTC
        131 AAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAA-TCTGACGTAAATAAG-TTTTAAATTC

                                   
        699 AAAGACCAAAAAGTTGTTTACAA
        194 AAAGACCAAAAAGTTGTTTACAA

                       *                        *    *           *       *   
        722 AATGACAAACTAATTTGGACCAAATGATGCGATTTCTCGAGTATGGAATGCTTTGAAAAATTGCT
          1 AATGACAAAC-CATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATG-TTCGAAAAATGGCT

                          * *                 * *     *               * *    
        787 CAAAGGAATGGATCGTTTTGAATACTTTAAGGAATCGAAGTTGTAAAAGAACTCGTAACATTTTG
         64 CAAAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTG

                 *   *      *                           *  *            *    
        852 ACAAGCTCGTAAGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTAATT
        129 ACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAA-TCTGACGTAAATAAGTTTTAAATT

            *   *         *  *      
        917 TAAAAACC-AAAAGCTGCTTAC-A
        193 CAAAGACCAAAAAGTTGTTTACAA

                      *                          *      *              **   *
        939 AATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGCATGAAATGTTCGAAAAATTACTCG
          1 AATGACAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCA

             *                                                 *          *  
       1004 ATGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTGTAAAAGTTTCAC
         66 AAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC

                  **                *                                        
       1069 AAGTTCATAAGTTCGTCCAAGAACAAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAA
        131 AAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAA

                               * 
       1134 AGACC-AAAAGTTGTTTACGA
        196 AGACCAAAAAGTTGTTTACAA

                     *                 *                                    *
       1154 AATGACAAAGCATTTGGACCAAATGATACGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCG
          1 AATGACAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCA

                        *  *   *                                             
       1219 AAGGAATGGATCGTCGTGACTACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC
         66 AAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC

                 *    *          *       *                                *  
       1284 AAGTTTGGAAATTCGTCCAAGTACCAAAAAAGAAACAATCTGACGTAAATAAGTTTTAAATTTAA
        131 AAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAA

                                *
       1349 AGACCAAAAAGTTGTTTACAG
        196 AGACCAAAAAGTTGTTTACAA

                               *                
       1370 AATGACAAACCATTTGGACTAAATGATGCGATTTCC
          1 AATGACAAACCATTTGGACCAAATGATGCGATTTCC


Statistics
Matches: 587,  Mismatches: 90, Indels: 13
        0.85            0.13        0.02

Matches are distributed among these distances:
 214   38  0.06
 215  292  0.50
 216  115  0.20
 217   91  0.16
 218   16  0.03
 219   35  0.06

ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26


Consensus pattern (216 bp):   
AATGACAAACCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATGGCTCA
AAGGAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGAC
AAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAA
AGACCAAAAAGTTGTTTACAA
Done.