Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009591.1 Kokia drynarioides strain JFW-HI SEQ_124306, 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, 919

Length: 1533
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:1017 original size:431 final size:433

Alignment explanation


    Indices: 222--1017  Score: 1027
    Period size: 431  Copynumber: 1.8  Consensus size: 433

        212 AACACAAAAT

                      *         **                                     * *   
        222 AAGTGGTATATAATGTTAAATGATAAAAGAAAAAAACTACTGTTTCTGAAGATATTTAAGCGAAA
          1 AAGTGGTATACAATGTTAAAAAATAAAAGAAAAAAACTACTGTTTCTGAAGATATTTAAACAAAA

               *                  *   *                                  *   
        287 TTTTCAAAGAAAGATTAGAGTCTTAATTACAATGGAAACAACAAACAAATATGGTAGGAAATATG
         66 TTTCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACAAACAAATATGGTAGGAAACATG

                               *               *     *                  **   
        352 TATCACGGTTCGCATCTAAGAAATTGGATACACTCTATTTTTAGACTTTTTAAATGGGTCCGCCT
        131 TATCACGGTTCGCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTCAACCT

                                                 *             **            
        417 CGACTTTGTCTTCACTACTCTTTTTTATTTATTTCCAGCCCTCAATATCGCTGCATGTTGCAATG
        196 CGACTTTGTCTTCACTACTCTTTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGCAATG

                                                                    *        
        482 CAATTACACTCTATTTATTTATATGGATATTCTGGAAACATATAGAAACTTGGCACTTTTACCGT
        261 CAATTACACTCTATTTATTTATATGGATATTCTGGAAACATATAGAAACTTGGCACATTTACCGT

                *        *                *                                  
        547 AAGCTGTTGCTGTCTTCTTGAGATTGTTTAGACAATTTTTTTGCCATCCTTTTTCCACTCGGTTC
        326 AAGCCGTTGCTGTATTCTTGAGATTGTTTAAACAATTTTTTTGCCATCCTTTTTCCACTCGGTTC

                                                       
        612 ATGTAGGAAACATGAATTGCTATTAATGTTGGTAATGCGAAAC
        391 ATGTAGGAAACATGAATTGCTATTAATGTTGGTAATGCGAAAC

                                                                             
        655 AAGTGGTATACAATGTTAAAAAAATAAAAGAAAAATAA-TA-T-TTTC-GAAGATATTTAAACAA
          1 AAGTGGTATACAATGTT-AAAAAATAAAAGAAAAA-AACTACTGTTTCTGAAGATATTTAAACAA

                     *     *  *             *                                
        716 AATTTCCAATGAAAGGTTGGAGTCATAACTACGATGGAAACAACAGAA-AAATATGGTAGGAAAC
         64 AATTTCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACA-AACAAATATGGTAGGAAAC

                    * *  *  *                 *                        *     
        780 ATGTATCATGTTTGGCCTCTAACAAATTGGATACTCTCCATTTTCAGACTTTTTAAATGTGTCAA
        128 ATGTATCACGGTTCGCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTCAA

            *     *                                             *    *       
        845 TCTCGATTTTGTCTTCA-T-CTCTCTTTTTATTTATTTCC-CCCCTCAATATTGCAATATGTTGC
        193 CCTCGACTTTGTCTTCACTACTCT-TTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGC

             *  * *    *                   *      *           *      *       
        907 ACTGTAGTTACTCTCTATTTATTTTATATGGTTATTCTTGAAACATATAGGAACTTGTCACATTT
        257 AATGCAATTACACTCTATTTA-TTTATATGGATATTCTGGAAACATATAGAAACTTGGCACATTT

              *  *           *    *                   *     
        972 ACTGTGAGCCGTTAG-TTTATTGTTGAGATAT-TTTAAACAAATTTTT
        321 ACCGTAAGCCGTT-GCTGTATTCTTGAGAT-TGTTTAAACAATTTTTT

       1018 ACGTATAAAA


Statistics
Matches: 308,  Mismatches: 48, Indels: 17
        0.83            0.13        0.05

Matches are distributed among these distances:
 429   40  0.13
 430   88  0.29
 431  138  0.45
 432    6  0.02
 433   17  0.06
 434   17  0.06
 435    2  0.01

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Consensus pattern (433 bp):   
AAGTGGTATACAATGTTAAAAAATAAAAGAAAAAAACTACTGTTTCTGAAGATATTTAAACAAAA
TTTCCAAAGAAAGATTAGAGTCATAACTACAATGGAAACAACAAACAAATATGGTAGGAAACATG
TATCACGGTTCGCATCTAACAAATTGGATACACTCCATTTTCAGACTTTTTAAATGGGTCAACCT
CGACTTTGTCTTCACTACTCTTTTTTATTTATTTCCACCCCTCAATATCGCAACATGTTGCAATG
CAATTACACTCTATTTATTTATATGGATATTCTGGAAACATATAGAAACTTGGCACATTTACCGT
AAGCCGTTGCTGTATTCTTGAGATTGTTTAAACAATTTTTTTGCCATCCTTTTTCCACTCGGTTC
ATGTAGGAAACATGAATTGCTATTAATGTTGGTAATGCGAAAC
Done.