Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009501.1 Kokia drynarioides strain JFW-HI SEQ_124212, 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: 7301
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34


Found at i:2677 original size:21 final size:21

Alignment explanation


    Indices: 2651--2723  Score: 92
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       2641 AGTGTAGACC

                                 
       2651 TCTACCGATACAAGTAATAGT
          1 TCTACCGATACAAGTAATAGT

                  *        * *   
       2672 TCTACCAATACAAGTGACAGT
          1 TCTACCGATACAAGTAATAGT

                           **  * 
       2693 TCTACCGATACAAGTCTTACT
          1 TCTACCGATACAAGTAATAGT

                      
       2714 TCTACCGATA
          1 TCTACCGATA

       2724 ACAAAAACTC


Statistics
Matches: 44,  Mismatches: 8, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   44  1.00

ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29


Consensus pattern (21 bp):   
TCTACCGATACAAGTAATAGT

Found at i:3569 original size:52 final size:52

Alignment explanation


    Indices: 3448--3633  Score: 232
    Period size: 52  Copynumber: 3.6  Consensus size: 52

       3438 ATTTCATTTA

                   *                       **      *  *         
       3448 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCAT-TAGGATTCAT
          1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                                         *      * **             
       3499 ATACTCACT-ATGACACATAGTCATCGGATCTCATATTTTGTAAAGGATTCAT
          1 ATACTCA-TGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                *        *                                      
       3551 ATACGCATGATGAGACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
          1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                   *                  *    
       3603 ATACTCACGATGACACATAGTCATCGAACCT
          1 ATACTCATGATGACACATAGTCATCGGACCT

       3634 TTTTGCATTT


Statistics
Matches: 113,  Mismatches: 19, Indels: 5
        0.82            0.14        0.04

Matches are distributed among these distances:
  51   33  0.29
  52   80  0.71

ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29


Consensus pattern (52 bp):   
ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

Found at i:5783 original size:41 final size:41

Alignment explanation


    Indices: 5726--5862  Score: 193
    Period size: 41  Copynumber: 3.3  Consensus size: 41

       5716 CCGAGTCATA

                                     *       *   *    
       5726 AGTCTTCCTTTAAATATAATCTCATTCTCATCTTGAGTCACG
          1 AGTCTTCCTTT-AATATAATCTCATGCTCATCTCGAGACACG

                  *            *             *       
       5768 AGTCTTGCTTTAATATAATATCATGCTCATCTCAAGACACG
          1 AGTCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACG

                                                   * 
       5809 AGTCTTCCTTTAATATAATCTCATGCTCATCTCGAGACATG
          1 AGTCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACG

                         
       5850 AGTCTTCCATTTA
          1 AGTCTTCC-TTTA

       5863 TATGTCAAGT


Statistics
Matches: 84,  Mismatches: 10, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  41   70  0.83
  42   14  0.17

ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38


Consensus pattern (41 bp):   
AGTCTTCCTTTAATATAATCTCATGCTCATCTCGAGACACG
Done.