Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003716.1 Kokia drynarioides strain JFW-HI SEQ_116667, 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: 11478
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36


Found at i:147 original size:17 final size:15

Alignment explanation


    Indices: 113--156  Score: 70
    Period size: 17  Copynumber: 2.8  Consensus size: 15

        103 AACACATTAC

                           
        113 CTTTCTTTCCTTCTT
          1 CTTTCTTTCCTTCTT

                             
        128 CTTTCTTTCCTCTCCTT
          1 CTTTCTTTCCT-T-CTT

                        
        145 CTTTCTTTCCTT
          1 CTTTCTTTCCTT

        157 TGTTTCTTTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  15   11  0.41
  16    2  0.07
  17   14  0.52

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (15 bp):   
CTTTCTTTCCTTCTT

Found at i:3440 original size:51 final size:51

Alignment explanation


    Indices: 3385--3492  Score: 128
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       3375 GTCGTCAAAT

                      * *           *           *   *           
       3385 TTTACATATTTTGTCAAATTGA-TTTTAATTTAACACATTTAACCCACAACA
          1 TTTACATATTCTATC-AATTGAGTCTTAATTTAACAAATTCAACCCACAACA

                               *      *              *         
       3436 TTTACATATTCTATCAATTTAGTCTTGATTTAACAAATTCAGCCCACAACA
          1 TTTACATATTCTATCAATTGAGTCTTAATTTAACAAATTCAACCCACAACA

                  
       3487 TTTACA
          1 TTTACA

       3493 CAGAATATAT


Statistics
Matches: 48,  Mismatches: 8, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  50    5  0.10
  51   43  0.90

ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40


Consensus pattern (51 bp):   
TTTACATATTCTATCAATTGAGTCTTAATTTAACAAATTCAACCCACAACA

Found at i:10076 original size:52 final size:52

Alignment explanation


    Indices: 9993--10283  Score: 395
    Period size: 52  Copynumber: 5.6  Consensus size: 52

       9983 TGCATATTTA

                         *             *     * **  *        *    
       9993 ATACTCACGATGATACAG-AGTCATCGAACCTCTTGTTCTGTAAAGGAATCAT
          1 ATACTCACGATGACAC-GTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

             *             **    * *                            
      10045 ACACTCACGATGACATATAGTTACCGGACCTCATAATCCGTAAAGGATTCAT
          1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                 *                                      *       
      10097 ATACTTACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
          1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                                 *  * *                         
      10149 ATACTCACGATGACACGTAGTTATTGAACCTCATAATCCGTAAAGGATTCAT
          1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                                                 *              
      10201 ATACTCACGATGACACGTAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
          1 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

                            *              
      10253 ATACTCACGATGACACATAGTCATCGGACCT
          1 ATACTCACGATGACACGTAGTCATCGGACCT

      10284 TTCTCATTTA


Statistics
Matches: 209,  Mismatches: 29, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  52  209  1.00

ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27


Consensus pattern (52 bp):   
ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT

Done.