Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008196.1 Kokia drynarioides strain JFW-HI SEQ_122856, 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: 9670
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31


Found at i:3470 original size:28 final size:28

Alignment explanation


    Indices: 3422--3487  Score: 89
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       3412 TAAGGAATTT

                           *             
       3422 ATCAAATTAATCCTTTTACTATTAAATAA
          1 ATCAAATTAATCCTTATACTATTAAA-AA

                 *                      
       3451 ATCAATTTAAT-CTTATACTATTAAAAA
          1 ATCAAATTAATCCTTATACTATTAAAAA

              *       
       3478 ATTAAATTAA
          1 ATCAAATTAA

       3488 AATAGAATTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  27   10  0.30
  28   13  0.39
  29   10  0.30

ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41


Consensus pattern (28 bp):   
ATCAAATTAATCCTTATACTATTAAAAA

Found at i:6228 original size:53 final size:53

Alignment explanation


    Indices: 6139--6506  Score: 411
    Period size: 53  Copynumber: 7.0  Consensus size: 53

       6129 TTCAAATTTG

                  *                    *    *        *      *    *
       6139 ATAACTTACGATGACAC-GAAGTCATCAGACCATTAATACATAATAGGGTTCAT
          1 ATAACTCACGATGACACAG-AGTCATCGGACCTTTAATACACAATAGGATTCAA

                                                  **       *     
       6192 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATATGCAATAGGGTTCAA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCAA

                              *  *               *       *       
       6245 ATAACTCACGATGACACACAGACATCGGACCTTTAATCCACAATACGATTCAA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCAA

                    *     * * *                     *   *         
       6298 ATAACTCATGATGATATAAAGTCATCGGACCTTTAAT-CTGCAACAGGATTCAA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATAC-ACAATAGGATTCAA

                     *                *          * *             
       6351 ATAACTCACAATGACAC--AGTCATCTGACCTTTAATCCGCAATAGGATTCAA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCAA

                              *                  * *             
       6402 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGCAATAGGATTCAA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCAA

                     *       *                    * **          
       6455 ATAACTCACAATGACACCGAGTCATCGGACCTTTAATATATGATAGGATTCA
          1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCA

       6507 TTTCTCATTT


Statistics
Matches: 272,  Mismatches: 38, Indels: 10
        0.85            0.12        0.03

Matches are distributed among these distances:
  51   46  0.17
  52    2  0.01
  53  223  0.82
  54    1  0.00

ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25


Consensus pattern (53 bp):   
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATACACAATAGGATTCAA

Found at i:6408 original size:157 final size:158

Alignment explanation


    Indices: 6139--6491  Score: 451
    Period size: 157  Copynumber: 2.2  Consensus size: 158

       6129 TTCAAATTTG

                  *  *       *        *    *             *   *    *         *
       6139 ATAACTTACGATGACACGAAGTCATCAGACCATTAATACAT--AATAGGGTTCATATAACTCACG
          1 ATAACTCACAATGACACAAAGTCATCGGACCTTTAAT-C-TGCAACAGGATTCAAATAACTCACA

                                        *        *                       *   
       6202 ATGACACAGAGTCATCGGACCTTTAATATGCAATAGGGTTCAAATAACTCACGATGACACACAGA
         64 ATGACACA-AGTCATCGGACCTTTAATACGCAATAGGATTCAAATAACTCACGATGACACAAAGA

                                           
       6267 CATCGGACCTTTAATCCACAATACGATTCAA
        128 CATCGGACCTTTAATCCACAATACGATTCAA

                    **    * *                                                
       6298 ATAACTCATGATGATATAAAGTCATCGGACCTTTAATCTGCAACAGGATTCAAATAACTCACAAT
          1 ATAACTCACAATGACACAAAGTCATCGGACCTTTAATCTGCAACAGGATTCAAATAACTCACAAT

                         *          *                                    *   
       6363 GACAC-AGTCATCTGACCTTTAATCCGCAATAGGATTCAAATAACTCACGATGACACAAAGTCAT
         66 GACACAAGTCATCGGACCTTTAATACGCAATAGGATTCAAATAACTCACGATGACACAAAGACAT

                          *     *       
       6427 CGGACCTTTAATCCGCAATAGGATTCAA
        131 CGGACCTTTAATCCACAATACGATTCAA

                             **                  
       6455 ATAACTCACAATGACACCGAGTCATCGGACCTTTAAT
          1 ATAACTCACAATGACACAAAGTCATCGGACCTTTAAT

       6492 ATATGATAGG


Statistics
Matches: 167,  Mismatches: 25, Indels: 6
        0.84            0.13        0.03

Matches are distributed among these distances:
 157  111  0.66
 158    1  0.01
 159   55  0.33

ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25


Consensus pattern (158 bp):   
ATAACTCACAATGACACAAAGTCATCGGACCTTTAATCTGCAACAGGATTCAAATAACTCACAAT
GACACAAGTCATCGGACCTTTAATACGCAATAGGATTCAAATAACTCACGATGACACAAAGACAT
CGGACCTTTAATCCACAATACGATTCAA

Found at i:8910 original size:16 final size:16

Alignment explanation


    Indices: 8889--8923  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       8879 TAATCACAAA

                     *    * 
       8889 AAACCAAAAGAAAAGG
          1 AAACCAAAAAAAAAAG

                            
       8905 AAACCAAAAAAAAAAG
          1 AAACCAAAAAAAAAAG

               
       8921 AAA
          1 AAA

       8924 TAAGAAGAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.77, C:0.11, G:0.11, T:0.00


Consensus pattern (16 bp):   
AAACCAAAAAAAAAAG
Done.