Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007176.1 Kokia drynarioides strain JFW-HI SEQ_121788, 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: 1846
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30


Found at i:1676 original size:249 final size:246

Alignment explanation


    Indices: 858--1846  Score: 1295
    Period size: 249  Copynumber: 4.1  Consensus size: 246

        848 AGCAACCTCT

                        *          * *  **       *          *                
        858 TTACTCACTTTTTCTTTTCCTTTCAGCAAATTAACATCAACTAACAAAAAGTA-AAAGATGAAGA
          1 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAG-AGAAAGATGAAGA

                *     *               *   *                             *    
        922 AATGGGAGAAAAGAAGAAATAAGTTTTAATGGGAGAAGAATTAAGTTTATCTAAGTGAGACGAGA
         65 AATGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGA

               *                   *    **    * **    * *                    
        987 GAAAATATATAA-GTTCATTTTGGCATTCTGTAAAGCCAAATGTCAATATATATAAAT-CTAAGA
        130 GAATATATA-AAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATAT-AATGCTAAGA

              *                                                *  *    * 
       1050 TGTTGTCAATCTATATACATATATATAAAGG-TT-TACCTGAAGGTTTGGCAGCAACCTCA
        193 TGATGTC-A---ATAT--ATATATATAAAGGCTTATA-CTGAAGGTTTGGCGGCGACCTGA

                                       *               *        *            
       1109 TTACTCACTTTTCCTTTTCCTTTAATCGTCTTAACATAAACTAGCAAAGAGAAAAAGATGAAGAA
          1 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA

                                                          *    *             
       1174 ATGAGAGAAGAGAAGAAATAAGTTTGAAT-GG-G-AG----AAG--AATCTGAGTGAGAAGAGAG
         66 ATGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAG

                    *       *         *        *                             
       1230 AATATATACAGGTTCACTTTGACATTAAGTAATGGCAAATATAAATATATATAATGCTAAGATGA
        131 AATATATAAAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATATAATGCTAAGATGA

                                *                 *            
       1295 TGTCAATATATATATATAAACGCTTATA-TGAAGGTTTTGC-G-G-CCTGA
        196 TGTCAATATATATATATAAAGGCTTATACTGAAGGTTTGGCGGCGACCTGA

                                                                             
       1342 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA
          1 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA

            *                                                   *            
       1407 CTGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTATGTGAGAAGAGAG
         66 ATGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAG

                                                                  *          
       1472 AATATATAAAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATATAACGCTAAGATGA
        131 AATATATAAAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATATAATGCTAAGATGA

                                                                   
       1537 TGTCAATATATATATATATATAAAGGCTTATAC-GAAGGTTTGGCGGCGACCTGA
        196 TGTC---A-ATATATATATATAAAGGCTTATACTGAAGGTTTGGCGGCGACCTGA

                                                                             
       1591 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA
          1 TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA

            *        *                                                       
       1656 CTGAGAGAATAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAG
         66 ATGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAG

                    *             *                                          
       1721 AATATATACAGGTTCATTTTGAAATTGAGTAATGGAAAATATAAATATATATAATGCTAAGATGA
        131 AATATATAAAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATATAATGCTAAGATGA

                                                                
       1786 TGTC-A-ATATATATATAAAGGCTTAT-CTGAAGGTTTGGCGGCGACC-GCA
        196 TGTCAATATATATATATAAAGGCTTATACTGAAGGTTTGGCGGCGACCTG-A

                         
       1834 TTACTCACTTTTC
          1 TTACTCACTTTTC


Statistics
Matches: 665,  Mismatches: 49, Indels: 56
        0.86            0.06        0.07

Matches are distributed among these distances:
 233   94  0.14
 234    2  0.00
 235    2  0.00
 236   25  0.04
 237    2  0.00
 238    6  0.01
 240    3  0.00
 241    5  0.01
 242  150  0.23
 243   52  0.08
 244    4  0.01
 245    1  0.00
 246   32  0.05
 247    1  0.00
 248    3  0.00
 249  200  0.30
 250    3  0.00
 251   80  0.12

ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30


Consensus pattern (246 bp):   
TTACTCACTTTTCCTTTTCCTTTAATCATCTTAACATAAACTAACAAAGAGAGAAAGATGAAGAA
ATGAGAGAAGAGAAGAAATAAGTTTGAATAGGAGAAGAATTAAGTTTATCTAAGTGAGAAGAGAG
AATATATAAAGGTTCATTTTGACATTGAGTAATGGAAAATATAAATATATATAATGCTAAGATGA
TGTCAATATATATATATAAAGGCTTATACTGAAGGTTTGGCGGCGACCTGA
Done.