Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007629.1 Kokia drynarioides strain JFW-HI SEQ_122260, 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: 5972
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26


Found at i:2290 original size:49 final size:49

Alignment explanation


    Indices: 2185--2531  Score: 249
    Period size: 49  Copynumber: 7.1  Consensus size: 49

       2175 GTTTCATTAC

                                       *         *     *       
       2185 CATGAAGGGAAAGATTTAAGCC-CAACAACAAATCCAATACCATGAAAGGA
          1 CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACG-AA-GA

                                *     *                      
       2235 CA--AAGGGAAAGATTTAAGTCGCAATGACAAATCCAGTACCACGAAGA
          1 CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACGAAGA

            *                           ***            *   * 
       2282 TATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCATGAAAA
          1 CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACGAAGA

               **   *            *    *    *  *     *   *       
       2331 CACAAAAGAGAAAGATTTAAGTCGCATCGACGAACCTCA-CACCTCAGAAGA
          1 CA-TGAAGGGAAAGATTTAAGCCGCAACGACAAATC-CAGTACCAC-GAAGA

            *                             *                   
       2382 TAT-AAGGGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCACGAAGA
          1 CATGAA-GGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACGAAGA

            * **  *    *              *    *           *      
       2431 TACAAAAGGAATGATTTAAGCCGCAATGAC-GATCCAAGTACCTCGAA-A
          1 CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCC-AGTACCACGAAGA

               * *                       * *    *      *      
       2479 GCACGGAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCGCGAAGA
          1 -CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACGAAGA

               
       2529 CAT
          1 CAT

       2532 TATAACCATA


Statistics
Matches: 230,  Mismatches: 54, Indels: 27
        0.74            0.17        0.09

Matches are distributed among these distances:
  47    3  0.01
  48   24  0.10
  49  133  0.58
  50   63  0.27
  51    7  0.03

ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16


Consensus pattern (49 bp):   
CATGAAGGGAAAGATTTAAGCCGCAACGACAAATCCAGTACCACGAAGA

Found at i:2401 original size:100 final size:97

Alignment explanation


    Indices: 2186--2507  Score: 319
    Period size: 100  Copynumber: 3.3  Consensus size: 97

       2176 TTTCATTACC

                                      * *       *          **     *          
       2186 ATGAAGGGAAAGATTTAAGCC-CAACAACAAATCCAATACCATGAAAGGACAAAGGGAAAGATTT
          1 ATGAAGGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCATGAAAACACAAAAGGAAAGATTT

                            *    *           
       2250 AAGTCGCAATGACAAATCCAGTACCACGAAGAT
         66 AAGTCGC-ATGACAAACCCAGCACCACGAAGAT

                                       * *                                   
       2283 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCATGAAAACACAAAAGAGAAAGATT
          1 ATGAAGGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCATGAAAACACAAAAG-GAAAGATT

                          *            *        
       2348 TAAGTCGCATCGACGAACCTCA-CACCTCAGAAGAT
         65 TAAGTCGCAT-GACAAACC-CAGCACCAC-GAAGAT

                                                       *   * *          *    
       2383 AT-AAGGGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCACGAAGATACAAAAGGAATGATT
          1 ATGAA-GGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCATGAAAACACAAAAGGAAAGATT

                *         * *  *  *   *       *
       2447 TAAGCCGCAATGACGATCCAAGTACCTCGAA-AGC
         65 TAAGTCGC-ATGACAAACCCAGCACCACGAAGA-T

             * *                       
       2481 ACGGAGGGAAAGATTTAAGCCGCAACG
          1 ATGAAGGGAAAGATTTAAGCCGCAACG

       2508 GCGAATCTAG


Statistics
Matches: 190,  Mismatches: 25, Indels: 19
        0.81            0.11        0.08

Matches are distributed among these distances:
  97   22  0.12
  98   55  0.29
  99   55  0.29
 100   58  0.31

ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16


Consensus pattern (97 bp):   
ATGAAGGGAAAGATTTAAGCCGCAACGATAAATCCAGTACCATGAAAACACAAAAGGAAAGATTT
AAGTCGCATGACAAACCCAGCACCACGAAGAT
Done.