Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006684.1 Kokia drynarioides strain JFW-HI SEQ_121278, 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: 4379
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31


Found at i:2611 original size:41 final size:40

Alignment explanation


    Indices: 2556--2671  Score: 106
    Period size: 41  Copynumber: 2.9  Consensus size: 40

       2546 TACCTAATAC

                   * *        * *  *   *       *    
       2556 AATACACCGACACGAAACTTGCTGGGCTCAAAGCCTGATA
          1 AATACACAGGCACGAAACCTACTAGGCACAAAGCCAGATA

                    *        *                       
       2596 ATATACACTGGCACGAAGCCTACTAGGCACAAAGCCAGATA
          1 A-ATACACAGGCACGAAACCTACTAGGCACAAAGCCAGATA

                            *   *    *   *     
       2637 AATACACAGGCACGAAGCCTGCTAGACACTAAGCC
          1 AATACACAGGCACGAAACCTACTAGGCACAAAGCC

       2672 CAATAAACTC


Statistics
Matches: 63,  Mismatches: 12, Indels: 2
        0.82            0.16        0.03

Matches are distributed among these distances:
  40   31  0.49
  41   32  0.51

ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15


Consensus pattern (40 bp):   
AATACACAGGCACGAAACCTACTAGGCACAAAGCCAGATA

Found at i:2653 original size:40 final size:41

Alignment explanation


    Indices: 2584--2671  Score: 124
    Period size: 40  Copynumber: 2.2  Consensus size: 41

       2574 TTGCTGGGCT

                   *            *                 *  
       2584 CAAAGCCTGATAATATACACTGGCACGAAGCCTACTAGGCA
          1 CAAAGCCAGATAATATACACAGGCACGAAGCCTACTAGACA

                                             *       
       2625 CAAAGCCAGATAA-ATACACAGGCACGAAGCCTGCTAGACA
          1 CAAAGCCAGATAATATACACAGGCACGAAGCCTACTAGACA

             *     
       2665 CTAAGCC
          1 CAAAGCC

       2672 CAATAAACTC


Statistics
Matches: 42,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  40   30  0.71
  41   12  0.29

ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14


Consensus pattern (41 bp):   
CAAAGCCAGATAATATACACAGGCACGAAGCCTACTAGACA

Found at i:2776 original size:38 final size:38

Alignment explanation


    Indices: 2607--2795  Score: 146
    Period size: 38  Copynumber: 4.9  Consensus size: 38

       2597 TATACACTGG

                               *                 * *
       2607 CACGAAGCCTACTAGGCACAAAGCCAGATAAATACACAGG
          1 CACGAAGCCTACTAGGCACTAAGCCAGAT-AA-ACACCGA

                      *    *                  *   *
       2647 CACGAAGCCTGCTAGACACTAAGCCCA-ATAAACTCCGG
          1 CACGAAGCCTACTAGGCACTAAG-CCAGATAAACACCGA

             **     * *            * *        * * 
       2685 CGTGAAGCTTGCTAGGCACTAAGACTGATAAACATCAA
          1 CACGAAGCCTACTAGGCACTAAGCCAGATAAACACCGA

            *  *      *                           
       2723 TACAAAGCCTTCTAGGCACTAAGCCAGATAAACACCGA
          1 CACGAAGCCTACTAGGCACTAAGCCAGATAAACACCGA

                  *           *  *   *         
       2761 CACGAACCCTACTAGGCATTAGGCCCGATAAACAC
          1 CACGAAGCCTACTAGGCACTAAGCCAGATAAACAC

       2796 TGCTTACAAC


Statistics
Matches: 115,  Mismatches: 32, Indels: 6
        0.75            0.21        0.04

Matches are distributed among these distances:
  37    1  0.01
  38   87  0.76
  39    2  0.02
  40   22  0.19
  41    3  0.03

ACGTcount: A:0.38, C:0.29, G:0.19, T:0.15


Consensus pattern (38 bp):   
CACGAAGCCTACTAGGCACTAAGCCAGATAAACACCGA
Done.