Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007121.1 Kokia drynarioides strain JFW-HI SEQ_121732, 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, 970

Length: 1618
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37


Found at i:306 original size:30 final size:30

Alignment explanation


    Indices: 242--659  Score: 371
    Period size: 30  Copynumber: 14.2  Consensus size: 30

        232 GGAGACCCCG

                    *                      
        242 AAACTTCCTAAAATTCCA-TTTT-ACCCTC-
          1 AAACTTCCAAAAATTCCATTTTTGA-CCTCA

                          *               
        270 AAACTTCCAAAAATGCCATTTTTGACCTCA
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                    *                  * *
        300 AAACTTCCCAAAATTCCATTTTT-ACCCCT
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                           *               
        329 AAACTTCCAAAAATTTCA-TTTTGACC-CAA
          1 AAACTTCCAAAAATTCCATTTTTGACCTC-A

                           *       *   * *
        358 AAACTTCCAAAAATTTCATTTTTTACCCCC
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                   *            *      *  
        388 AAACTTCAAAAAATTCCATTATTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                         *                 
        418 AAACTTCCAAAAACTCCATTTTT-ACCCTC-
          1 AAACTTCCAAAAATTCCATTTTTGA-CCTCA

                                           
        447 AAACTTCCAAAAATTCCATTTTTGACAC-CA
          1 AAACTTCCAAAAATTCCATTTTTGAC-CTCA

                                        * *
        477 AAACTTCCAAAAATTCCATTTTT-ACCCCCC
          1 AAACTTCCAAAAATTCCATTTTTGA-CCTCA

            *    *    *            *     *
        507 GAACTACCAAGAATTCCATTTTTTACCTCG
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                                          *
        537 AAACTTCCAAAAATTCCATTTTT-ACAC-CT
          1 AAACTTCCAAAAATTCCATTTTTGAC-CTCA

                *       *     *        *  
        566 AAACCTCCAAAATTTCCAATTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTGACCTCA

                  *                       *
        596 AAACTTTCAAAAATTACC-TTTTTG-CCTCC
          1 AAACTTCCAAAAATT-CCATTTTTGACCTCA

            **            *        *       
        625 GGA-TGTCCAAAAACTCCATTTTCGACCTCA
          1 AAACT-TCCAAAAATTCCATTTTTGACCTCA

                 
        655 AAACT
          1 AAACT

        660 CTCAAAATTA


Statistics
Matches: 319,  Mismatches: 49, Indels: 41
        0.78            0.12        0.10

Matches are distributed among these distances:
  28   24  0.08
  29  117  0.37
  30  173  0.54
  31    5  0.02

ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32


Consensus pattern (30 bp):   
AAACTTCCAAAAATTCCATTTTTGACCTCA

Found at i:341 original size:59 final size:59

Alignment explanation


    Indices: 242--710  Score: 451
    Period size: 59  Copynumber: 8.0  Consensus size: 59

        232 GGAGACCCCG

                    *                                   *               
        242 AAACTTCCTAAAATTCCA-TTTTA-CCCTCAAACTTCCAAAAATGCCATTTTTGACCTCA
          1 AAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCTCA

                    *                                   *               
        300 AAACTTCCCAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTTCA-TTTTGACC-CAA
          1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTC-A

                           *             *       *            *      *  
        358 AAACTTCCAAAAATTTCATTTTTTACCCCCAAACTTCAAAAAATTCCATTATTGACCCCA
          1 AAACTTCCAAAAATTCCA-TTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCA

                         *                                               
        418 AAACTTCCAAAAACTCCATTTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTGACAC-CA
          1 AAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGAC-CTCA

                                         **    *    *            *     *
        477 AAACTTCCAAAAATTCCATTTTTACCCCCCGAACTACCAAGAATTCCATTTTTTACCTCG
          1 AAACTTCCAAAAATTCCATTTTTA-CCCCTAAACTTCCAAAAATTCCATTTTTGACCTCA

                                     *       *       *     *        *  
        537 AAACTTCCAAAAATTCCATTTTTACACCTAAACCTCCAAAATTTCCAATTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCA

                  *                 *      **            *        *       
        596 AAACTTTCAAAAATTACC-TTTTTGCCTCC-GGA-TGTCCAAAAACTCCATTTTCGACCTCA
          1 AAACTTCCAAAAATT-CCATTTTTACC-CCTAAACT-TCCAAAAATTCCATTTTTGACCTCA

                                *         **       *               *    
        655 AAAC-TCTC-AAAATTACC-CTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTAACCT
          1 AAACTTC-CAAAAATT-CCATTTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGACCT

        711 TGAATTTTCT


Statistics
Matches: 344,  Mismatches: 51, Indels: 32
        0.81            0.12        0.07

Matches are distributed among these distances:
  57    3  0.01
  58   84  0.24
  59  173  0.50
  60   80  0.23
  61    4  0.01

ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32


Consensus pattern (59 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCTCA

Done.