Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012326.1 Kokia drynarioides strain JFW-HI SEQ_127328, 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: 3914
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:1781 original size:30 final size:30

Alignment explanation


    Indices: 1714--2062  Score: 311
    Period size: 30  Copynumber: 11.8  Consensus size: 30

       1704 GGAGGTCCCT

                           ** *           *
       1714 AAACTTTCCAAAAATTTCGTTTTT-ACCCCC
          1 AAAC-TTCCAAAAATCCCATTTTTAACCCCA

            *                          ** 
       1744 GAACTTCCAAAAATCCCATTTTTAACCTTA
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                          *               
       1774 AAACTTCCAAAAATTCCATTTTT-ACCCCA
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                                       * *
       1803 AAACTTCCAAAAATCCCATTTTTAACCTCG
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                          *              *
       1833 AAACTTCCAAAAATTCCATTTTT-ACCCCT
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                           *               
       1862 AAACTTCCAAAAATCTCATTTTTAACCCTC-
          1 AAACTTCCAAAAATCCCATTTTTAACCC-CA

            *              *       *   * *
       1892 GAACTTCCAAAAATCTCA--TTTGACCTCG
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                   *      ***             
       1920 AAACTTCTAAAAATTATATTTTT-ACCCC-
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

               *              *           
       1948 AAATTTCCAAAAATCCCAATTTTAACCCCA
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

                          *             **
       1978 AAACTTCCAAAAATTCCATTTTT-ACCCTT
          1 AAACTTCCAAAAATCCCATTTTTAACCCCA

            *       *                    * 
       2007 GAACTTCAAAAAAATCCCATTTTTAACCCTA
          1 AAACTTC-CAAAAATCCCATTTTTAACCCCA

                   *      **         
       2038 AAACTTCTAAAAATTTCATTTTTAA
          1 AAACTTCCAAAAATCCCATTTTTAA

       2063 ACCCTAAATT


Statistics
Matches: 261,  Mismatches: 47, Indels: 22
        0.79            0.14        0.07

Matches are distributed among these distances:
  27    1  0.00
  28   36  0.14
  29   86  0.33
  30  126  0.48
  31   12  0.05

ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34


Consensus pattern (30 bp):   
AAACTTCCAAAAATCCCATTTTTAACCCCA

Found at i:1808 original size:59 final size:59

Alignment explanation


    Indices: 1714--2062  Score: 341
    Period size: 59  Copynumber: 5.9  Consensus size: 59

       1704 GGAGGTCCCT

                            * *          **                            *
       1714 AAACTTTCCAAAAATTTCGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTTA
          1 AAAC-TTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

                                                                       
       1774 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACC-TC
          1 AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

                                         *               *           *  
       1832 GAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCTC
          1 -AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

            *                      *   * *       *      ***           * 
       1892 GAACTTCCAAAAA-TCTCA-TTTGACCTCGAAACTTCTAAAAATTATATTTTT-ACC-CC
          1 AAACTTCCAAAAATTC-CATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

               *          *        *                    *         *     
       1948 AAATTTCCAAAAATCCCAATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTT-
          1 AAACTTCCAAAAATTCC-ATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

            *       *      *             *        *      **         
       2007 GAACTTCAAAAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATTTCATTTTTAA
          1 AAACTTC-CAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATCCCATTTTTAA

       2063 ACCCTAAATT


Statistics
Matches: 244,  Mismatches: 35, Indels: 20
        0.82            0.12        0.07

Matches are distributed among these distances:
  56   13  0.05
  57    5  0.02
  58   56  0.23
  59  128  0.52
  60   42  0.17

ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34


Consensus pattern (59 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTAACCTTC

Done.