Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013438.1 Kokia drynarioides strain JFW-HI SEQ_128464, 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: 3245
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2769 original size:29 final size:29

Alignment explanation


    Indices: 2736--3023  Score: 235
    Period size: 30  Copynumber: 9.7  Consensus size: 29

       2726 GGGAATTCAA

                                         
       2736 GGTTAAAATGTAATTTTGGAAAAGTTTAG
          1 GGTTAAAATGTAATTTTGGAAAAGTTTAG

                                         *
       2765 GGTTAAAATGTAATTTTAGG-AAAGTTTAA
          1 GGTTAAAATGTAATTTT-GGAAAAGTTTAG

                         *   *             
       2794 GGTTAAAATTGTAGTTTAGGAGAAA-TTTAG
          1 GGTTAAAA-TGTAATTTTGGA-AAAGTTTAG

                                *         
       2824 GGTTAAAATGTAATTTTGGAGAAGTTTAAG
          1 GGTTAAAATGTAATTTTGGAAAAGTTT-AG

               *             *  *         
       2854 GGTCAAAATGTAATTTTAGAGAAGTTTTAG
          1 GGTTAAAATGTAATTTTGGAAAAG-TTTAG

                     *    *     * *     * 
       2884 GGTTAAAATATAATATTGGAGATGTTTTGG
          1 GGTTAAAATGTAATTTTGGAAAAG-TTTAG

                       *        *      * 
       2914 GGTTAAAATGTGATTTTGG-GAAGTTTGG
          1 GGTTAAAATGTAATTTTGGAAAAGTTTAG

               * *           *        *   
       2942 GGTCAGAATGTAATTTTAGAGAAA-TATAG
          1 GGTTAAAATGTAATTTTGGA-AAAGTTTAG

                *                        * 
       2971 GAGTCAAAATGTAATTTT-GAAGAAGTTTTG
          1 G-GTTAAAATGTAATTTTGGAA-AAGTTTAG

                *       *          
       3001 AGGTCAAAATGTGATTTTAGGAA
          1 -GGTTAAAATGTAATTTT-GGAA

       3024 GTTTGGGGTC


Statistics
Matches: 214,  Mismatches: 30, Indels: 27
        0.79            0.11        0.10

Matches are distributed among these distances:
  28   23  0.11
  29   59  0.28
  30  122  0.57
  31    7  0.03
  32    3  0.01

ACGTcount: A:0.36, C:0.01, G:0.26, T:0.36


Consensus pattern (29 bp):   
GGTTAAAATGTAATTTTGGAAAAGTTTAG

Found at i:2980 original size:88 final size:88

Alignment explanation


    Indices: 2736--3037  Score: 281
    Period size: 88  Copynumber: 3.4  Consensus size: 88

       2726 GGGAATTCAA

                       *        *      *    *                       *  *   * 
       2736 GGTTAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTAG-GAA-AGTTTAAGGTTA
          1 GGTTAAAATGTGATTTTGG-GAAGTTTGGGGTCAAAATGTAATTTTAGAGAAGA-TATAGGGTCA

                 *  *      *     *   * 
       2799 AAATTGTAGT-TTAGGAGAA-ATTTAG
         64 AAA-TATAATATT-GAAGAAGTTTTGG

                       *                *                         * *      * 
       2824 GGTTAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTTAGAGAAGTTTTAGGGTTA
          1 GGTTAAAATGTGATTTTGG-GAAGTTT-GGGGTCAAAATGTAATTTTAGAGAAGATATAGGGTCA

                         *   *       
       2889 AAATATAATATTGGAGATGTTTTGG
         64 AAATATAATATTGAAGAAGTTTTGG

                                             *                               
       2914 GGTTAAAATGTGATTTTGGGAAGTTTGGGGTCAGAATGTAATTTTAGAGAA-ATATAGGAGTCAA
          1 GGTTAAAATGTGATTTTGGGAAGTTTGGGGTCAAAATGTAATTTTAGAGAAGATATAGG-GTCAA

               *    *              *
       2978 AATGTAATTTTGAAGAAGTTTTGA
         65 AATATAATATTGAAGAAGTTTTGG

               *             *                  
       3002 GGTCAAAATGTGATTTTAGGAAGTTTGGGGTCAAAA
          1 GGTTAAAATGTGATTTTGGGAAGTTTGGGGTCAAAA

       3038 CATGATTTCT


Statistics
Matches: 185,  Mismatches: 23, Indels: 12
        0.84            0.10        0.05

Matches are distributed among these distances:
  87    5  0.03
  88  105  0.57
  89   36  0.19
  90   39  0.21

ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36


Consensus pattern (88 bp):   
GGTTAAAATGTGATTTTGGGAAGTTTGGGGTCAAAATGTAATTTTAGAGAAGATATAGGGTCAAA
ATATAATATTGAAGAAGTTTTGG

Done.