Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001302.1 Kokia drynarioides strain JFW-HI SEQ_112714, 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: 1951
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34


Found at i:590 original size:30 final size:30

Alignment explanation


    Indices: 490--821  Score: 277
    Period size: 30  Copynumber: 11.2  Consensus size: 30

        480 TTTTGGAGAA

                             *       *   *
        490 TTTA-GGGTTAAAATGTAATTTTGGAAAAA
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                  *  *       *     *      
        519 TTT-GGTGTCAAAATGTAATTTTAGGAAAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                 **        *              
        548 TTT-GATGTTAAAATATGATTTTGGGAAAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                           *              
        577 TTTAGGGGTTAAAATATGATTTTGGG-AAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                     *   * *         *    
        606 TTTAGGGGTCAAATTTTGATTTTGGAAAAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                 *   *     *        *     
        636 TTTAGAGGTGAAAATATGATTTTGAGAAAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                                           
        666 TTTTA-GGGTTAAAATGTGATTTTGGGAAA-
          1 -TTTAGGGGTTAAAATGTGATTTTGGGAAAG

               *                           
        695 TTTTGGGGTTTAAAATGTGATTTTGGGAAAG
          1 TTTAGGGG-TTAAAATGTGATTTTGGGAAAG

                              *       *   *
        726 TTTAGGGG-TAAAAGTGTAATTTTGGAAAAA
          1 TTTAGGGGTTAAAA-TGTGATTTTGGGAAAG

            *   *    * *     *       *    
        756 ATTATGGGTGAGAATGTAATTTT-GAAAAG
          1 TTTAGGGGTTAAAATGTGATTTTGGGAAAG

                      *     *       *      
        785 TTT-GAGGGTCAAAATATGATTTTTGGAAAG
          1 TTTAG-GGGTTAAAATGTGATTTTGGGAAAG

                   
        815 TTTAGGG
          1 TTTAGGG

        822 ACCTTTTGGG


Statistics
Matches: 248,  Mismatches: 43, Indels: 23
        0.79            0.14        0.07

Matches are distributed among these distances:
  28    3  0.01
  29  104  0.42
  30  126  0.51
  31   15  0.06

ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38


Consensus pattern (30 bp):   
TTTAGGGGTTAAAATGTGATTTTGGGAAAG

Found at i:772 original size:90 final size:89

Alignment explanation


    Indices: 488--821  Score: 257
    Period size: 89  Copynumber: 3.8  Consensus size: 89

        478 ATTTTTGGAG

                       *       *       *   *     *        * *     *          
        488 AATT-TAGGGTTAAAATGTAATTTTGGAAAAATTTGGTGTCAAAATGTAATTTTAGGAAAGTTT-
          1 AATTATAGGGTGAAAATGTGATTTTGGGAAATTTTGGGGTCAAAATATGATTTTGGGAAAGTTTA

             **  *       *      **  
        551 GATGTTAAAATATGATTTTGGGAA
         66 GGGGTGAAAATATAATTTTGAAAA

             *          *     *            *   *         * *         *       
        575 AGTT-TAGGGGTTAAAATATGATTTTGGGAAGTTTAGGGGTCAAATTTTGATTTTGGAAAAGTTT
          1 AATTATA-GGGTGAAAATGTGATTTTGGGAAATTTTGGGGTCAAAATATGATTTTGGGAAAGTTT

              *           *       *  
        639 AGAGGTGAAAATATGATTTTGAGAA
         65 AGGGGTGAAAATATAATTTTGAAAA

             *  *      *                             *     *                 
        664 AGTTTTAGGGTTAAAATGTGATTTTGGGAAATTTTGGGGTTTAAAATGTGATTTTGGGAAAGTTT
          1 AATTATAGGGTGAAAATGTGATTTTGGGAAATTTTGGGG-TCAAAATATGATTTTGGGAAAGTTT

                         *             
        729 AGGGGT-AAAAGTGTAATTTTGGAAAA
         65 AGGGGTGAAAA-TATAATTTT-GAAAA

                         *     *       *   *                       *         
        755 AATTAT-GGGTGAGAATGTAATTTT-GAAAAGTTTGAGGGTCAAAATATGATTTTTGGAAAGTTT
          1 AATTATAGGGTGAAAATGTGATTTTGGGAAATTTTG-GGGTCAAAATATGATTTTGGGAAAGTTT

                
        818 AGGG
         65 AGGG

        822 ACCTTTTGGG


Statistics
Matches: 203,  Mismatches: 37, Indels: 12
        0.81            0.15        0.05

Matches are distributed among these distances:
  87    5  0.02
  88   45  0.22
  89   92  0.45
  90   53  0.26
  91    8  0.04

ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38


Consensus pattern (89 bp):   
AATTATAGGGTGAAAATGTGATTTTGGGAAATTTTGGGGTCAAAATATGATTTTGGGAAAGTTTA
GGGGTGAAAATATAATTTTGAAAA

Found at i:785 original size:59 final size:57

Alignment explanation


    Indices: 480--813  Score: 246
    Period size: 59  Copynumber: 5.6  Consensus size: 57

        470 AAAAATGAAT

                                       *                     *       * 
        480 TTTTGGAGAA-TTTAGGGTTAAAATGTAATTTTGGAAAAATT-TGGTGTCAAAATGTAA
          1 TTTTGGA-AAGTTTAGGGTTAAAATGTGATTTTGGAAAAATTATGG-GTGAAAATGTGA

                             *        *             **   *    *     *   
        537 TTTTAGGAAAGTTT-GATGTTAAAATATGATTTTGGGAAAGTTTAGGGGTTAAAATATGA
          1 TTTT-GGAAAGTTTAG-GGTTAAAATGTGATTTT-GGAAAAATTATGGGTGAAAATGTGA

                  *            *   * *             *                *   
        596 TTTTGGGAAGTTTAGGGGTCAAATTTTGATTTTGGAAAAGTT-TAGAGGTGAAAATATGA
          1 TTTTGGAAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAATTAT-G-GGTGAAAATGTGA

                                                 *     *       *         
        655 TTTTGAGAAAGTTTTAGGGTTAAAATGTGATTTTGG-GAAATTTTGGGGTTTAAAATGTGA
          1 TTTTG-GAAAG-TTTAGGGTTAAAATGTGATTTTGGAAAAATTAT-GGG-TGAAAATGTGA

                              *         *                       *     * 
        715 TTTTGGGAAAGTTTAGGGGTAAAAGTGTAATTTTGGAAAAAATTATGGGTGAGAATGTAA
          1 TTTT-GGAAAGTTTAGGGTTAAAA-TGTGATTTTGG-AAAAATTATGGGTGAAAATGTGA

                 *             *     *             
        775 TTTTGAAAAGTTTGAGGGTCAAAATATGATTTTTGGAAA
          1 TTTTGGAAAGTTT-AGGGTTAAAATGTGA-TTTTGGAAA

        814 GTTTAGGGAC


Statistics
Matches: 219,  Mismatches: 39, Indels: 36
        0.74            0.13        0.12

Matches are distributed among these distances:
  57    7  0.03
  58   36  0.16
  59   82  0.37
  60   80  0.37
  61    8  0.04
  62    6  0.03

ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38


Consensus pattern (57 bp):   
TTTTGGAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAATTATGGGTGAAAATGTGA
Done.