Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008966.1 Kokia drynarioides strain JFW-HI SEQ_123662, 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, 667

Length: 1112
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29


Found at i:412 original size:30 final size:30

Alignment explanation


    Indices: 378--697  Score: 282
    Period size: 30  Copynumber: 10.8  Consensus size: 30

        368 TTTGAGGTCC

                                 *        
        378 AAAATGGAGATTTTTGGAAGTATGGGGGTA
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA

                 *                 **  *   
        408 AAAATAGA-ATTTTTGGAAGTTTTAGGATCA
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGT-A

                                   *      *
        438 AAAATGGA-ATTTTTGGAAGTTTTGGGGTCG
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGT-A

                                  **     *
        468 AAAATGG-GATTTTTGGAAGTTCAGGGGTG
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA

                                   * *  *  
        497 AAAATGGA-ATTTTTGGAAGCTTCGAGGTTA
          1 AAAATGGAGATTTTTGGAAG-TTTGGGGGTA

                                * *       
        527 AAAATGGA-ATTTTTGGAAGCTCGGGGGTA
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA

                                    *  **  
        556 AAAAT-GAGATTTTTGGAAGTTTCAGGATTA
          1 AAAATGGAGATTTTTGGAAGTTT-GGGGGTA

                                   **     
        586 AAAATGG-GATTTTTGGAAGTTTAAGGGTA
          1 AAAATGGAGATTTTTGGAAGTTTGGGGGTA

                         * *            *  
        615 AAAATGG-GATTTATAGAAGTTTTGGGGTTA
          1 AAAATGGAGATTTTTGGAAG-TTTGGGGGTA

                                  *       *
        645 AAAAT-GAGATTTTTGGAAGTTCGAGGGGTG
          1 AAAATGGAGATTTTTGGAAGTTTG-GGGGTA

                                    
        675 AAAATGGA-ATTTTTGGATAGTTT
          1 AAAATGGAGATTTTTGGA-AGTTT

        698 AGGAACCTCC


Statistics
Matches: 241,  Mismatches: 37, Indels: 23
        0.80            0.12        0.08

Matches are distributed among these distances:
  28    2  0.01
  29   84  0.35
  30  148  0.61
  31    7  0.03

ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34


Consensus pattern (30 bp):   
AAAATGGAGATTTTTGGAAGTTTGGGGGTA

Found at i:449 original size:89 final size:88

Alignment explanation


    Indices: 365--701  Score: 383
    Period size: 89  Copynumber: 3.8  Consensus size: 88

        355 TAATTTTGAG

                   *    *                        *           *               
        365 AGTTTTGAGGTCCAAAATGGAGATTTTTGGAAGTAT-GGGGGTAAAAATAGAATTTTTGGAAGTT
          1 AGTTTTGGGGTCAAAAAT-GAGATTTTTGGAAGT-TCAGGGGTAAAAATGGAATTTTTGGAAGTT

                                      
        429 TTAGGATCAAAAATGGAATTTTTGGA
         64 TTAGGAT-AAAAATGGAATTTTTGGA

                        *      *                     *                      *
        455 AGTTTTGGGGTCGAAAATGGGATTTTTGGAAGTTCAGGGGTGAAAATGGAATTTTTGGAAGCTTC
          1 AGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGGAAG-TTT

            *   *                   
        520 GAGGTTAAAAATGGAATTTTTGGA
         65 TAGGATAAAAATGGAATTTTTGGA

              * **                                 **         *              
        544 AGCTCGGGGGT-AAAAATGAGATTTTTGGAAGTTTCAGGATTAAAAATGGGATTTTTGGAAGTTT
          1 AGTTTTGGGGTCAAAAATGAGATTTTTGGAAG-TTCAGGGGTAAAAATGGAATTTTTGGAAGTTT

            *   *         *    * *  
        608 AAGGGTAAAAATGGGATTTATAGA
         65 TAGGATAAAAATGGAATTTTTGGA

                       *                              *                      
        632 AGTTTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGGTGAAAATGGAATTTTTGGATAG-T
          1 AGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTC-AGGGGTAAAAATGGAATTTTTGGA-AGTT

                  
        696 TTAGGA
         64 TTAGGA

        702 ACCTCCAAGG


Statistics
Matches: 208,  Mismatches: 33, Indels: 13
        0.82            0.13        0.05

Matches are distributed among these distances:
  88   51  0.25
  89  133  0.64
  90   24  0.12

ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34


Consensus pattern (88 bp):   
AGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGGAAGTTTT
AGGATAAAAATGGAATTTTTGGA

Found at i:453 original size:59 final size:58

Alignment explanation


    Indices: 378--697  Score: 304
    Period size: 59  Copynumber: 5.4  Consensus size: 58

        368 TTTGAGGTCC

                                 *     *       *                *   *   
        378 AAAATGGAGATTTTTGGAAGTATGGGGGTAAAAATAGAATTTTTGGAAGTTTTAGGATCA
          1 AAAATGGA-ATTTTTGGAAGTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGT-A

                                        **       *              *      *
        438 AAAATGGAATTTTTGGAAGTTTTGGGGTCGAAAATGGGATTTTTGGAAG-TTCAGGGGTG
          1 AAAATGGAATTTTTGGAAG-TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGA-GGGTA

                                  * *                        * * *     
        497 AAAATGGAATTTTTGGAAGCTTCGAGGTTAAAAATGGAATTTTTGGAAGCTCGGGGGTA
          1 AAAATGGAATTTTTGGAAG-TTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTA

                                    *  *          *              *      
        556 AAAAT-GAGATTTTTGGAAGTTTCAGGATTAAAAATGGGATTTTTGGAAGTTTAAGGGTA
          1 AAAATGGA-ATTTTTGGAAGTTT-GGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTA

                   *    * *                                     *       *
        615 AAAATGGGATTTATAGAAGTTTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTCGAGGGGTG
          1 AAAATGGAATTTTTGGAAG-TTTGGGGTTAAAAATGGA-ATTTTTGGAAGTTTGA-GGGTA

                                   
        675 AAAATGGAATTTTTGGATAGTTT
          1 AAAATGGAATTTTTGGA-AGTTT

        698 AGGAACCTCC


Statistics
Matches: 210,  Mismatches: 40, Indels: 20
        0.78            0.15        0.07

Matches are distributed among these distances:
  58    5  0.02
  59  143  0.68
  60   60  0.29
  61    2  0.01

ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34


Consensus pattern (58 bp):   
AAAATGGAATTTTTGGAAGTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTA
Done.