Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014157.1 Kokia drynarioides strain JFW-HI SEQ_129190, 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: 6198
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33

Warning! 74 characters in sequence are not A, C, G, or T


Found at i:5642 original size:29 final size:28

Alignment explanation


    Indices: 5613--6022  Score: 217
    Period size: 29  Copynumber: 14.0  Consensus size: 28

       5603 TTTTGAGAGT

                                        
       5613 TTCGAGTCGAAAATGGGATTTTTGGAAG
          1 TTCGAGTCGAAAATGGGATTTTTGGAAG

               *  **          *   *       
       5641 TT-TAGGGGAAAAATGGTAATTCTTGGAAG
          1 TTCGAGTCG-AAAATGG-GATTTTTGGAAG

                  *   *      *  *         
       5670 ATTCAGGGTCAAAAAT-AGAATTTTGGAAG
          1 -TTC-GAGTCGAAAATGGGATTTTTGGAAG

                   *          *           
       5699 TTCGAG-GGTAAAATGGTAATTTTTGGAAG
          1 TTCGAGTCG-AAAATGG-GATTTTTGGAAG

                                     *    
       5728 ATTCGAGGTCGAAAATGGGATTTTTAGAAG
          1 -TTCGA-GTCGAAAATGGGATTTTTGGAAG

                  **          *            
       5758 TTCG-GGGGTAAAATGGTAATTTTTGGAAGG
          1 TTCGAGTCG-AAAATGG-GATTTTTGGAA-G

               *     *                   
       5788 ATTGGAGTCAAAAATGGGATTTTTGGAAG
          1 -TTCGAGTCGAAAATGGGATTTTTGGAAG

                               *            
       5817 TTCGGGAGT--AAAATGGTAATTTTTGGAAGG
          1 TTC--GAGTCGAAAATGG-GATTTTTGGAA-G

                     *                   
       5847 TTCGAGGTCAAAAATGGGATTTTTGGAAG
          1 TTCGA-GTCGAAAATGGGATTTTTGGAAG

                          *  **            
       5876 TTCGAGGGT-GAAATTGTAATTTTTGGAAGG
          1 TTCGA--GTCGAAAATGGGATTTTTGGAA-G

            *    *   *                   
       5906 GTCGGGGTCAAAAATGGGATTTTTGGAAG
          1 TTC-GAGTCGAAAATGGGATTTTTGGAAG

                  **         **            
       5935 TTCG-GGGGTAAAATGATAATTTTTGGAAGG
          1 TTCGAGTCG-AAAATG-GGATTTTTGGAA-G

                     *                   
       5965 TTCGAGGTCAAAAATGGGATTTTTGGAAG
          1 TTCGA-GTCGAAAATGGGATTTTTGGAAG

                  **          *           
       5994 TTC-AGGGGTAAAATGGTAATTTTTGGAAG
          1 TTCGAGTCG-AAAATGG-GATTTTTGGAAG

       6023 GTTTAGGGAC


Statistics
Matches: 288,  Mismatches: 60, Indels: 67
        0.69            0.14        0.16

Matches are distributed among these distances:
  27   14  0.05
  28   45  0.16
  29  106  0.37
  30   82  0.28
  31   37  0.13
  32    4  0.01

ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32


Consensus pattern (28 bp):   
TTCGAGTCGAAAATGGGATTTTTGGAAG

Found at i:5777 original size:59 final size:59

Alignment explanation


    Indices: 5613--6022  Score: 576
    Period size: 59  Copynumber: 7.0  Consensus size: 59

       5603 TTTTGAGAGT

                     *                     **    *            *        
       5613 TTCGA-GTCGAAAATGGGATTTTTGGAAGTTTAGGGGAAAAATGGTAATTCTTGGAAGA
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

                             *  *             *                         
       5671 TTC-AGGGTCAAAAAT-AGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGA
          1 TTCGA-GGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

                     *              *                                   
       5729 TTCGAGGTCGAAAATGGGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGA
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAA-GA

              *                                *                      *
       5789 TTGGA-GTCAAAAATGGGATTTTTGGAAGTTCGGGAGTAAAATGGTAATTTTTGGAAGG
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

                                             *    *    *              *
       5847 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTGAAATTGTAATTTTTGGAAGG
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

            *   *                                       *             *
       5906 GTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTTGGAAGG
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

                                            *                         
       5965 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAG
          1 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG

       6023 GTTTAGGGAC


Statistics
Matches: 313,  Mismatches: 33, Indels: 11
        0.88            0.09        0.03

Matches are distributed among these distances:
  57    1  0.00
  58   56  0.18
  59  250  0.80
  60    6  0.02

ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32


Consensus pattern (59 bp):   
TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGA

Done.