Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012334.1 Kokia drynarioides strain JFW-HI SEQ_127336, 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: 2382
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Found at i:549 original size:29 final size:29

Alignment explanation


    Indices: 457--765  Score: 250
    Period size: 30  Copynumber: 10.5  Consensus size: 29

        447 CAAAAAGGTA

                                *       **
        457 ATTTTTGGAAGTTTCGGGGACAAAAATGAT
          1 ATTTTTGGAAGTTTCGGGG-TAAAAATGGG

                          *             *
        487 ATTTTTGGAAGTTTGGGGGT-AAAATGGT
          1 ATTTTTGGAAGTTTCGGGGTAAAAATGGG

                          *               
        515 ATTTTTGGAAGTTTTGGGGTCAAAAATGGG
          1 ATTTTTGGAAGTTTCGGGGT-AAAAATGGG

                        *                *
        545 ATTTTTGGAAG-CTCGAGGGTAAAAATGGA
          1 ATTTTTGGAAGTTTCG-GGGTAAAAATGGG

                  *        *   *        * 
        574 ATTTTTAGAAGTTTTAGGGTTAAAAATGAG
          1 ATTTTTGGAAG-TTTCGGGGTAAAAATGGG

                       *              ****
        604 ATTTTTGGAAGCTT-GAGGGTAAAAACAAA
          1 ATTTTTGGAAGTTTCG-GGGTAAAAATGGG

                      *                 * 
        633 ATTTTTGGAAATTTCGGGGTTAAAAATGAG
          1 ATTTTTGGAAGTTTCGGGG-TAAAAATGGG

                 * *                     *
        663 ATTTTCGAAAG-TTCGAGGGTAAAAATGGA
          1 ATTTTTGGAAGTTTCG-GGGTAAAAATGGG

                  *       *       *       
        692 ATTTTTAGAAGTTTTGGGGTTAGAAATGGG
          1 ATTTTTGGAAGTTTCGGGG-TAAAAATGGG

                                       * *
        722 ATTTTTGGAAG-TTCGAGGGTAAAAATAGA
          1 ATTTTTGGAAGTTTCG-GGGTAAAAATGGG

                           
        751 ATTTTTGGACAGTTT
          1 ATTTTTGGA-AGTTT

        766 AGGGACCTCC


Statistics
Matches: 224,  Mismatches: 41, Indels: 27
        0.77            0.14        0.09

Matches are distributed among these distances:
  28   27  0.12
  29   88  0.39
  30  105  0.47
  31    4  0.02

ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35


Consensus pattern (29 bp):   
ATTTTTGGAAGTTTCGGGGTAAAAATGGG

Found at i:599 original size:59 final size:59

Alignment explanation


    Indices: 421--765  Score: 374
    Period size: 59  Copynumber: 5.9  Consensus size: 59

        411 TTCGAGGTCG

                    *          *        *                        *    ** 
        421 AAAATG-GGTTTTTGGACATCT-GAGGGCAAAAA-GGTAATTTTTGGAAGTTTCGGGGACA
          1 AAAATGAGATTTTTGGA-AGCTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTTA

                   *           * * *            *                    * 
        479 AAAATGATATTTTTGGAAGTTTGGGGGT-AAAATGGTATTTTTGGAAGTTTTGGGGTCA
          1 AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA

                  *                                    *        *      
        537 AAAATGGGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGTTA
          1 AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA

                                 *           ***           *   *       
        596 AAAATGAGATTTTTGGAAGCTTGAGGGTAAAAACAAAATTTTTGGAAATTTCGGGGTTA
          1 AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA

                         * *   *                       *               
        655 AAAATGAGATTTTCGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTA
          1 AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA

            *     *            *              *                 
        714 GAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGACAGTTT
          1 AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT

        766 AGGGACCTCC


Statistics
Matches: 239,  Mismatches: 43, Indels: 8
        0.82            0.15        0.03

Matches are distributed among these distances:
  58   55  0.23
  59  179  0.75
  60    5  0.02

ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34


Consensus pattern (59 bp):   
AAAATGAGATTTTTGGAAGCTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA

Found at i:1757 original size:3 final size:3

Alignment explanation


    Indices: 1749--1793  Score: 54
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       1739 TTTTCCCTTT

                                * * *                                  
       1749 TTA TTA TTA TTA TTA ATG CTA TTA TTAA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT

       1794 CATTCAATGT


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
   3   33  0.92
   4    3  0.08

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62


Consensus pattern (3 bp):   
TTA

Done.