Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002947.1 Kokia drynarioides strain JFW-HI SEQ_115401, 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: 21167
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:6597 original size:18 final size:17

Alignment explanation


    Indices: 6576--6626  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       6566 CTAACAAAAT

                        * *   
       6576 TGTCGAGACAACTATCAA
          1 TGTCGAG-CAACCAGCAA

                              
       6594 TGTCGATGCAACCAGCAA
          1 TGTCGA-GCAACCAGCAA

                           
       6612 TGTCGAGGCAACCAG
          1 TGTCGA-GCAACCAG

       6627 ATGTATCCAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  18   28  0.97
  19    1  0.03

ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18


Consensus pattern (17 bp):   
TGTCGAGCAACCAGCAA

Found at i:16491 original size:28 final size:27

Alignment explanation


    Indices: 16427--16492  Score: 64
    Period size: 28  Copynumber: 2.4  Consensus size: 27

      16417 GAAATTTAAG

                                       
      16427 AGAATG-AAAAGAAGGAGAAGAACCAA
          1 AGAATGAAAAAGAAGGAGAAGAACCAA

                  *                   *    
      16453 ATTGAAGGAAAAAGGAAAGGAGAA-AGCCAA
          1 A--GAATGAAAAA-G-AAGGAGAAGAACCAA

                      
      16483 AGAATGAAAA
          1 AGAATGAAAA

      16493 GGGATTATCT


Statistics
Matches: 32,  Mismatches: 3, Indels: 8
        0.74            0.07        0.19

Matches are distributed among these distances:
  26    1  0.03
  28   12  0.38
  29    4  0.12
  30    7  0.22
  31    8  0.25

ACGTcount: A:0.61, C:0.06, G:0.27, T:0.06


Consensus pattern (27 bp):   
AGAATGAAAAAGAAGGAGAAGAACCAA

Found at i:20469 original size:22 final size:21

Alignment explanation


    Indices: 20442--20493  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 21

      20432 CAATACACCA

                    * *          
      20442 GGTTGTGGTTTAACTACCAAT
          1 GGTTGTGGATAAACTACCAAT

                   *          *   
      20463 GGTTTGTAGATAAACTACTAAT
          1 GG-TTGTGGATAAACTACCAAT

                     
      20485 GGTTGTGGA
          1 GGTTGTGGA

      20494 CACGCAACAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 2
        0.78            0.16        0.06

Matches are distributed among these distances:
  21    8  0.32
  22   17  0.68

ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37


Consensus pattern (21 bp):   
GGTTGTGGATAAACTACCAAT

Found at i:20561 original size:45 final size:46

Alignment explanation


    Indices: 20498--20594  Score: 108
    Period size: 45  Copynumber: 2.2  Consensus size: 46

      20488 TGTGGACACG

                        * *     *                         
      20498 CAAC-AAAATCTTGTAGATGGAATTTACCTCTAGCTATGG-GTACA
          1 CAACAAAAATCTAGCAGATGAAATTTACCTCTAGCTATGGAGTACA

                                      *   * *   *    *    
      20542 CAACAAAAATCTAGCAGATGAAATTTGCCTTTGGCTGTGGATTACA
          1 CAACAAAAATCTAGCAGATGAAATTTACCTCTAGCTATGGAGTACA

                   
      20588 CAACAAA
          1 CAACAAA

      20595 CAACCATAGA


Statistics
Matches: 43,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  44    4  0.09
  45   28  0.65
  46   11  0.26

ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27


Consensus pattern (46 bp):   
CAACAAAAATCTAGCAGATGAAATTTACCTCTAGCTATGGAGTACA
Done.