Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004432.1 Kokia drynarioides strain JFW-HI SEQ_117825, 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, 688

Length: 1147
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28


Found at i:589 original size:17 final size:17

Alignment explanation


    Indices: 537--613  Score: 68
    Period size: 17  Copynumber: 4.5  Consensus size: 17

        527 TTCAATGAAC

                       *     
        537 AAAGAAAAAAATAA-AA
          1 AAAGAAAAAAAAAAGAA

                *     *    * 
        553 AAAGGAAAAAGAAAGCA
          1 AAAGAAAAAAAAAAGAA

                              
        570 AAAGAAAAGAAAAAAGAA
          1 AAAGAAAA-AAAAAAGAA

                        *     
        588 AAA-AAAAACAAGAAGAA
          1 AAAGAAAAA-AAAAAGAA

               *     
        605 AAACAAAAA
          1 AAAGAAAAA

        614 TAGAAAAAAG


Statistics
Matches: 49,  Mismatches: 8, Indels: 6
        0.78            0.13        0.10

Matches are distributed among these distances:
  16   12  0.24
  17   22  0.45
  18   15  0.31

ACGTcount: A:0.82, C:0.04, G:0.13, T:0.01


Consensus pattern (17 bp):   
AAAGAAAAAAAAAAGAA

Found at i:603 original size:29 final size:29

Alignment explanation


    Indices: 550--622  Score: 85
    Period size: 28  Copynumber: 2.4  Consensus size: 29

        540 GAAAAAAATA

                         *   *           *
        550 AAAAAAGGAAAAAGAAAGCAAAAG-AAAAG
          1 AAAAAA-GAAAAAAAAAACAAAAGAAAAAC

                                          
        579 AAAAAAGAAAAAAAAAACAAGAAGAAAAAC
          1 AAAAAAGAAAAAAAAAACAA-AAGAAAAAC

                          
        609 AAAAATAGAAAAAA
          1 AAAAA-AGAAAAAA

        623 GGGAGAGGTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  28   12  0.32
  29    9  0.24
  30    9  0.24
  31    8  0.21

ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01


Consensus pattern (29 bp):   
AAAAAAGAAAAAAAAAACAAAAGAAAAAC

Found at i:1071 original size:35 final size:34

Alignment explanation


    Indices: 1032--1130  Score: 117
    Period size: 35  Copynumber: 2.8  Consensus size: 34

       1022 CCATACTCCC

                                      *        
       1032 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
          1 TTTAAATTTATTTTAAAATTAAATTTATTT-AAAA

                                           *  *
       1067 TTTAAATTTATTTTAAAATTTAAATTTATTTTAAG
          1 TTTAAATTTATTTTAAAA-TTAAATTTATTTAAAA

                  *           *          
       1102 TTTAAAATTATTTTCAAATTTAAAATTTA
          1 TTTAAATTTATTTT-AAAATT-AAATTTA

       1131 AAATAAATAA


Statistics
Matches: 56,  Mismatches: 5, Indels: 5
        0.85            0.08        0.08

Matches are distributed among these distances:
  35   35  0.62
  36   21  0.38

ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54


Consensus pattern (34 bp):   
TTTAAATTTATTTTAAAATTAAATTTATTTAAAA

Found at i:1073 original size:18 final size:18

Alignment explanation


    Indices: 1032--1130  Score: 130
    Period size: 18  Copynumber: 5.6  Consensus size: 18

       1022 CCATACTCCC

                              
       1032 TTTAAATTTATTTTAAAA
          1 TTTAAATTTATTTTAAAA

                     *   *    
       1050 -TTAAATTTGTTTAAAAA
          1 TTTAAATTTATTTTAAAA

                              
       1067 TTTAAATTTATTTTAAAA
          1 TTTAAATTTATTTTAAAA

                             *
       1085 TTTAAATTTATTTT-AAG
          1 TTTAAATTTATTTTAAAA

                  *       *   
       1102 TTTAAAATTATTTTCAAA
          1 TTTAAATTTATTTTAAAA

                       
       1120 TTTAAAATTTA
          1 TTT-AAATTTA

       1131 AAATAAATAA


Statistics
Matches: 70,  Mismatches: 8, Indels: 5
        0.84            0.10        0.06

Matches are distributed among these distances:
  17   30  0.43
  18   34  0.49
  19    6  0.09

ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54


Consensus pattern (18 bp):   
TTTAAATTTATTTTAAAA
Done.