Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003838.1 Kokia drynarioides strain JFW-HI SEQ_116854, 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: 10029
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33


Found at i:3016 original size:39 final size:33

Alignment explanation


    Indices: 2942--3008  Score: 80
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       2932 AATTTCATAG

                       *                 *   
       2942 AAATAAAAATATAAATTTTAAATTTTAAATTTA
          1 AAATAAAAATAAAAATTTTAAATTTTAAAGTTA

                                              
       2975 AAATAAAAATAAAAATATTTGATATATTTTAAAG
          1 AAATAAAAATAAAAAT-TTT-A-A-ATTTTAAAG

       3009 CGTTAAAAAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  33   15  0.54
  34    3  0.11
  35    1  0.04
  36    1  0.04
  37    8  0.29

ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39


Consensus pattern (33 bp):   
AAATAAAAATAAAAATTTTAAATTTTAAAGTTA

Found at i:4838 original size:31 final size:30

Alignment explanation


    Indices: 4770--4847  Score: 95
    Period size: 31  Copynumber: 2.6  Consensus size: 30

       4760 CATTGAAGCT

                    *                     
       4770 AAACTTAGTTACCAAATTAGAAAAAAAAAA
          1 AAACTTAGATACCAAATTAGAAAAAAAAAA

                                     *    **
       4800 AAACTTAGATACCAAATTA-AACATGAAAACC
          1 AAACTTAGATACCAAATTAGAA-A-AAAAAAA

                             
       4831 AAACTTAGATACCAAAT
          1 AAACTTAGATACCAAAT

       4848 AGTATATTAC


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  29    2  0.05
  30   19  0.45
  31   21  0.50

ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21


Consensus pattern (30 bp):   
AAACTTAGATACCAAATTAGAAAAAAAAAA

Found at i:5268 original size:108 final size:110

Alignment explanation


    Indices: 5076--5316  Score: 360
    Period size: 108  Copynumber: 2.2  Consensus size: 110

       5066 TGTTGGTATG

                                                                             
       5076 AAATTTTGAAATAAAAAAATACTCACATAACAACAATATAACTAAAAAGAATGATACTATAATGA
          1 AAATTTTGAAATAAAAAAATAC-CACATAACAACAATATAACTAAAAAGAATGATACTATAATGA

                                                     *    
       5141 ACTTAAATTTAAGAAAATAATTTTAACAGTATTAACAGTTATATCT
         65 ACTTAAATTTAAGAAAATAATTTTAACAGTATTAACAGTTAGATCT

                                                      *           ** *       
       5187 AAATTTTGAAATAAAAAAATA-CACATAACAACAATATAACTTAAAA-AATGATGTTGTAATGAA
          1 AAATTTTGAAATAAAAAAATACCACATAACAACAATATAACTAAAAAGAATGATACTATAATGAA

                                    **   *    *          
       5250 CTTAAATTTAAGAAAATAATTTTAGGAGTGTTAATAGTTAGATCT
         66 CTTAAATTTAAGAAAATAATTTTAACAGTATTAACAGTTAGATCT

                         *        
       5295 AAATTTTGAAATTTAAAAAATA
          1 AAATTTTGAAA-TAAAAAAATA

       5317 AAGAAACTAA


Statistics
Matches: 119,  Mismatches: 10, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 108   65  0.55
 109   33  0.28
 111   21  0.18

ACGTcount: A:0.52, C:0.07, G:0.08, T:0.32


Consensus pattern (110 bp):   
AAATTTTGAAATAAAAAAATACCACATAACAACAATATAACTAAAAAGAATGATACTATAATGAA
CTTAAATTTAAGAAAATAATTTTAACAGTATTAACAGTTAGATCT

Found at i:9428 original size:30 final size:30

Alignment explanation


    Indices: 9394--9623  Score: 265
    Period size: 30  Copynumber: 7.8  Consensus size: 30

       9384 GGGAAAATTC

                 *                       *
       9394 GGGGTCAAAAATGGGATTTTTAGAAG-TTC
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                *            *              
       9423 GGGGGTAAAAAT-GGACCTTTT-GAAAGTTTT
          1 GGGGTTAAAAATGGGA-TTTTTAG-AAGTTTT

                                 * *    **
       9453 GGGGTTAAAAATGGGATTTTTGGTAGTTCA
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                          *           *   
       9483 GGGG-TAAAAATGGAATTTTTAGAA-CTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                      *           *   *   
       9511 GGGGTTAAAATTGGGATTTTTAAAAGCTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                                 *        
       9541 GGGGTTAAAAATGGGATTTTTGGAAGTTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                        *                 
       9571 GGGGTTAAAAATTGGATTTTTAGAAGTTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTTT

                                    
       9601 GGGG-TAAAAATGGGATTTTTAGA
          1 GGGGTTAAAAATGGGATTTTTAGA

       9624 CAATTTAGGG


Statistics
Matches: 169,  Mismatches: 25, Indels: 14
        0.81            0.12        0.07

Matches are distributed among these distances:
  28    9  0.05
  29   69  0.41
  30   87  0.51
  31    4  0.02

ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37


Consensus pattern (30 bp):   
GGGGTTAAAAATGGGATTTTTAGAAGTTTT

Found at i:9457 original size:59 final size:58

Alignment explanation


    Indices: 9394--9619  Score: 256
    Period size: 59  Copynumber: 3.8  Consensus size: 58

       9384 GGGAAAATTC

                 *                                       *             
       9394 GGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGACCTTTTGAAAGTTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGA-ATTTTGAAAGTTTT

                                 * *     *                   *     *   
       9453 GGGGTTAAAAATGGGATTTTTGGTAGTTCAGGGGTAAAAATGGAATTTTTAGAA-CTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTGA-AAGTTTT

                      *           *      *    *           *     *       
       9511 GGGGTTAAAATTGGGATTTTTAAAAGCTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAG-TTCGGGGGTAAAAAT-GGAATTTTGAAAGTTTT

                        *               **             *     
       9571 GGGGTTAAAAATTGGATTTTTAGAAGTTTTGGGGTAAAAATGGGATTTT
          1 GGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTT

       9620 TAGACAATTT


Statistics
Matches: 138,  Mismatches: 25, Indels: 9
        0.80            0.15        0.05

Matches are distributed among these distances:
  58   36  0.26
  59   69  0.50
  60   33  0.24

ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37


Consensus pattern (58 bp):   
GGGGTTAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGAATTTTGAAAGTTTT
Done.