Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008267.1 Kokia drynarioides strain JFW-HI SEQ_122932, 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: 3116
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27


Found at i:2731 original size:6 final size:6

Alignment explanation


    Indices: 2715--2818  Score: 75
    Period size: 6  Copynumber: 16.3  Consensus size: 6

       2705 TTCAATGAAT

                                              *                         
       2715 AAAGAAA AAAGAA AAAGAAGA AGAAGAA AATGAA AAAGAA AAAGAA AAAGAAA
          1 AAAG-AA AAAGAA AAAG-A-A A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-AA

                        *             *       *  *       **          
       2768 AAAGAGGA AAACAA AAAGAA AAACAA AAA-TA GAAGAA ATGGAA AAAGAA
          1 AAAGA--A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA

              
       2817 AA
          1 AA

       2819 GGAGAGGTCG


Statistics
Matches: 77,  Mismatches: 13, Indels: 15
        0.73            0.12        0.14

Matches are distributed among these distances:
   5    3  0.04
   6   50  0.65
   7   13  0.17
   8    8  0.10
   9    3  0.04

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03


Consensus pattern (6 bp):   
AAAGAA

Found at i:2749 original size:21 final size:19

Alignment explanation


    Indices: 2715--2818  Score: 84
    Period size: 21  Copynumber: 5.1  Consensus size: 19

       2705 TTCAATGAAT

                                 
       2715 AAAGAAAAAAGAAAAAGAAGA
          1 AAAG-AAAAAGAAAAAGAA-A

                     *          
       2736 AGAAGAAAATGAAAAAG-AA
          1 A-AAGAAAAAGAAAAAGAAA

                               * 
       2755 AAAGAAAAAGAAAAAAGAGGA
          1 AAAGAAAAAG-AAAAAGA-AA

               *           *   
       2776 AAACAAAAAGAAAAACAAA
          1 AAAGAAAAAGAAAAAGAAA

                                   
       2795 AATAGAAGAAATGGAAAAAGAAA
          1 AA-AGAA-AAA--GAAAAAGAAA

             
       2818 A
          1 A

       2819 GGAGAGGTCG


Statistics
Matches: 67,  Mismatches: 8, Indels: 14
        0.75            0.09        0.16

Matches are distributed among these distances:
  18    8  0.12
  19   11  0.16
  20   10  0.15
  21   25  0.37
  22    3  0.04
  23   10  0.15

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03


Consensus pattern (19 bp):   
AAAGAAAAAGAAAAAGAAA

Found at i:2757 original size:27 final size:25

Alignment explanation


    Indices: 2715--2818  Score: 100
    Period size: 27  Copynumber: 3.8  Consensus size: 25

       2705 TTCAATGAAT

                               *       
       2715 AAAGAAAAAAGAAAAAGAAGAAGAAGA
          1 AAAG-AAAAAGAAAAAGAAAAAGAA-A

                                      
       2742 AAATGAAAAAGAAAAAGAAAAAGAAA
          1 AAA-GAAAAAGAAAAAGAAAAAGAAA

                       *           *   
       2768 AAAGAGGAAAACAAAAAGAAAAACAAA
          1 AAAGA--AAAAGAAAAAGAAAAAGAAA

                                    
       2795 AATAGAAGAAATGGAAAAAGAAAA
          1 AA-AGAA-AAA--GAAAAAGAAAA

       2819 GGAGAGGTCG


Statistics
Matches: 66,  Mismatches: 4, Indels: 12
        0.80            0.05        0.15

Matches are distributed among these distances:
  25    2  0.03
  26    5  0.08
  27   45  0.68
  28    4  0.06
  29   10  0.15

ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03


Consensus pattern (25 bp):   
AAAGAAAAAGAAAAAGAAAAAGAAA

Found at i:2761 original size:33 final size:33

Alignment explanation


    Indices: 2708--2804  Score: 108
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       2698 ACTCGGATTC

                                               
       2708 AATGAATAAAGAAAAAAGAAAAAGAAGAAGAAGAA
          1 AATGAA-AAAG-AAAAAGAAAAAGAAGAAGAAGAA

                                     *    *   
       2743 AATGAAAAAGAAAAAGAAAAAGAAAAAAGAGGAA
          1 AATGAAAAAGAAAAAGAAAAAG-AAGAAGAAGAA

               *           *      *       
       2777 AA-CAAAAAGAAAAACAAAAA-TAGAAGAA
          1 AATGAAAAAGAAAAAGAAAAAGAAGAAGAA

       2805 ATGGAAAAAG


Statistics
Matches: 54,  Mismatches: 7, Indels: 6
        0.81            0.10        0.09

Matches are distributed among these distances:
  31    5  0.09
  33   28  0.52
  34   15  0.28
  35    6  0.11

ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04


Consensus pattern (33 bp):   
AATGAAAAAGAAAAAGAAAAAGAAGAAGAAGAA
Done.