Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000508.1 Kokia drynarioides strain JFW-HI SEQ_111388, 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: 22576
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35


Found at i:1283 original size:24 final size:24

Alignment explanation


    Indices: 1241--1299  Score: 77
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       1231 ATCAGTATTC

                  *        *        
       1241 TTAAAAGTC-AAACCTATTAAAAT
          1 TTAAAACTCAAAACCCATTAAAAT

                                 *  
       1264 TTAAAACTCAAAACCCATTAATAT
          1 TTAAAACTCAAAACCCATTAAAAT

                         
       1288 TTAAAAC-CAAAA
          1 TTAAAACTCAAAA

       1300 TTGTTAATTT


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  23   13  0.41
  24   19  0.59

ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27


Consensus pattern (24 bp):   
TTAAAACTCAAAACCCATTAAAAT

Found at i:6335 original size:22 final size:23

Alignment explanation


    Indices: 6289--6336  Score: 62
    Period size: 22  Copynumber: 2.1  Consensus size: 23

       6279 TTAAAGACAA

                                   
       6289 TCATATAAAGAATATTAAATTAT
          1 TCATATAAAGAATATTAAATTAT

                  *         * *    
       6312 TCATATTAA-AATATTTATTTAT
          1 TCATATAAAGAATATTAAATTAT

               
       6334 TCA
          1 TCA

       6337 ATCAATATGA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  22   14  0.64
  23    8  0.36

ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46


Consensus pattern (23 bp):   
TCATATAAAGAATATTAAATTAT

Found at i:11718 original size:21 final size:21

Alignment explanation


    Indices: 11679--11719  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11669 ATTACTAGTA

                        *        
      11679 TATATTTTTATTTTATTTTAT
          1 TATATTTTTATTGTATTTTAT

                                 
      11700 TATATTTTATATTGT-TTTTA
          1 TATATTTT-TATTGTATTTTA

      11720 AAAGGGGTTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73


Consensus pattern (21 bp):   
TATATTTTTATTGTATTTTAT

Found at i:14984 original size:17 final size:17

Alignment explanation


    Indices: 14964--15025  Score: 67
    Period size: 17  Copynumber: 3.6  Consensus size: 17

      14954 GTAAAATAGA

                             
      14964 AGGTTAAAGGTCAAGGG
          1 AGGTTAAAGGTCAAGGG

                               
      14981 AGGTT-AAGG--AAGTTGG
          1 AGGTTAAAGGTCAAG--GG

                     *        
      14997 AAGGTTAAAAGTCAAGGG
          1 -AGGTTAAAGGTCAAGGG

                       
      15015 AGGTTAAAGGT
          1 AGGTTAAAGGT

      15026 TGAACATCCA


Statistics
Matches: 37,  Mismatches: 2, Indels: 12
        0.73            0.04        0.24

Matches are distributed among these distances:
  14    3  0.08
  16    6  0.16
  17   20  0.54
  18    5  0.14
  20    3  0.08

ACGTcount: A:0.37, C:0.03, G:0.39, T:0.21


Consensus pattern (17 bp):   
AGGTTAAAGGTCAAGGG

Found at i:14987 original size:34 final size:34

Alignment explanation


    Indices: 14947--15021  Score: 105
    Period size: 34  Copynumber: 2.2  Consensus size: 34

      14937 AGAATATGAA

                    *                *        
      14947 AGGTTAAGTAAAATAGAAGGTTAAAGGTCAAGGG
          1 AGGTTAAGGAAAATAGAAGGTTAAAAGTCAAGGG

                       ** *                   
      14981 AGGTTAAGGAAGTTGGAAGGTTAAAAGTCAAGGG
          1 AGGTTAAGGAAAATAGAAGGTTAAAAGTCAAGGG

                   
      15015 AGGTTAA
          1 AGGTTAA

      15022 AGGTTGAACA


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   36  1.00

ACGTcount: A:0.41, C:0.03, G:0.35, T:0.21


Consensus pattern (34 bp):   
AGGTTAAGGAAAATAGAAGGTTAAAAGTCAAGGG

Found at i:15881 original size:30 final size:31

Alignment explanation


    Indices: 15847--15908  Score: 99
    Period size: 30  Copynumber: 2.0  Consensus size: 31

      15837 ATTATCACTT

                                           
      15847 AATTCTCTTCAAGAGACTT-ATGATATTTAA
          1 AATTCTCTTCAAGAGACTTAATGATATTTAA

                       *   *               
      15877 AATTCTCTTCAGGAGTCTTAATGATATTTAA
          1 AATTCTCTTCAAGAGACTTAATGATATTTAA

             
      15908 A
          1 A

      15909 TCCTCAACAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  30   17  0.59
  31   12  0.41

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40


Consensus pattern (31 bp):   
AATTCTCTTCAAGAGACTTAATGATATTTAA

Found at i:20441 original size:34 final size:34

Alignment explanation


    Indices: 20392--20475  Score: 105
    Period size: 34  Copynumber: 2.4  Consensus size: 34

      20382 AGAATATGAA

                   *  *              **       
      20392 AAGTTAAAGAAGATAGAAGGTTAAAGGTCAAGGG
          1 AAGTTAAGGATGATAGAAGGTTAAAAATCAAGGG

             *                                
      20426 AGGTTAAGGATGATAGAAGGTTAAAAATCAAGGG
          1 AAGTTAAGGATGATAGAAGGTTAAAAATCAAGGG

                      *     
      20460 AAGTTAAAGGCTGATA
          1 AAGTT-AAGGATGATA

      20476 ATCCATTCAA


Statistics
Matches: 42,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  34   33  0.79
  35    9  0.21

ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20


Consensus pattern (34 bp):   
AAGTTAAGGATGATAGAAGGTTAAAAATCAAGGG
Done.