Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001429.1 Kokia drynarioides strain JFW-HI SEQ_112936, 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: 10814
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36

Warning! 42 characters in sequence are not A, C, G, or T


Found at i:4516 original size:30 final size:30

Alignment explanation


    Indices: 4472--4529  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       4462 GATAAGACAC

                 *   *                    
       4472 TTTGAGAAAGGTTTTCAATAGAAATGATAT
          1 TTTGAAAAAAGTTTTCAATAGAAATGATAT

                               *  *     
       4502 TTTGAAAAAAGTTTTCAATGGATATGAT
          1 TTTGAAAAAAGTTTTCAATAGAAATGAT

       4530 GATATCTTTA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38


Consensus pattern (30 bp):   
TTTGAAAAAAGTTTTCAATAGAAATGATAT

Found at i:7014 original size:31 final size:30

Alignment explanation


    Indices: 6967--7082  Score: 91
    Period size: 31  Copynumber: 4.0  Consensus size: 30

       6957 AATCTAAAAA

                   *   *                   
       6967 AAGTTTAGGTATCAAATTAAGAAAAAATGTC
          1 AAGTTTAAGTACCAAATTAAGAAAAAA-GTC

                                         **
       6998 AAGTTTAAGTACCAAATTAAGTAAAAAA-AA
          1 AAGTTTAAGTACCAAATTAAG-AAAAAAGTC

                     *            *        
       7028 AAGTTT-AGAATCCAAATTAAGTAAAAAG--
          1 AAGTTTAAGTA-CCAAATTAAGAAAAAAGTC

            *          *                 
       7056 GA-TTTAAGTATCAAATTAA-AAAAAAGT
          1 AAGTTTAAGTACCAAATTAAGAAAAAAGT

       7083 GTCAAGTTGA


Statistics
Matches: 70,  Mismatches: 10, Indels: 14
        0.74            0.11        0.15

Matches are distributed among these distances:
  26    6  0.09
  27   11  0.16
  28    4  0.06
  29    8  0.11
  30   16  0.23
  31   19  0.27
  32    6  0.09

ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27


Consensus pattern (30 bp):   
AAGTTTAAGTACCAAATTAAGAAAAAAGTC

Found at i:7034 original size:30 final size:30

Alignment explanation


    Indices: 6962--7054  Score: 100
    Period size: 30  Copynumber: 3.1  Consensus size: 30

       6952 AATTGAATCT

                        *   *             
       6962 AAAAAAAGTTTAGGTATCAAATTAAG-AAA
          1 AAAAAAAGTTTAAGTACCAAATTAAGTAAA

                 **                         
       6991 AAATGTCAAGTTTAAGTACCAAATTAAGTAAA
          1 AAA--AAAAGTTTAAGTACCAAATTAAGTAAA

                          *                
       7023 AAAAAAAGTTT-AGAATCCAAATTAAGTAAA
          1 AAAAAAAGTTTAAGTA-CCAAATTAAGTAAA

              
       7053 AA
          1 AA

       7055 GGATTTAAGT


Statistics
Matches: 53,  Mismatches: 7, Indels: 7
        0.79            0.10        0.10

Matches are distributed among these distances:
  29    6  0.11
  30   22  0.42
  31   19  0.36
  32    6  0.11

ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25


Consensus pattern (30 bp):   
AAAAAAAGTTTAAGTACCAAATTAAGTAAA

Found at i:7080 original size:27 final size:26

Alignment explanation


    Indices: 7019--7080  Score: 63
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       7009 CCAAATTAAG

                                      
       7019 TAAAAAAAAAAGTTTAGAATCCAAAT
          1 TAAAAAAAAAAGTTTAGAATCCAAAT

               **     *        *        
       7045 TAAGTAAAAAGGATTTAAGTAT-CAAAT
          1 TAAAAAAAAAAG-TTT-AGAATCCAAAT

                     
       7072 TAAAAAAAA
          1 TAAAAAAAA

       7081 GTGTCAAGTT


Statistics
Matches: 28,  Mismatches: 6, Indels: 3
        0.76            0.16        0.08

Matches are distributed among these distances:
  26    9  0.32
  27   15  0.54
  28    4  0.14

ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24


Consensus pattern (26 bp):   
TAAAAAAAAAAGTTTAGAATCCAAAT
Done.