Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013565.1 Kokia drynarioides strain JFW-HI SEQ_128591, 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: 35608
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:417 original size:21 final size:21

Alignment explanation


    Indices: 391--431  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        381 TCATCGCGAT

                  *              
        391 ACTCTATTCCTCCCGGGCAAG
          1 ACTCTACTCCTCCCGGGCAAG

                         *      
        412 ACTCTACTCCTCCGGGGCAA
          1 ACTCTACTCCTCCCGGGCAA

        432 ATGGACCTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22


Consensus pattern (21 bp):   
ACTCTACTCCTCCCGGGCAAG

Found at i:2199 original size:21 final size:21

Alignment explanation


    Indices: 2173--2213  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2163 TCATCGCGAT

                  *              
       2173 ACTCTATTCCTCCCGGGCAAG
          1 ACTCTACTCCTCCCGGGCAAG

                         *      
       2194 ACTCTACTCCTCCGGGGCAA
          1 ACTCTACTCCTCCCGGGCAA

       2214 ATGGACCTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22


Consensus pattern (21 bp):   
ACTCTACTCCTCCCGGGCAAG

Found at i:7207 original size:45 final size:45

Alignment explanation


    Indices: 7158--7255  Score: 196
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       7148 TGTTTTGCTG

                                                         
       7158 AAATCCCAAATTTATTAATTGCTTAGATACAAGGGTTTAGAGTGA
          1 AAATCCCAAATTTATTAATTGCTTAGATACAAGGGTTTAGAGTGA

                                                         
       7203 AAATCCCAAATTTATTAATTGCTTAGATACAAGGGTTTAGAGTGA
          1 AAATCCCAAATTTATTAATTGCTTAGATACAAGGGTTTAGAGTGA

                    
       7248 AAATCCCA
          1 AAATCCCA

       7256 CTAGTTCAAC


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   53  1.00

ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32


Consensus pattern (45 bp):   
AAATCCCAAATTTATTAATTGCTTAGATACAAGGGTTTAGAGTGA

Found at i:13843 original size:2 final size:2

Alignment explanation


    Indices: 13836--13862  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      13826 TTATTAGAAA

                                                    
      13836 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

      13863 AGTTCTTGTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:15120 original size:37 final size:37

Alignment explanation


    Indices: 15073--15152  Score: 151
    Period size: 37  Copynumber: 2.2  Consensus size: 37

      15063 CGTCTGTTAG

                *                                
      15073 TTAACAATATGGTAAGTAGAAACACTATATATATTAC
          1 TTAAAAATATGGTAAGTAGAAACACTATATATATTAC

                                                 
      15110 TTAAAAATATGGTAAGTAGAAACACTATATATATTAC
          1 TTAAAAATATGGTAAGTAGAAACACTATATATATTAC

                  
      15147 TTAAAA
          1 TTAAAA

      15153 TCCTAGGTCC


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  37   42  1.00

ACGTcount: A:0.49, C:0.09, G:0.10, T:0.33


Consensus pattern (37 bp):   
TTAAAAATATGGTAAGTAGAAACACTATATATATTAC

Found at i:17088 original size:31 final size:32

Alignment explanation


    Indices: 17050--17120  Score: 90
    Period size: 31  Copynumber: 2.2  Consensus size: 32

      17040 TTAATATAAC

                        *    *              
      17050 ATTTGGTACCTGTACTTGACA-CTTTTTCCTA
          1 ATTTGGTACCTGAACTTCACATCTTTTTCCTA

                               *  *         
      17081 ATTTGGTACCTGAACTTCATATTTTTTTCCTA
          1 ATTTGGTACCTGAACTTCACATCTTTTTCCTA

            *       
      17113 TTTTGGTA
          1 ATTTGGTA

      17121 TCTAAGTATT


Statistics
Matches: 34,  Mismatches: 5, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  31   18  0.53
  32   16  0.47

ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49


Consensus pattern (32 bp):   
ATTTGGTACCTGAACTTCACATCTTTTTCCTA

Found at i:20446 original size:21 final size:21

Alignment explanation


    Indices: 20407--20463  Score: 89
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      20397 TTTTTTTTTT

                                   
      20407 TTTGCTTTAT-ATTCCTTAATGA
          1 TTTGCTTTATGA--CCTTAATGA

                                 
      20429 TTTGCTTTATGACCTTAATGA
          1 TTTGCTTTATGACCTTAATGA

                          
      20450 TTTGCTTTATGACC
          1 TTTGCTTTATGACC

      20464 GTGTTCTTAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  21   23  0.68
  22   10  0.29
  23    1  0.03

ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51


Consensus pattern (21 bp):   
TTTGCTTTATGACCTTAATGA
Done.