Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000718.1 Kokia drynarioides strain JFW-HI SEQ_111736, 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: 17270
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2773 original size:43 final size:45

Alignment explanation


    Indices: 2725--2812  Score: 153
    Period size: 43  Copynumber: 2.0  Consensus size: 45

       2715 TTCGTTTTCC

                        *                                
       2725 AAATTTAAGCACTTCCCTATCATATG-TT-TATATATTTATGTTT
          1 AAATTTAAGCACGTCCCTATCATATGTTTATATATATTTATGTTT

                                                         
       2768 AAATTTAAGCACGTCCCTATCATATGTTTATATATATTTATGTTT
          1 AAATTTAAGCACGTCCCTATCATATGTTTATATATATTTATGTTT

       2813 TCTCTCAATA


Statistics
Matches: 42,  Mismatches: 1, Indels: 2
        0.93            0.02        0.04

Matches are distributed among these distances:
  43   25  0.60
  44    2  0.05
  45   15  0.36

ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48


Consensus pattern (45 bp):   
AAATTTAAGCACGTCCCTATCATATGTTTATATATATTTATGTTT

Found at i:4621 original size:42 final size:40

Alignment explanation


    Indices: 4562--4647  Score: 127
    Period size: 42  Copynumber: 2.1  Consensus size: 40

       4552 GTGTTTATGG

                        *         *                   
       4562 GTTTAAGAGTGAGATACTTTATTATTGTTAATACTTAGTGGT
          1 GTTTAAGAGTGACATACTTTATCATTGTTAATAC-T-GTGGT

                 *                                  
       4604 GTTTATGAGTGACATACTTTATCATTGTTAATACTGTGGT
          1 GTTTAAGAGTGACATACTTTATCATTGTTAATACTGTGGT

                
       4644 GTTT
          1 GTTT

       4648 TTGTGTTTTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  40    9  0.22
  41    1  0.02
  42   31  0.76

ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47


Consensus pattern (40 bp):   
GTTTAAGAGTGACATACTTTATCATTGTTAATACTGTGGT

Found at i:5035 original size:18 final size:18

Alignment explanation


    Indices: 5012--5047  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       5002 GAAGGTGTCG

                              
       5012 AATATTTTTATTGCTTTA
          1 AATATTTTTATTGCTTTA

                              
       5030 AATATTTTTATTGCTTTA
          1 AATATTTTTATTGCTTTA

       5048 TTAAAGTAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61


Consensus pattern (18 bp):   
AATATTTTTATTGCTTTA

Found at i:16586 original size:23 final size:23

Alignment explanation


    Indices: 16560--16615  Score: 69
    Period size: 23  Copynumber: 2.4  Consensus size: 23

      16550 AAAATGATTA

                      **    *      
      16560 TTGAATTATTTTAAAGTTTTTCT
          1 TTGAATTATTCAAAAGATTTTCT

                                   
      16583 TTGAATTATTCAAAAGATTTTCT
          1 TTGAATTATTCAAAAGATTTTCT

                       
      16606 TT-AAGTTATT
          1 TTGAA-TTATT

      16616 GGATTGTTAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  22    2  0.07
  23   27  0.93

ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55


Consensus pattern (23 bp):   
TTGAATTATTCAAAAGATTTTCT
Done.