Examples
of pattern descriptions.
1:
GAATTC
EcoRI site
2: {GAATTC}[1]
Same as #1 but allowing one error (mismatch)
3: (RY)[10:]
Alternating purine-pyrimidine pattern repeated
ten times or
more (upper limit can be omitted)
4: {(RY)[10:]}[3]
Same as #3 but allowing up to 3 errors
5: NNNNN-5-4-3-2-1
Any exact 10-bp palindrome (like ACTTGCAAGT)
6: NNNNN(N)[0:20]-5-4-3-2-1
or (N)[
A close inverted 5bp repeat separated by up to 20 bp of any
sequence
7: NNNNN(N)[0:20]{-5-4-3-2-1}[1]
Same as #6 but allowing one error
8: {SSSSS}[1](N)[0:20]{-5-4-3-2-1}[1]
Same as #7 but with an additional requirement that at least 4
of the first 5 nucleotides are C or G
9: NNN(+1+2+3)[9:]
Exact tandem repeat of any trinucleotide at
least ten times in
a row
10: NNNNN((N)[0:10]+1+2+3+4+5)[5:]
Any pentanucleotide repeated 6 or more times
with gaps not
exceeding 10 bp
11: NNNNN((N)[0:10]{+1+2+3+4+5}[1])[5:]
Same as #10 but allowing one mismatch in each repeat relative
to the first pentanucleotide
12:
<>{SSSSSSSS}[3](N)[
A subset of E. coli rho-independent
terminators (a G+C rich
stem-loop structure followed by a T-rich segment).
'<>' at the beginning
signifies that both direct and complementary DNA
strands will be
searched.