#
# Sample scoring matrix that rewards both purine-purine
# and pyrimidine-pyrimidine transitions.  This matrix
# or one like it may be useful in developing better PCR
# primers or in finding candidate noncoding RNA genes.
# Simultaneous use of a shorter word length than the
# default W=11 may be advisable.
#
# Specify matrix=pupy on the BLASTN command line
#
# The complete 4-bit (.4) alphabet is
# ACGT RYMKWSBDHVN -
#      acagaccaaaa g
#      gtcttgggccc a
#            tttgg p
#                t
#
#   Subject letters ->
# Query
# letters
# |
# V
#
# Ungapped Lambda = 0.267098 bits, H = 0.510588 bits
	A	C	G	T
A	4	-8	2	-8
C	-8	4	-8	2
G	2	-8	4	-8
T	-8	2	-8	4
R	3	-8	3	-8
Y	-8	3	-8	3
M	-2	-2	-3	-3
K	-3	-3	-2	-2
W	-2	-3	-3	-2
S	-3	-2	-2	-3
B	-5	-1	-4	-1
D	-1	-5	-1	-4
H	-4	-1	-5	-1
V	-1	-4	-1	-5
N	-3	-3	-3	-3
