ScoreMatrix DNA
ACGTUIXRYN -
#
# A DNA substitution matrix.
# This is an ad-hoc matrix which, in addition to penalising mutations between the common 
# nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA. 
# In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, 
# and N is allowed to match any other base weakly. 
# This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match
# any of (ACGTU), and unfavourably match each other.
#
# The first line declares a ScoreMatrix with the name DNA (shown in menus)
# The second line gives the symbols for which scores are held in the matrix
# These may include a space (but not as the first or last character)
# Scores are not case sensitive, unless column(s) are provided for lower case characters
#
#
# Header line with symbols is provided as a guide
# Values may be integer or floating point, delimited by tab, space, comma or combinations
#
	A	C	G	T	U	I	X	R	Y	N		-
	10	-8	-8	-8	-8	1	1	1	-8	1	1	1 
	-8	10	-8	-8	-8	1	1	-8	1	1	1	1
	-8	-8	10	-8	-8	1	1	1	-8	1	1	1
	-8	-8	-8	10	10	1	1	-8	1	1	1	1
	-8	-8	-8	10	10	1	1	-8	1	1	1	1
	1	1	1	1	1	10	0	0	0	1	1	1
	1	1	1	1	1	0	10	0	0	1	1	1
	1	-8	1	-8	-8	0	0	10	-8	1	1	1
	-8	1	-8	1	1	0	0	-8	10	1	1	1
	1	1	1	1	1	1	1	1	1	10	1	1
	1	1	1	1	1	1	1	1	1	1	1	1
	1	1	1	1	1	1	1	1	1	1	1	1
#
#	A	C	G	T	U	I	X	R	Y	N		-