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+ScoreMatrix DNA
+#
+# 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)
+# Scores are not case sensitive, unless column(s) are provided for lower case characters
+#
+# Values may be integer or floating point, delimited by tab, space, comma or combinations
+#
+	 A	 C	 G	 T	 U	 I	 X	 R	 Y	 N	-
+A	10	-8	-8	-8	-8	 1	 1	 1	-8	 1	1 
+C	-8	10	-8	-8	-8	 1	 1	-8	 1	 1	1
+G	-8	-8	10	-8	-8	 1	 1	 1	-8	 1	1
+T	-8	-8	-8	10	10	 1	 1	-8	 1	 1	1
+U	-8	-8	-8	10	10	 1	 1	-8	 1	 1	1
+I	 1	 1	 1	 1	 1	10	 0	 0	 0	 1	1
+X	 1	 1	 1	 1	 1	 0	10	 0	 0	 1	1
+R	 1	-8	 1	-8	-8	 0	 0	10	-8	 1	1
+Y	-8	 1	-8	 1	 1	 0	 0	-8	10	 1	1
+N	 1	 1	 1	 1	 1	 1	 1	 1	 1	10	1
+-	 1	 1	 1	 1	 1	 1	 1	 1	 1	 1	1