X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fdna.scm;h=0d7cbc102a730490c604f99ba7bf5872a63f7874;hb=0a0cce2e9671916ffa893bff2b3e3187def66049;hp=e66864a89a4a436f8f66f72af5f636eaab6327d8;hpb=613a7a5d1fe2758f0bb620e49eeb87fa45b5458f;p=jalview.git

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
index e66864a..0d7cbc1 100644
--- a/resources/scoreModel/dna.scm
+++ b/resources/scoreModel/dna.scm
@@ -1,5 +1,4 @@
 ScoreMatrix DNA
-ACGTUIXRYN-
 #
 # A DNA substitution matrix.
 # This is an ad-hoc matrix which, in addition to penalising mutations between the common 
@@ -14,17 +13,15 @@ ACGTUIXRYN-
 #
 # 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
-#
-#	A	C	G	T	U	I	X	R	Y	N		-
+	 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