X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fblosum62.scm;h=b0e927d38fb36e8d318637d0a7f1bcc6ab26a81a;hb=refs%2Fheads%2Fpatch%2FJAL-4024_jumpScrollHang;hp=c7af6b0b55e84df3d16715df6252a58fffa2f935;hpb=6129931bfa23eec90e6556a4d0412ef34aff5759;p=jalview.git

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index c7af6b0..b0e927d 100644
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -1,43 +1,34 @@
 ScoreMatrix BLOSUM62
-ARNDCQEGHILKMFPSTWYVBZX *
 #
 # The BLOSUM62 substitution matrix, as at https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
 # The first line declares a ScoreMatrix with the name BLOSUM62 (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 symbol case sensitive, unless column(s) are provided for lower case characters
 # The 'guide symbol' at the start of each row of score values is optional
-#
-# Comment header line with symbols is provided as a guide
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
-#	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	    *
-#
-A	4	-1	-2	-2	0	-1	-1	0	-2	-1	-1	-1	-1	-2	-1	1	0	-3	-2	0	-2	-1	0	-4 -4
-R	-1	5	0	-2	-3	1	0	-2	0	-3	-2	2	-1	-3	-2	-1	-1	-3	-2	-3	-1	0	-1	-4 -4
-N	-2	0	6	1	-3	0	0	0	1	-3	-3	0	-2	-3	-2	1	0	-4	-2	-3	3	0	-1	-4 -4
-D	-2	-2	1	6	-3	0	2	-1	-1	-3	-4	-1	-3	-3	-1	0	-1	-4	-3	-3	4	1	-1	-4 -4
-C	0	3	-3	-3	9	-3	-4	-3	-3	-1	-1	-3	-1	-2	-3	-1	-1	-2	-2	-1	-3	-3	-2	-4 -4
-Q	-1	1	0	0	-3	5	2	-2	0	-3	-2	1	0	-3	-1	0	-1	-2	-1	-2	0	3	-1	-4 -4
-E	-1	0	0	2	-4	2	5	-2	0	-3	-3	1	-2	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
-G	0	-2	0	-1	-3	-2	-2	6	-2	-4	-4	-2	-3	-3	-2	0	-2	-2	-3	-3	-1	-2	-1	-4 -4
-H	-2	0	1	-1	-3	0	0	-2	8	-3	-3	-1	-2	-1	-2	-1	-2	-2	2	-3	0	0	-1	-4 -4
-I	-1	-3	-3	-3	-1	-3	-3	-4	-3	4	2	-3	1	0	-3	-2	-1	-3	-1	3	-3	-3	-1	-4 -4
-L	-1	-2	-3	-4	-1	-2	-3	-4	-3	2	4	-2	2	0	-3	-2	-1	-2	-1	1	-4	-3	-1	-4 -4
-K	-1	2	0	-1	-3	1	1	-2	-1	-3	-2	5	-1	-3	-1	0	-1	-3	-2	-2	0	1	-1	-4 -4
-M	-1	-1	-2	-3	-1	0	-2	-3	-2	1	2	-1	5	0	-2	-1	-1	-1	-1	1	-3	-1	-1	-4 -4
-F	-2	-3	-3	-3	-2	-3	-3	-3	-1	0	0	-3	0	6	-4	-2	-2	1	3	-1	-3	-3	-1	-4 -4
-P	-1	-2	-2	-1	-3	-1	-1	-2	-2	-3	-3	-1	-2	-4	7	-1	-1	-4	-3	-2	-2	-1	-2	-4 -4
-S	1	-1	1	0	-1	0	0	0	-1	-2	-2	0	-1	-2	-1	4	1	-3	-2	-2	0	0	0	-4 -4
-T	0	-1	0	-1	-1	-1	-1	-2	-2	-1	-1	-1	-1	-2	-1	1	5	-2	-2	0	-1	-1	0	-4 -4
-W	-3	-3	-4	-4	-2	-2	-3	-2	-2	-3	-2	-3	-1	1	-4	-3	-2	11	2	-3	-4	-3	-2	-4 -4
-Y	-2	-2	-2	-3	-2	-1	-2	-3	2	-1	-1	-2	-1	3	-3	-2	-2	2	7	-1	-3	-2	-1	-4 -4
-V	0	-3	-3	-3	-1	-2	-2	-3	-3	3	1	-2	1	-1	-2	-2	0	-3	-1	4	-3	-2	-1	-4 -4
-B	-2	-1	3	4	-3	0	1	-1	0	-3	-4	0	-3	-3	-2	0	-1	-4	-3	-3	4	1	-1	-4 -4
-Z	-1	0	0	1	-3	3	4	-2	0	-3	-3	1	-1	-3	-1	0	-1	-3	-2	-2	1	4	-1	-4 -4
-X	0	-1	-1	-1	-2	-1	-1	-1	-1	-1	-1	-1	-1	-1	-2	0	0	-2	-1	-1	-1	-1	-1	-4 -4
-	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	1  1
-*	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	1  1
-#
-#	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	*
+	 A	 R	 N	 D	 C	 Q	 E	 G	 H	 I	 L	 K	 M	 F	 P	 S	 T	 W	 Y	 V	 B	 Z	 X	 * 
+A	 4	-1	-2	-2	 0	-1	-1	 0	-2	-1	-1	-1	-1	-2	-1	 1	 0	-3	-2	 0	-2	-1	 0	-4
+R	-1	 5	 0	-2	-3	 1	 0	-2	 0	-3	-2	 2	-1	-3	-2	-1	-1	-3	-2	-3	-1	 0	-1	-4
+N	-2	 0	 6	 1	-3	 0	 0	 0	 1	-3	-3	 0	-2	-3	-2	 1	 0	-4	-2	-3	 3	 0	-1	-4
+D	-2	-2	 1	 6	-3	 0	 2	-1	-1	-3	-4	-1	-3	-3	-1	 0	-1	-4	-3	-3	 4	 1	-1	-4
+C	 0	-3	-3	-3	 9	-3	-4	-3	-3	-1	-1	-3	-1	-2	-3	-1	-1	-2	-2	-1	-3	-3	-2	-4
+Q	-1	 1	 0	 0	-3	 5	 2	-2	 0	-3	-2	 1	 0	-3	-1	 0	-1	-2	-1	-2	 0	 3	-1	-4
+E	-1	 0	 0	 2	-4	 2	 5	-2	 0	-3	-3	 1	-2	-3	-1	 0	-1	-3	-2	-2	 1	 4	-1	-4
+G	 0	-2	 0	-1	-3	-2	-2	 6	-2	-4	-4	-2	-3	-3	-2	 0	-2	-2	-3	-3	-1	-2	-1	-4
+H	-2	 0	 1	-1	-3	 0	 0	-2	 8	-3	-3	-1	-2	-1	-2	-1	-2	-2	 2	-3	 0	 0	-1	-4
+I	-1	-3	-3	-3	-1	-3	-3	-4	-3	 4	 2	-3	 1	 0	-3	-2	-1	-3	-1	 3	-3	-3	-1	-4
+L	-1	-2	-3	-4	-1	-2	-3	-4	-3	 2	 4	-2	 2	 0	-3	-2	-1	-2	-1	 1	-4	-3	-1	-4
+K	-1	 2	 0	-1	-3	 1	 1	-2	-1	-3	-2	 5	-1	-3	-1	 0	-1	-3	-2	-2	 0	 1	-1	-4
+M	-1	-1	-2	-3	-1	 0	-2	-3	-2	 1	 2	-1	 5	 0	-2	-1	-1	-1	-1	 1	-3	-1	-1	-4
+F	-2	-3	-3	-3	-2	-3	-3	-3	-1	 0	 0	-3	 0	 6	-4	-2	-2	 1	 3	-1	-3	-3	-1	-4
+P	-1	-2	-2	-1	-3	-1	-1	-2	-2	-3	-3	-1	-2	-4	 7	-1	-1	-4	-3	-2	-2	-1	-2	-4
+S	 1	-1	 1	 0	-1	 0	 0	 0	-1	-2	-2	 0	-1	-2	-1	 4	 1	-3	-2	-2	 0	 0	 0	-4
+T	 0	-1	 0	-1	-1	-1	-1	-2	-2	-1	-1	-1	-1	-2	-1	 1	 5	-2	-2	 0	-1	-1	 0	-4
+W	-3	-3	-4	-4	-2	-2	-3	-2	-2	-3	-2	-3	-1	 1	-4	-3	-2	11	 2	-3	-4	-3	-2	-4
+Y	-2	-2	-2	-3	-2	-1	-2	-3	 2	-1	-1	-2	-1	 3	-3	-2	-2	 2	 7	-1	-3	-2	-1	-4
+V	 0	-3	-3	-3	-1	-2	-2	-3	-3	 3	 1	-2	 1	-1	-2	-2	 0	-3	-1	 4	-3	-2	-1	-4
+B	-2	-1	 3	 4	-3	 0	 1	-1	 0	-3	-4	 0	-3	-3	-2	 0	-1	-4	-3	-3	 4	 1	-1	-4
+Z	-1	 0	 0	 1	-3	 3	 4	-2	 0	-3	-3	 1	-1	-3	-1	 0	-1	-3	-2	-2	 1	 4	-1	-4
+X	 0	-1	-1	-1	-2	-1	-1	-1	-1	-1	-1	-1	-1	-1	-2	 0	 0	-2	-1	-1	-1	-1	-1	-4
+*	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	-4	 1