/usr/lib/R/site-library/bio3d/matrices/bio3d.mat is in r-other-bio3d 1.1-5-1build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | # PET91 Matrix - Jones, Taylor and Thornton 1991
# This is an update of the MDM78 Dayhoff matrix normalised such that
# all maxima are on the diagonal with a score of 10
A R N D C Q E G H I L K M F P S T W Y V B Z X -
A 10 -1 0 -1 -1 -1 -1 1 -2 0 -1 -1 -1 -3 1 1 2 -4 -3 1 0 -1 0 0
R -1 10 0 -1 -1 2 0 0 2 -3 -3 4 -2 -4 -1 -1 -1 0 -2 -3 0 1 0 0
N 0 0 10 2 -1 0 1 0 1 -2 -3 1 -2 -3 -1 1 1 -4 -1 -2 2 0 0 0
D -1 -1 2 10 -3 0 4 1 0 -3 -4 0 -3 -5 -2 0 -1 -5 -2 -3 3 2 0 0
C -1 -1 -1 -3 10 -3 -4 -1 0 -2 -3 -3 -2 0 -2 1 -1 1 2 -2 -2 -3 0 0
Q -1 2 0 0 -3 10 2 -1 3 -3 -2 2 -2 -4 0 -1 -1 -3 -1 -3 0 3 0 0
E -1 0 1 4 -4 2 10 1 0 -3 -4 1 -3 -5 -2 -1 -1 -5 -4 -2 2 3 0 0
G 1 0 0 1 -1 -1 1 10 -2 -3 -4 -1 -3 -5 -1 1 0 -2 -4 -2 0 0 0 0
H -2 2 1 0 0 3 0 -2 10 -3 -2 1 -2 0 0 -1 -1 -3 4 -3 0 1 0 0
I 0 -3 -2 -3 -2 -3 -3 -3 -3 10 2 -3 3 0 -2 -1 1 -4 -2 4 -2 -3 0 0
L -1 -3 -3 -4 -3 -2 -4 -4 -2 2 10 -3 3 2 0 -2 -1 -2 -1 2 -3 -3 0 0
K -1 4 1 0 -3 2 1 -1 1 -3 -3 10 -2 -5 -2 -1 -1 -3 -3 -3 0 1 0 0
M -1 -2 -2 -3 -2 -2 -3 -3 -2 3 3 -2 10 0 -2 -1 0 -3 -3 2 -2 -2 0 0
F -3 -4 -3 -5 0 -4 -5 -5 0 0 2 -5 0 10 -2 -2 -2 -1 5 0 -4 -4 0 0
P 1 -1 -1 -2 -2 0 -2 -1 0 -2 0 -2 -2 -2 10 1 1 -5 -3 -1 -1 -1 0 0
S 1 -1 1 0 1 -1 -1 1 -1 -1 -2 -1 -1 -2 1 10 1 -3 -1 -1 0 -1 0 0
T 2 -1 1 -1 -1 -1 -1 0 -1 1 -1 -1 0 -2 1 1 10 -4 -3 0 0 -1 0 0
W -4 0 -4 -5 1 -3 -5 -2 -3 -4 -2 -3 -3 -1 -5 -3 -4 10 0 -4 -4 -4 0 0
Y -3 -2 -1 -2 2 -1 -4 -4 4 -2 -1 -3 -3 5 -3 -1 -3 0 10 -3 -1 -2 0 0
V 1 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 0 -1 -1 0 -4 -3 10 -2 -2 0 0
B 0 0 2 3 -2 0 2 0 0 -2 -3 0 -2 -4 -1 0 0 -4 -1 -2 10 1 0 0
Z -1 1 0 2 -3 3 3 0 1 -3 -3 1 -2 -4 -1 -1 -1 -4 -2 -2 1 10 0 0
X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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