X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5fbbc194f2dde467cf88aad0e748c9d188dd40c7;hb=adca107ff292173bc844ad4a5c6c7eba958ad24a;hp=ef9eceb7580a838c0c05f170fedae816ea3d6f1d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index ef9eceb..5fbbc19 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -1,119 +1,1572 @@ + -->
Jalview includes a small number of built in substitution matrices, used for different types of analysis.
-A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W | X | Y | Z | |
A | 4 | -2 | 0 | -2 | -1 | -2 | 0 | -2 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | -1 | 1 | 0 | 0 | 0 | -3 | 0 | -2 | -1 |
B | -2 | 4 | -3 | 4 | 1 | -3 | -1 | 0 | -3 | 0 | -4 | -3 | 3 | -2 | 0 | -1 | 0 | -1 | -1 | -3 | -4 | -1 | -3 | 1 |
C | 0 | -3 | 9 | -3 | -4 | -2 | -3 | -3 | -1 | -3 | -1 | -1 | -3 | -3 | -3 | 3 | -1 | -1 | -2 | -1 | -2 | -2 | -2 | -3 |
D | -2 | 4 | -3 | 6 | 2 | -3 | -1 | -1 | -3 | -1 | -4 | -3 | 1 | -1 | 0 | -2 | 0 | -1 | -1 | -3 | -4 | -1 | -3 | 1 |
E | -1 | 1 | -4 | 2 | 5 | -3 | -2 | 0 | -3 | 1 | -3 | -2 | 0 | -1 | 2 | 0 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 4 |
F | -2 | -3 | -2 | -3 | -3 | 6 | -3 | -1 | 0 | -3 | 0 | 0 | -3 | -4 | -3 | -3 | -2 | -2 | -1 | -1 | 1 | -1 | 3 | -3 |
G | 0 | -1 | -3 | -1 | -2 | -3 | 6 | -2 | -4 | -2 | -4 | -3 | 0 | -2 | -2 | -2 | 0 | -2 | -1 | -3 | -2 | -1 | -3 | -2 |
H | -2 | 0 | -3 | -1 | 0 | -1 | -2 | 8 | -3 | -1 | -3 | -2 | 1 | -2 | 0 | 0 | -1 | -2 | -1 | -3 | -2 | -1 | 2 | 0 |
I | -1 | -3 | -1 | -3 | -3 | 0 | -4 | -3 | 4 | -3 | 2 | 1 | -3 | -3 | -3 | -3 | -2 | -1 | -1 | 3 | -3 | -1 | -1 | -3 |
K | -1 | 0 | -3 | -1 | 1 | -3 | -2 | -1 | -3 | 5 | -2 | -1 | 0 | -1 | 1 | 2 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 1 |
L | -1 | -4 | -1 | -4 | -3 | 0 | -4 | -3 | 2 | -2 | 4 | 2 | -3 | -3 | -2 | -2 | -2 | -1 | -1 | 1 | -2 | -1 | -1 | -3 |
M | -1 | -3 | -1 | -3 | -2 | 0 | -3 | -2 | 1 | -1 | 2 | 5 | -2 | -2 | 0 | -1 | -1 | -1 | -1 | 1 | -1 | -1 | -1 | -1 |
N | -2 | 3 | -3 | 1 | 0 | -3 | 0 | 1 | -3 | 0 | -3 | -2 | 6 | -2 | 0 | 0 | 1 | 0 | -1 | -3 | -4 | -1 | -2 | 0 |
P | -1 | -2 | -3 | -1 | -1 | -4 | -2 | -2 | -3 | -1 | -3 | -2 | -2 | 7 | -1 | -2 | -1 | -1 | -2 | -2 | -4 | -2 | -3 | -1 |
Q | -1 | 0 | -3 | 0 | 2 | -3 | -2 | 0 | -3 | 1 | -2 | 0 | 0 | -1 | 5 | 1 | 0 | -1 | -1 | -2 | -2 | -1 | -1 | 3 |
R | -1 | -1 | -3 | -2 | 0 | -3 | -2 | 0 | -3 | 2 | -2 | -1 | 0 | -2 | 1 | 5 | -1 | -1 | -1 | -3 | -3 | -1 | -2 | 0 |
S | 1 | 0 | -1 | 0 | 0 | -2 | 0 | -1 | -2 | 0 | -2 | -1 | 1 | -1 | 0 | -1 | 4 | 1 | 0 | -2 | -3 | 0 | -2 | 0 |
T | 0 | -1 | -1 | -1 | -1 | -2 | -2 | -2 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 1 | 5 | 0 | 0 | -2 | 0 | -2 | -1 |
U | 0 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | 0 | 0 | -1 | -1 | -2 | -1 | -1 | -1 |
V | 0 | -3 | -1 | -3 | -2 | -1 | -3 | -3 | 3 | -2 | 1 | 1 | -3 | -2 | -2 | -3 | -2 | 0 | -1 | 4 | -3 | -1 | -1 | -2 |
W | -3 | -4 | -2 | -4 | -3 | 1 | -2 | -2 | -3 | -3 | -2 | -1 | -4 | -4 | -2 | -3 | -3 | -2 | -2 | -3 | 11 | -2 | 2 | -3 |
X | 0 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | 0 | 0 | -1 | -1 | -2 | -1 | -1 | -1 |
Y | -2 | -3 | -2 | -3 | -2 | 3 | -3 | 2 | -1 | -2 | -1 | -1 | -2 | -3 | -1 | -2 | -2 | -2 | -1 | -1 | 2 | -1 | 7 | -2 |
Z | -1 | 1 | -3 | 1 | 4 | -3 | -2 | 0 | -3 | 1 | -3 | -1 | 0 | -1 | 3 | 0 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 4 |
PAM250
-Percentage Accepted Mutation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).
-Jalview 2.8.1 introduced support for PAM250 based PCA and tree calculations.
-
A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W | X | Y | Z | |
A | 2 | 0 | -2 | 0 | 0 | -3 | 1 | -1 | -1 | -1 | -2 | -1 | 0 | 1 | 0 | -2 | 1 | 1 | 0 | 0 | -6 | 0 | -3 | 0 |
B | 0 | 3 | -4 | 3 | 3 | -4 | 0 | 1 | -2 | 1 | -3 | -2 | 2 | -1 | 1 | -1 | 0 | 0 | -1 | -2 | -5 | -1 | -3 | 2 |
C | -2 | -4 | 12 | -5 | -5 | -4 | -3 | -3 | -2 | -5 | -6 | -5 | -4 | -3 | -5 | -4 | 0 | -2 | -3 | -2 | -8 | -3 | 0 | -5 |
D | 0 | 3 | -5 | 4 | 3 | -6 | 1 | 1 | -2 | 0 | -4 | -3 | 2 | -1 | 2 | -1 | 0 | 0 | -1 | -2 | -7 | -1 | -4 | 3 |
E | 0 | 3 | -5 | 3 | 4 | -5 | 0 | 1 | -2 | 0 | -3 | -2 | 1 | -1 | 2 | -1 | 0 | 0 | -1 | -2 | -7 | -1 | -4 | 3 |
F | -3 | -4 | -4 | -6 | -5 | 9 | -5 | -2 | 1 | -5 | 2 | 0 | -3 | -5 | -5 | -4 | -3 | -3 | -2 | -1 | 0 | -2 | 7 | -5 |
G | 1 | 0 | -3 | 1 | 0 | -5 | 5 | -2 | -3 | -2 | -4 | -3 | 0 | 0 | -1 | -3 | 1 | 0 | -1 | -1 | -7 | -1 | -5 | 0 |
H | -1 | 1 | -3 | 1 | 1 | -2 | -2 | 6 | -2 | 0 | -2 | -2 | 2 | 0 | 3 | 2 | -1 | -1 | -1 | -2 | -3 | -1 | 0 | 2 |
I | -1 | -2 | -2 | -2 | -2 | 1 | -3 | -2 | 5 | -2 | 2 | 2 | -2 | -2 | -2 | -2 | -1 | 0 | -1 | 4 | -5 | -1 | -1 | -2 |
K | -1 | 1 | -5 | 0 | 0 | -5 | -2 | 0 | -2 | 5 | -3 | 0 | 1 | -1 | 1 | 3 | 0 | 0 | -1 | -2 | -3 | -1 | -4 | 0 |
L | -2 | -3 | -6 | -4 | -3 | 2 | -4 | -2 | 2 | -3 | 6 | 4 | -3 | -3 | -2 | -3 | -3 | -2 | -1 | 2 | -2 | -1 | -1 | -3 |
M | -1 | -2 | -5 | -3 | -2 | 0 | -3 | -2 | 2 | 0 | 4 | 6 | -2 | -2 | -1 | 0 | -2 | -1 | -1 | 2 | -4 | -1 | -2 | -2 |
N | 0 | 2 | -4 | 2 | 1 | -3 | 0 | 2 | -2 | 1 | -3 | -2 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | -2 | -4 | 0 | -2 | 1 |
P | 1 | -1 | -3 | -1 | -1 | -5 | 0 | 0 | -2 | -1 | -3 | -2 | 0 | 6 | 0 | 0 | 1 | 0 | -1 | -1 | -6 | -1 | -5 | 0 |
Q | 0 | 1 | -5 | 2 | 2 | -5 | -1 | 3 | -2 | 1 | -2 | -1 | 1 | 0 | 4 | 1 | -1 | -1 | -1 | -2 | -5 | -1 | -4 | 3 |
R | -2 | -1 | -4 | -1 | -1 | -4 | -3 | 2 | -2 | 3 | -3 | 0 | 0 | 0 | 1 | 6 | 0 | -1 | -1 | -2 | 2 | -1 | -4 | 0 |
S | 1 | 0 | 0 | 0 | 0 | -3 | 1 | -1 | -1 | 0 | -3 | -2 | 1 | 1 | -1 | 0 | 2 | 1 | 0 | -1 | -2 | 0 | -3 | 0 |
T | 1 | 0 | -2 | 0 | 0 | -3 | 0 | -1 | 0 | 0 | -2 | -1 | 0 | 0 | -1 | -1 | 1 | 3 | 0 | 0 | -5 | 0 | -3 | -1 |
U | 0 | -1 | -3 | -1 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 0 | 0 | -1 | -1 | -4 | -1 | -2 | -1 |
V | 0 | -2 | -2 | -2 | -2 | -1 | -1 | -2 | 4 | -2 | 2 | 2 | -2 | -1 | -2 | -2 | -1 | 0 | -1 | 4 | -6 | -1 | -2 | -2 |
W | -6 | -5 | -8 | -7 | -7 | 0 | -7 | -3 | -5 | -3 | -2 | -4 | -4 | -6 | -5 | 2 | -2 | -5 | -4 | -6 | 17 | -4 | 0 | -6 |
X | 0 | -1 | -3 | -1 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 0 | 0 | -1 | -1 | -4 | -1 | -2 | -1 |
Y | -3 | -3 | 0 | -4 | -4 | 7 | -5 | 0 | -1 | -4 | -1 | -2 | -2 | -5 | -4 | -4 | -3 | -3 | -2 | -2 | 0 | -2 | 10 | -4 |
Z | 0 | 2 | -5 | 3 | 3 | -5 | 0 | 2 | -2 | 0 | -3 | -2 | 1 | 0 | 3 | 0 | 0 | -1 | -1 | -2 | -6 | -1 | -4 | 3 |
+ | A | +B | +C | +D | +E | +F | +G | +H | +I | +K | +L | +M | +N | +P | +Q | +R | +S | +T | +U | +V | +W | +X | +Y | +Z | +
A | +4 | +-2 | +0 | +-2 | +-1 | +-2 | +0 | +-2 | +-1 | +-1 | +-1 | +-1 | +-2 | +-1 | +-1 | +-1 | +1 | +0 | +0 | +0 | +-3 | +0 | +-2 | +-1 | +
B | +-2 | +4 | +-3 | +4 | +1 | +-3 | +-1 | +0 | +-3 | +0 | +-4 | +-3 | +3 | +-2 | +0 | +-1 | +0 | +-1 | +-1 | +-3 | +-4 | +-1 | +-3 | +1 | +
C | +0 | +-3 | +9 | +-3 | +-4 | +-2 | +-3 | +-3 | +-1 | +-3 | +-1 | +-1 | +-3 | +-3 | +-3 | +3 | +-1 | +-1 | +-2 | +-1 | +-2 | +-2 | +-2 | +-3 | +
D | +-2 | +4 | +-3 | +6 | +2 | +-3 | +-1 | +-1 | +-3 | +-1 | +-4 | +-3 | +1 | +-1 | +0 | +-2 | +0 | +-1 | +-1 | +-3 | +-4 | +-1 | +-3 | +1 | +
E | +-1 | +1 | +-4 | +2 | +5 | +-3 | +-2 | +0 | +-3 | +1 | +-3 | +-2 | +0 | +-1 | +2 | +0 | +0 | +-1 | +-1 | +-2 | +-3 | +-1 | +-2 | +4 | +
F | +-2 | +-3 | +-2 | +-3 | +-3 | +6 | +-3 | +-1 | +0 | +-3 | +0 | +0 | +-3 | +-4 | +-3 | +-3 | +-2 | +-2 | +-1 | +-1 | +1 | +-1 | +3 | +-3 | +
G | +0 | +-1 | +-3 | +-1 | +-2 | +-3 | +6 | +-2 | +-4 | +-2 | +-4 | +-3 | +0 | +-2 | +-2 | +-2 | +0 | +-2 | +-1 | +-3 | +-2 | +-1 | +-3 | +-2 | +
H | +-2 | +0 | +-3 | +-1 | +0 | +-1 | +-2 | +8 | +-3 | +-1 | +-3 | +-2 | +1 | +-2 | +0 | +0 | +-1 | +-2 | +-1 | +-3 | +-2 | +-1 | +2 | +0 | +
I | +-1 | +-3 | +-1 | +-3 | +-3 | +0 | +-4 | +-3 | +4 | +-3 | +2 | +1 | +-3 | +-3 | +-3 | +-3 | +-2 | +-1 | +-1 | +3 | +-3 | +-1 | +-1 | +-3 | +
K | +-1 | +0 | +-3 | +-1 | +1 | +-3 | +-2 | +-1 | +-3 | +5 | +-2 | +-1 | +0 | +-1 | +1 | +2 | +0 | +-1 | +-1 | +-2 | +-3 | +-1 | +-2 | +1 | +
L | +-1 | +-4 | +-1 | +-4 | +-3 | +0 | +-4 | +-3 | +2 | +-2 | +4 | +2 | +-3 | +-3 | +-2 | +-2 | +-2 | +-1 | +-1 | +1 | +-2 | +-1 | +-1 | +-3 | +
M | +-1 | +-3 | +-1 | +-3 | +-2 | +0 | +-3 | +-2 | +1 | +-1 | +2 | +5 | +-2 | +-2 | +0 | +-1 | +-1 | +-1 | +-1 | +1 | +-1 | +-1 | +-1 | +-1 | +
N | +-2 | +3 | +-3 | +1 | +0 | +-3 | +0 | +1 | +-3 | +0 | +-3 | +-2 | +6 | +-2 | +0 | +0 | +1 | +0 | +-1 | +-3 | +-4 | +-1 | +-2 | +0 | +
P | +-1 | +-2 | +-3 | +-1 | +-1 | +-4 | +-2 | +-2 | +-3 | +-1 | +-3 | +-2 | +-2 | +7 | +-1 | +-2 | +-1 | +-1 | +-2 | +-2 | +-4 | +-2 | +-3 | +-1 | +
Q | +-1 | +0 | +-3 | +0 | +2 | +-3 | +-2 | +0 | +-3 | +1 | +-2 | +0 | +0 | +-1 | +5 | +1 | +0 | +-1 | +-1 | +-2 | +-2 | +-1 | +-1 | +3 | +
R | +-1 | +-1 | +-3 | +-2 | +0 | +-3 | +-2 | +0 | +-3 | +2 | +-2 | +-1 | +0 | +-2 | +1 | +5 | +-1 | +-1 | +-1 | +-3 | +-3 | +-1 | +-2 | +0 | +
S | +1 | +0 | +-1 | +0 | +0 | +-2 | +0 | +-1 | +-2 | +0 | +-2 | +-1 | +1 | +-1 | +0 | +-1 | +4 | +1 | +0 | +-2 | +-3 | +0 | +-2 | +0 | +
T | +0 | +-1 | +-1 | +-1 | +-1 | +-2 | +-2 | +-2 | +-1 | +-1 | +-1 | +-1 | +0 | +-1 | +-1 | +-1 | +1 | +5 | +0 | +0 | +-2 | +0 | +-2 | +-1 | +
U | +0 | +-1 | +-2 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-2 | +-1 | +-1 | +0 | +0 | +-1 | +-1 | +-2 | +-1 | +-1 | +-1 | +
V | +0 | +-3 | +-1 | +-3 | +-2 | +-1 | +-3 | +-3 | +3 | +-2 | +1 | +1 | +-3 | +-2 | +-2 | +-3 | +-2 | +0 | +-1 | +4 | +-3 | +-1 | +-1 | +-2 | +
W | +-3 | +-4 | +-2 | +-4 | +-3 | +1 | +-2 | +-2 | +-3 | +-3 | +-2 | +-1 | +-4 | +-4 | +-2 | +-3 | +-3 | +-2 | +-2 | +-3 | +11 | +-2 | +2 | +-3 | +
X | +0 | +-1 | +-2 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +-2 | +-1 | +-1 | +0 | +0 | +-1 | +-1 | +-2 | +-1 | +-1 | +-1 | +
Y | +-2 | +-3 | +-2 | +-3 | +-2 | +3 | +-3 | +2 | +-1 | +-2 | +-1 | +-1 | +-2 | +-3 | +-1 | +-2 | +-2 | +-2 | +-1 | +-1 | +2 | +-1 | +7 | +-2 | +
Z | +-1 | +1 | +-3 | +1 | +4 | +-3 | +-2 | +0 | +-3 | +1 | +-3 | +-1 | +0 | +-1 | +3 | +0 | +0 | +-1 | +-1 | +-2 | +-3 | +-1 | +-2 | +4 | +
+ PAM250
Percentage
+ Accepted Mutation matrix. PAM250
+ estimates substitutions after 250% of sites have changed (each
+ site can be mutated multple times).
Jalview 2.8.1
+ introduced support for PAM250 based PCA and tree calculations.
+
+ | A | +B | +C | +D | +E | +F | +G | +H | +I | +K | +L | +M | +N | +P | +Q | +R | +S | +T | +U | +V | +W | +X | +Y | +Z | +
A | +2 | +0 | +-2 | +0 | +0 | +-3 | +1 | +-1 | +-1 | +-1 | +-2 | +-1 | +0 | +1 | +0 | +-2 | +1 | +1 | +0 | +0 | +-6 | +0 | +-3 | +0 | +
B | +0 | +3 | +-4 | +3 | +3 | +-4 | +0 | +1 | +-2 | +1 | +-3 | +-2 | +2 | +-1 | +1 | +-1 | +0 | +0 | +-1 | +-2 | +-5 | +-1 | +-3 | +2 | +
C | +-2 | +-4 | +12 | +-5 | +-5 | +-4 | +-3 | +-3 | +-2 | +-5 | +-6 | +-5 | +-4 | +-3 | +-5 | +-4 | +0 | +-2 | +-3 | +-2 | +-8 | +-3 | +0 | +-5 | +
D | +0 | +3 | +-5 | +4 | +3 | +-6 | +1 | +1 | +-2 | +0 | +-4 | +-3 | +2 | +-1 | +2 | +-1 | +0 | +0 | +-1 | +-2 | +-7 | +-1 | +-4 | +3 | +
E | +0 | +3 | +-5 | +3 | +4 | +-5 | +0 | +1 | +-2 | +0 | +-3 | +-2 | +1 | +-1 | +2 | +-1 | +0 | +0 | +-1 | +-2 | +-7 | +-1 | +-4 | +3 | +
F | +-3 | +-4 | +-4 | +-6 | +-5 | +9 | +-5 | +-2 | +1 | +-5 | +2 | +0 | +-3 | +-5 | +-5 | +-4 | +-3 | +-3 | +-2 | +-1 | +0 | +-2 | +7 | +-5 | +
G | +1 | +0 | +-3 | +1 | +0 | +-5 | +5 | +-2 | +-3 | +-2 | +-4 | +-3 | +0 | +0 | +-1 | +-3 | +1 | +0 | +-1 | +-1 | +-7 | +-1 | +-5 | +0 | +
H | +-1 | +1 | +-3 | +1 | +1 | +-2 | +-2 | +6 | +-2 | +0 | +-2 | +-2 | +2 | +0 | +3 | +2 | +-1 | +-1 | +-1 | +-2 | +-3 | +-1 | +0 | +2 | +
I | +-1 | +-2 | +-2 | +-2 | +-2 | +1 | +-3 | +-2 | +5 | +-2 | +2 | +2 | +-2 | +-2 | +-2 | +-2 | +-1 | +0 | +-1 | +4 | +-5 | +-1 | +-1 | +-2 | +
K | +-1 | +1 | +-5 | +0 | +0 | +-5 | +-2 | +0 | +-2 | +5 | +-3 | +0 | +1 | +-1 | +1 | +3 | +0 | +0 | +-1 | +-2 | +-3 | +-1 | +-4 | +0 | +
L | +-2 | +-3 | +-6 | +-4 | +-3 | +2 | +-4 | +-2 | +2 | +-3 | +6 | +4 | +-3 | +-3 | +-2 | +-3 | +-3 | +-2 | +-1 | +2 | +-2 | +-1 | +-1 | +-3 | +
M | +-1 | +-2 | +-5 | +-3 | +-2 | +0 | +-3 | +-2 | +2 | +0 | +4 | +6 | +-2 | +-2 | +-1 | +0 | +-2 | +-1 | +-1 | +2 | +-4 | +-1 | +-2 | +-2 | +
N | +0 | +2 | +-4 | +2 | +1 | +-3 | +0 | +2 | +-2 | +1 | +-3 | +-2 | +2 | +0 | +1 | +0 | +1 | +0 | +0 | +-2 | +-4 | +0 | +-2 | +1 | +
P | +1 | +-1 | +-3 | +-1 | +-1 | +-5 | +0 | +0 | +-2 | +-1 | +-3 | +-2 | +0 | +6 | +0 | +0 | +1 | +0 | +-1 | +-1 | +-6 | +-1 | +-5 | +0 | +
Q | +0 | +1 | +-5 | +2 | +2 | +-5 | +-1 | +3 | +-2 | +1 | +-2 | +-1 | +1 | +0 | +4 | +1 | +-1 | +-1 | +-1 | +-2 | +-5 | +-1 | +-4 | +3 | +
R | +-2 | +-1 | +-4 | +-1 | +-1 | +-4 | +-3 | +2 | +-2 | +3 | +-3 | +0 | +0 | +0 | +1 | +6 | +0 | +-1 | +-1 | +-2 | +2 | +-1 | +-4 | +0 | +
S | +1 | +0 | +0 | +0 | +0 | +-3 | +1 | +-1 | +-1 | +0 | +-3 | +-2 | +1 | +1 | +-1 | +0 | +2 | +1 | +0 | +-1 | +-2 | +0 | +-3 | +0 | +
T | +1 | +0 | +-2 | +0 | +0 | +-3 | +0 | +-1 | +0 | +0 | +-2 | +-1 | +0 | +0 | +-1 | +-1 | +1 | +3 | +0 | +0 | +-5 | +0 | +-3 | +-1 | +
U | +0 | +-1 | +-3 | +-1 | +-1 | +-2 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +0 | +-1 | +-1 | +-1 | +0 | +0 | +-1 | +-1 | +-4 | +-1 | +-2 | +-1 | +
V | +0 | +-2 | +-2 | +-2 | +-2 | +-1 | +-1 | +-2 | +4 | +-2 | +2 | +2 | +-2 | +-1 | +-2 | +-2 | +-1 | +0 | +-1 | +4 | +-6 | +-1 | +-2 | +-2 | +
W | +-6 | +-5 | +-8 | +-7 | +-7 | +0 | +-7 | +-3 | +-5 | +-3 | +-2 | +-4 | +-4 | +-6 | +-5 | +2 | +-2 | +-5 | +-4 | +-6 | +17 | +-4 | +0 | +-6 | +
X | +0 | +-1 | +-3 | +-1 | +-1 | +-2 | +-1 | +-1 | +-1 | +-1 | +-1 | +-1 | +0 | +-1 | +-1 | +-1 | +0 | +0 | +-1 | +-1 | +-4 | +-1 | +-2 | +-1 | +
Y | +-3 | +-3 | +0 | +-4 | +-4 | +7 | +-5 | +0 | +-1 | +-4 | +-1 | +-2 | +-2 | +-5 | +-4 | +-4 | +-3 | +-3 | +-2 | +-2 | +0 | +-2 | +10 | +-4 | +
Z | +0 | +2 | +-5 | +3 | +3 | +-5 | +0 | +2 | +-2 | +0 | +-3 | +-2 | +1 | +0 | +3 | +0 | +0 | +-1 | +-1 | +-2 | +-6 | +-1 | +-4 | +3 | +
Simple Nucleotide Substitution
-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.
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A | C | G | I | N | R | T | U | X | Y | |
A | 10 | -8 | -8 | 1 | 1 | 1 | -8 | -8 | 1 | -8 |
C | -8 | 10 | -8 | 1 | 1 | -8 | -8 | -8 | 1 | 1 |
G | -8 | -8 | 10 | 1 | 1 | 1 | -8 | -8 | 1 | -8 |
I | 1 | 1 | 1 | 10 | 1 | 0 | 1 | 1 | 0 | 0 |
N | 1 | 1 | 1 | 1 | 10 | 1 | 1 | 1 | 1 | 1 |
R | 1 | -8 | 1 | 0 | 1 | 10 | -8 | -8 | 0 | -8 |
T | -8 | -8 | -8 | 1 | 1 | -8 | 10 | 10 | 1 | 1 |
U | -8 | -8 | -8 | 1 | 1 | -8 | 10 | 10 | 1 | 1 |
X | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 10 | 0 |
Y | -8 | 1 | -8 | 0 | 1 | -8 | 1 | 1 | 0 | 10 |