!!NA_SCORING_MATRIX_RECT 1.0
Default scoring matrix used by PROFILEMAKE to create a profile from a
group of aligned nucleic acid sequences.
This matrix weights all matches as 10
This matrix weights all matches to 2 way ambiguity symbols as 6
This matrix weights all matches to 3 way ambiguity symbols as 2
This matrix weights all matches to 4 way ambiguity symbols as 0
This matrix weights all gaps as 0
This matrix weights all mismatches as -6
March 26, 1996 10:30 ..
{
GAP_CREATE 31
GAP_EXTEND 3
}
A B C D G H K M R S T U V W Y
A 10 -6 -6 2 -6 2 -6 6 6 -6 -6 -6 2 6 -6
B -6 2 2 2 2 2 2 2 2 2 2 2 2 2 2
C -6 2 10 -6 -6 2 -6 6 -6 6 -6 -6 2 -6 6
D 2 2 -6 2 2 2 2 2 2 2 2 2 2 2 2
G -6 2 -6 2 10 -6 6 -6 6 6 -6 -6 2 -6 -6
H 2 2 2 2 -6 2 2 2 2 2 2 2 2 2 2
K -6 2 -6 2 6 2 6 -6 6 6 6 6 2 6 6
M 6 2 6 2 -6 2 -6 6 6 6 -6 -6 2 6 6
R 6 2 -6 2 6 2 6 6 6 6 -6 -6 2 6 -6
S -6 2 6 2 6 2 6 6 6 6 -6 -6 2 -6 6
T -6 2 -6 2 -6 2 6 -6 -6 -6 10 10 -6 6 6
U -6 2 -6 2 -6 2 6 -6 -6 -6 10 10 -6 6 6
V 2 2 2 2 2 2 2 2 2 2 -6 -6 2 2 2
W 6 2 -6 2 -6 2 6 6 6 -6 6 6 2 6 6
Y -6 2 6 2 -6 2 6 6 -6 6 6 6 2 6 6