!!NA_SCORING_MATRIX_RECT 1.0
Alternative scoring matrix that could be used by PROFILEMAKE to create a
profile from a group of aligned nucleic acid sequences. This matrix may
be appropriate if you use the /GLObal switch with PROFILEGAP or
PROFILESEGMENTS.
This matrix weights all matches as 10
This matrix weights all matches to 2 way ambiugity symbols as 6
This matrix weights all matches to 3 way ambiugity symbols as 2
This matrix weights all matches to 4 way ambiugity symbols as 0
This matrix weights all gaps as 0
This matrix weights all mismatches as 0
March 26, 1996 10:38 ..
{
GAP_CREATE 31
GAP_EXTEND 3
}
A B C D G H K M R S T U V W Y
A 10 0 0 2 0 2 0 6 6 0 0 0 2 6 0
B 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2
C 0 2 10 0 0 2 0 6 0 6 0 0 2 0 6
D 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2
G 0 2 0 2 10 0 6 0 6 6 0 0 2 0 0
H 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2
K 0 2 0 2 6 2 6 0 6 6 6 6 2 6 6
M 6 2 6 2 0 2 0 6 6 6 0 0 2 6 6
R 6 2 0 2 6 2 6 6 6 6 0 0 2 6 0
S 0 2 6 2 6 2 6 6 6 6 0 0 2 0 6
T 0 2 0 2 0 2 6 0 0 0 10 10 0 6 6
U 0 2 0 2 0 2 6 0 0 0 10 10 0 6 6
V 2 2 2 2 2 2 2 2 2 2 0 0 2 2 2
W 6 2 0 2 0 2 6 6 6 0 6 6 2 6 6
Y 0 2 6 2 0 2 6 6 0 6 6 6 2 6 6