!!NA_SCORING_MATRIX_RECT 1.0
Default scoring matrix used by SEGMENTS for the comparison of nucleic
acid sequences when /WHOle for VMS, or -WHOle for UNIX, is on the
command line. SEGMENTS /WHOle, or SEGMENTS -WHOle, uses the method of
Needleman/Wunsch/Sellers to make alignments.
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
February 20, 1996 14:35 ..
{
GAP_CREATE 50
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