!!NA_SCORING_MATRIX_RECT 1.0
Default scoring matrix used by SEGMENTS for the comparison of
nucleic acid sequences. SEGMENTS uses the method of Smith/Waterman 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 -6
February 20, 1996 14:34 ..
{
GAP_CREATE 50
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