!!NA_SCORING_MATRIX_RECT 1.0

Default scoring matrix used by PILEUP for the comparison of nucleic acid
sequences.  PILEUP uses the method of Needleman/Wunsch/Sellers to make
alignments.  This table scores a match for any overlap between any IUB
nucleic acid ambiguity symbols EXCEPT X/N.

                     February 20, 1996 14:34   ..

{
GAP_CREATE 5
GAP_EXTEND 1
}

      A    B    C    D    G     H    K    M    N    R     S    T    U    V    W     X    Y 
A     1    0    0    1    0     1    0    1    1    1     0    0    0    1    1     1    0 
B     0    1    1    1    1     1    1    1    1    1     1    1    1    1    1     1    1 
C     0    1    1    0    0     1    0    1    1    0     1    0    0    1    0     1    1 
D     1    1    0    1    1     1    1    1    1    1     1    1    1    1    1     1    1 
G     0    1    0    1    1     0    1    0    1    1     1    0    0    1    0     1    0 

H     1    1    1    1    0     1    1    1    1    1     1    1    1    1    1     1    1 
K     0    1    0    1    1     1    1    0    1    1     1    1    1    1    1     1    1 
M     1    1    1    1    0     1    0    1    1    1     1    0    0    1    1     1    1 
N     1    1    1    1    1     1    1    1    1    1     1    1    1    1    1     1    1 
R     1    1    0    1    1     1    1    1    1    1     1    0    0    1    1     1    0 

S     0    1    1    1    1     1    1    1    1    1     1    0    0    1    0     1    1 
T     0    1    0    1    0     1    1    0    1    0     0    1    1    0    1     1    1 
U     0    1    0    1    0     1    1    0    1    0     0    1    1    0    1     1    1 
V     1    1    1    1    1     1    1    1    1    1     1    0    0    1    1     1    1 
W     1    1    0    1    0     1    1    1    1    1     0    1    1    1    1     1    1 

X     1    1    1    1    1     1    1    1    1    1     1    1    1    1    1     1    1 
Y     0    1    1    1    0     1    1    1    1    0     1    1    1    1    1     1    1