# The contents of this file can serve both as the .4.4 file and the .4.2
# file, with the resultant consequences described below.  For more complicated
# scoring systems, the .4.2 file may have 15 rows and 4 columns; and the .4.4
# file may have 15 rows and 15 columns.
#
# A score of -10000 (or less) is interpreted by WU-BLAST 2.0
# to mean that the substitution is absolutely disallowed, although
# the letters involved may still appear within gaps.
# Other versions of BLAST may treat scores of -10000 or less
# differently (e.g., as literal substitution score values).
#
# By choice, only ACGT are specified below for Query ROW labels and Subject
# COLUMN headings.  Omitted letters are /implicitly/ not allowed to appear
# in alignments, but the letters involved may still appear within gaps.
# (See above for the analogous, explicit treatment of scores <= -10000).
#
# The statistics assume background frequencies P(A), P(C), P(G), and P(T)
# sum to 1.  Any ambiguity codes (letters other than A, C, G and T)
# are assumed to have background frequencies of 0, even though they
# may appear at some frequency in the actual query and database sequences.
#
# The 2-bit .2 alphabet is simply ACGT
#
# The complete 4-bit .4 alphabet is
# ACGT RYMKWSBDHVN -
#      acagaccaaaa
#      gtcttgggccc
#            tttgg
#                t
#
# NOTE: substitution scores for the gap character, -, should NOT be specified.
#
#   Subject letters ->
# Query
# letters
# |
# V
#
#
   A      C      G      T
A  1     -10000 -10000 -10000
C -10000  1     -10000 -10000
G -10000 -10000  1     -10000
T -10000 -10000 -10000  1
