4 # A DNA substitution matrix.
5 # This is an ad-hoc matrix which, in addition to penalising mutations between the common
6 # nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
7 # In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively,
8 # and N is allowed to match any other base weakly.
9 # This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match
10 # any of (ACGTU), and unfavourably match each other.
12 # The first line declares a ScoreMatrix with the name DNA (shown in menus)
13 # Scores are not case sensitive, unless column(s) are provided for lower case characters
15 # Values may be integer or floating point, delimited by tab, space, comma or combinations
18 A 10 -8 -8 -8 -8 1 1 1 -8 1 1
19 C -8 10 -8 -8 -8 1 1 -8 1 1 1
20 G -8 -8 10 -8 -8 1 1 1 -8 1 1
21 T -8 -8 -8 10 10 1 1 -8 1 1 1
22 U -8 -8 -8 10 10 1 1 -8 1 1 1
23 I 1 1 1 1 1 10 0 0 0 1 1
24 X 1 1 1 1 1 0 10 0 0 1 1
25 R 1 -8 1 -8 -8 0 0 10 -8 1 1
26 Y -8 1 -8 1 1 0 0 -8 10 1 1
27 N 1 1 1 1 1 1 1 1 1 10 1
28 - 1 1 1 1 1 1 1 1 1 1 1
30 # A C G T U I X R Y N -