ScoreMatrix DNA
-ACGTUIXRYN -
#
# A DNA substitution matrix.
# This is an ad-hoc matrix which, in addition to penalising mutations between the common
# any of (ACGTU), and unfavourably match each other.
#
# The first line declares a ScoreMatrix with the name DNA (shown in menus)
-# The second line gives the symbols for which scores are held in the matrix
-# These may include a space (but not as the first or last character)
# Scores are not case sensitive, unless column(s) are provided for lower case characters
#
-#
-# Comment line with symbols is provided as a guide
# Values may be integer or floating point, delimited by tab, space, comma or combinations
#
-# A C G T U I X R Y N -
-#
- 10 -8 -8 -8 -8 1 1 1 -8 1 1 1
- -8 10 -8 -8 -8 1 1 -8 1 1 1 1
- -8 -8 10 -8 -8 1 1 1 -8 1 1 1
- -8 -8 -8 10 10 1 1 -8 1 1 1 1
- -8 -8 -8 10 10 1 1 -8 1 1 1 1
- 1 1 1 1 1 10 0 0 0 1 1 1
- 1 1 1 1 1 0 10 0 0 1 1 1
- 1 -8 1 -8 -8 0 0 10 -8 1 1 1
- -8 1 -8 1 1 0 0 -8 10 1 1 1
- 1 1 1 1 1 1 1 1 1 10 1 1
- 1 1 1 1 1 1 1 1 1 1 1 1
- 1 1 1 1 1 1 1 1 1 1 1 1
-#
-# A C G T U I X R Y N -
+ A C G T U I X R Y N -
+A 10 -8 -8 -8 -8 1 1 1 -8 1 1
+C -8 10 -8 -8 -8 1 1 -8 1 1 1
+G -8 -8 10 -8 -8 1 1 1 -8 1 1
+T -8 -8 -8 10 10 1 1 -8 1 1 1
+U -8 -8 -8 10 10 1 1 -8 1 1 1
+I 1 1 1 1 1 10 0 0 0 1 1
+X 1 1 1 1 1 0 10 0 0 1 1
+R 1 -8 1 -8 -8 0 0 10 -8 1 1
+Y -8 1 -8 1 1 0 0 -8 10 1 1
+N 1 1 1 1 1 1 1 1 1 10 1
+- 1 1 1 1 1 1 1 1 1 1 1