Default symbol comparison table used by BESTFIT for the comparison of nucleic acid sequences. BESTFIT uses the method of Smith/Waterman to make alignments.X's and N's are treated as matches to any IUB ambiguity symbol (score = 1.0). All mismatches for IUB symbols are -0.9, making BESTFIT clip off the best fitting segment at the point where the sequences stop being very similar.
A B C D G H K M N R S T U V W X Y ..
1.0 -0.9 -0.9 1.0 -0.9 1.0 -0.9 1.0 1.0 1.0 -0.9 -0.9 -0.9 1.0 1.0 1.0 -0.9 A
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 B
1.0 -0.9 -0.9 1.0 -0.9 1.0 1.0 -0.9 1.0 -0.9 -0.9 1.0 -0.9 1.0 1.0 C
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 D
1.0 -0.9 1.0 -0.9 1.0 1.0 1.0 -0.9 -0.9 1.0 -0.9 1.0 -0.9 G
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 H
1.0 -0.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 K
1.0 1.0 1.0 1.0 -0.9 -0.9 1.0 1.0 1.0 1.0 M
1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 N
1.0 1.0 -0.9 -0.9 1.0 1.0 1.0 -0.9 R
1.0 -0.9 -0.9 1.0 -0.9 1.0 1.0 S
1.0 1.0 -0.9 1.0 1.0 1.0 T
1.0 -0.9 1.0 1.0 1.0 U
1.0 1.0 1.0 1.0 V
1.0 1.0 1.0 W
1.0 1.0 X
1.0 Y