!!NA_SCORING_MATRIX_RECT 1.0 Default scoring matrix 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. All mismatches for IUB symbols are -9, making BESTFIT clip off the best fitting segment at the point where the sequences stop being very similar. February 20, 1996 14:35 .. { GAP_CREATE 100 GAP_EXTEND 2 } A C G T U A -.9 0.01 -.9 0.5 0.5 C 0.01 -0.9 1 -.9 -.9 G -.9 1 -.9 0.25 0.25 T 0.5 -.9 0.25 -.9 -0.9 U 0.5 -.9 .25 -.9 -.9