# MMLSUM Exp_Change = 0.9 log odds matrix (in 1/4-bit units) # Default Gap-open = 15 # Default Gap-extn = 1 # Notes: Matrix derived from MMLSUM (t = 373) Markov Matrix # File generated on: 2020/10/02 12:50:15 A R N D C Q E G H I L K M F P S T W Y V A 1 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 -1 -1 0 R 0 3 1 0 -1 1 1 -1 1 -1 -1 2 -1 -1 0 0 0 -1 0 -1 N 0 1 2 2 -1 1 1 1 1 -2 -2 1 -1 -2 0 1 0 -2 -1 -2 D 0 0 2 4 -2 1 2 1 0 -3 -3 1 -2 -3 0 1 0 -3 -2 -2 C 0 -1 -1 -2 11 -1 -2 -2 -1 0 0 -2 0 0 -2 0 0 0 0 1 Q 0 1 1 1 -1 1 1 -1 1 -1 -1 1 -1 -1 0 0 0 -2 -1 -1 E 0 1 1 2 -2 1 2 0 0 -2 -2 1 -1 -2 0 0 0 -2 -1 -2 G 0 -1 1 1 -2 -1 0 6 -1 -3 -3 0 -2 -2 0 1 0 -3 -2 -2 H 0 1 1 0 -1 1 0 -1 5 -1 -1 1 -1 0 -1 0 0 0 1 -1 I 0 -1 -2 -3 0 -1 -2 -3 -1 3 2 -2 2 1 -1 -1 0 0 0 2 L 0 -1 -2 -3 0 -1 -2 -3 -1 2 3 -1 2 2 -2 -1 -1 0 0 2 K 0 2 1 1 -2 1 1 0 1 -2 -1 2 -1 -2 0 0 0 -2 -1 -1 M 0 -1 -1 -2 0 -1 -1 -2 -1 2 2 -1 2 1 -1 -1 0 0 0 1 F -1 -1 -2 -3 0 -1 -2 -2 0 1 2 -2 1 4 -2 -1 -1 3 3 1 P 0 0 0 0 -2 0 0 0 -1 -1 -2 0 -1 -2 6 0 0 -2 -1 -1 S 0 0 1 1 0 0 0 1 0 -1 -1 0 -1 -1 0 1 1 -2 -1 -1 T 0 0 0 0 0 0 0 0 0 0 -1 0 0 -1 0 1 1 -1 -1 0 W -1 -1 -2 -3 0 -2 -2 -3 0 0 0 -2 0 3 -2 -2 -1 12 3 -1 Y -1 0 -1 -2 0 -1 -1 -2 1 0 0 -1 0 3 -1 -1 -1 3 5 0 V 0 -1 -2 -2 1 -1 -2 -2 -1 2 2 -1 1 1 -1 -1 0 -1 0 2