# MMLSUM Exp_Change = 0.9 log odds matrix (in 1/4-bit units) # Default Gap-open = 14.6838 # Default Gap-extn = 0.8198 # 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 1.0177 -0.1825 -0.1897 -0.3525 0.2484 -0.0109 -0.0367 0.4428 -0.4544 -0.1987 -0.2873 -0.0777 -0.1717 -0.7046 0.0268 0.3742 0.1459 -1.3382 -0.7638 0.0522 R -0.1825 2.5567 0.5278 0.4784 -1.3811 1.0334 0.9055 -0.7066 0.8016 -1.3325 -1.1491 1.7281 -0.7013 -1.3801 -0.2652 0.1952 0.0499 -1.0855 -0.4939 -1.2201 N -0.1897 0.5278 2.3561 1.8457 -1.4115 0.6797 0.9065 0.7192 0.6763 -1.9516 -1.9369 0.8046 -1.2879 -1.7948 0.0225 0.7347 0.3312 -1.9443 -0.7189 -1.6609 D -0.3525 0.4784 1.8457 3.7400 -2.2904 0.9363 1.9545 0.5043 0.2847 -2.7310 -2.6493 0.9493 -1.8665 -2.6986 0.1659 0.7087 0.2282 -2.7349 -1.5585 -2.3207 C 0.2484 -1.3811 -1.4115 -2.2904 10.9276 -1.4492 -1.9731 -1.7056 -1.0166 0.4228 0.4828 -1.7314 0.2896 0.4465 -1.7897 -0.1988 -0.3339 -0.3229 -0.0582 0.6015 Q -0.0109 1.0334 0.6797 0.9363 -1.4492 1.4974 1.2961 -0.5225 0.7425 -1.2967 -1.1636 1.1180 -0.6405 -1.3988 0.0175 0.3659 0.2155 -1.5113 -0.6300 -1.0915 E -0.0367 0.9055 0.9065 1.9545 -1.9731 1.2961 2.2926 -0.3796 0.3166 -1.8664 -1.8104 1.2177 -1.1941 -2.1043 0.1938 0.4729 0.2292 -2.2879 -1.2174 -1.5263 G 0.4428 -0.7066 0.7192 0.5043 -1.7056 -0.5225 -0.3796 5.5389 -0.6606 -2.6157 -2.5181 -0.4301 -1.8787 -2.3547 -0.1553 0.5990 -0.3557 -2.7040 -1.9372 -2.1728 H -0.4544 0.8016 0.6763 0.2847 -1.0166 0.7425 0.3166 -0.6606 4.8770 -1.3358 -1.0705 0.5160 -0.7255 -0.2631 -0.6136 0.0066 -0.1753 0.1377 1.2151 -1.2200 I -0.1987 -1.3325 -1.9516 -2.7310 0.4228 -1.2967 -1.8664 -2.6157 -1.3358 2.7329 2.2267 -1.5504 1.6208 1.4030 -1.4951 -1.1947 -0.3875 -0.1401 0.0491 2.3315 L -0.2873 -1.1491 -1.9369 -2.6493 0.4828 -1.1636 -1.8104 -2.5181 -1.0705 2.2267 2.6332 -1.4737 1.8427 1.7538 -1.6300 -1.2643 -0.5886 0.4273 0.3859 1.7565 K -0.0777 1.7281 0.8046 0.9493 -1.7314 1.1180 1.2177 -0.4301 0.5160 -1.5504 -1.4737 1.9788 -0.9103 -1.8052 0.1472 0.3866 0.2232 -1.9451 -0.9619 -1.3504 M -0.1717 -0.7013 -1.2879 -1.8665 0.2896 -0.6405 -1.1941 -1.8787 -0.7255 1.6208 1.8427 -0.9103 2.2359 1.2463 -1.3917 -0.7931 -0.3339 0.4348 0.3875 1.2144 F -0.7046 -1.3801 -1.7948 -2.6986 0.4465 -1.3988 -2.1043 -2.3547 -0.2631 1.4030 1.7538 -1.8052 1.2463 4.0906 -1.6983 -1.3415 -0.8101 2.8242 2.8672 0.9909 P 0.0268 -0.2652 0.0225 0.1659 -1.7897 0.0175 0.1938 -0.1553 -0.6136 -1.4951 -1.6300 0.1472 -1.3917 -1.6983 6.3487 0.2805 -0.0818 -2.2382 -1.3696 -1.1091 S 0.3742 0.1952 0.7347 0.7087 -0.1988 0.3659 0.4729 0.5990 0.0066 -1.1947 -1.2643 0.3866 -0.7931 -1.3415 0.2805 1.0644 0.7104 -1.6454 -0.8597 -0.8708 T 0.1459 0.0499 0.3312 0.2282 -0.3339 0.2155 0.2292 -0.3557 -0.1753 -0.3875 -0.5886 0.2232 -0.3339 -0.8101 -0.0818 0.7104 1.2187 -1.2508 -0.6083 -0.1465 W -1.3382 -1.0855 -1.9443 -2.7349 -0.3229 -1.5113 -2.2879 -2.7040 0.1377 -0.1401 0.4273 -1.9451 0.4348 2.8242 -2.2382 -1.6454 -1.2508 11.9598 3.3731 -0.5233 Y -0.7638 -0.4939 -0.7189 -1.5585 -0.0582 -0.6300 -1.2174 -1.9372 1.2151 0.0491 0.3859 -0.9619 0.3875 2.8672 -1.3696 -0.8597 -0.6083 3.3731 4.6621 -0.0930 V 0.0522 -1.2201 -1.6609 -2.3207 0.6015 -1.0915 -1.5263 -2.1728 -1.2200 2.3315 1.7565 -1.3504 1.2144 0.9909 -1.1091 -0.8708 -0.1465 -0.5233 -0.0930 2.2889