# MMLSUM Exp_Change = 0.8 log odds matrix (in 1/4-bit units) # Default Gap-open = 17.0858 # Default Gap-extn = 1.4437 # Notes: Matrix derived from MMLSUM (t = 203) 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 4.4421 -1.0140 -1.2510 -1.8170 0.1281 -0.3195 -0.4614 0.3774 -1.7220 -1.0390 -1.0792 -0.6800 -0.6583 -2.2047 -0.4928 1.0126 -0.0466 -3.3608 -2.2628 0.0738 R -1.0140 7.3096 0.2228 -0.4700 -3.3916 1.8828 1.0178 -2.5441 1.1948 -3.2859 -2.6104 3.7531 -1.6413 -3.5777 -1.6408 -0.3449 -0.6291 -2.4241 -1.3077 -3.2493 N -1.2510 0.2228 7.1957 3.1668 -3.3181 0.8202 0.6995 0.4547 1.0409 -4.4844 -4.6209 1.0166 -2.9577 -4.1004 -0.9988 1.3517 0.3319 -4.4169 -1.4503 -4.0178 D -1.8170 -0.4700 3.1668 8.1703 -5.4303 0.8615 3.2777 -0.2961 -0.4794 -6.3872 -6.0685 0.7237 -4.4872 -6.0701 -0.8562 0.6960 -0.3244 -5.8244 -3.7954 -5.6126 C 0.1281 -3.3916 -3.3181 -5.4303 16.6552 -3.8456 -5.1003 -4.0528 -2.6213 -0.6332 -0.3154 -4.5327 -0.4629 -0.3090 -4.5099 -0.4688 -1.2579 -1.8362 -1.0953 0.0833 Q -0.3195 1.8828 0.8202 0.8615 -3.8456 5.9062 2.7360 -2.2634 1.4338 -3.3187 -2.6390 2.1625 -0.9645 -3.5466 -0.8354 0.2958 0.0469 -3.5158 -1.5897 -2.7734 E -0.4614 1.0178 0.6995 3.2777 -5.1003 2.7360 6.2459 -2.1912 -0.2701 -4.4530 -4.2115 1.9547 -2.7870 -5.0816 -0.6042 0.1988 -0.1662 -5.1805 -3.0836 -3.5406 G 0.3774 -2.5441 0.4547 -0.2961 -4.0528 -2.2634 -2.1912 9.3096 -2.2348 -5.8921 -5.5233 -2.0651 -4.1693 -4.8375 -1.4452 0.4044 -1.6817 -5.5302 -4.4686 -4.9756 H -1.7220 1.1948 1.0409 -0.4794 -2.6213 1.4338 -0.2701 -2.2348 11.3318 -3.6101 -2.7618 0.3183 -2.0611 -1.0485 -2.2206 -0.6463 -1.1349 -0.5828 2.3457 -3.3143 I -1.0390 -3.2859 -4.4844 -6.3872 -0.6332 -3.3187 -4.4530 -5.8921 -3.6101 5.9694 3.4436 -3.6259 2.5229 1.4428 -3.5649 -3.1110 -1.2086 -1.8102 -1.3629 4.3142 L -1.0792 -2.6104 -4.6209 -6.0685 -0.3154 -2.6390 -4.2115 -5.5233 -2.7618 3.4436 5.7274 -3.4704 3.3962 2.4123 -3.9023 -3.3413 -1.8974 -0.6108 -0.5675 2.3156 K -0.6800 3.7531 1.0166 0.7237 -4.5327 2.1625 1.9547 -2.0651 0.3183 -3.6259 -3.4704 5.9232 -2.0235 -4.5659 -0.5653 0.1386 -0.0152 -4.5788 -2.5953 -3.4403 M -0.6583 -1.6413 -2.9577 -4.4872 -0.4629 -0.9645 -2.7870 -4.1693 -2.0611 2.5229 3.3962 -2.0235 7.9648 1.5268 -3.6639 -1.8670 -1.0164 -0.2121 -0.0476 1.3271 F -2.2047 -3.5777 -4.1004 -6.0701 -0.3090 -3.5466 -5.0816 -4.8375 -1.0485 1.4428 2.4123 -4.5659 1.5268 8.8866 -3.8125 -3.2489 -2.3115 3.4611 4.8558 0.5970 P -0.4928 -1.6408 -0.9988 -0.8562 -4.5099 -0.8354 -0.6042 -1.4452 -2.2206 -3.5649 -3.9023 -0.5653 -3.6639 -3.8125 11.3397 -0.0986 -0.9419 -4.9373 -3.3579 -2.6059 S 1.0126 -0.3449 1.3517 0.6960 -0.4688 0.2958 0.1988 0.4044 -0.6463 -3.1110 -3.3413 0.1386 -1.8670 -3.2489 -0.0986 4.3900 2.1565 -3.7640 -2.2121 -2.2408 T -0.0466 -0.6291 0.3319 -0.3244 -1.2579 0.0469 -0.1662 -1.6817 -1.1349 -1.2086 -1.8974 -0.0152 -1.0164 -2.3115 -0.9419 2.1565 5.2302 -3.0713 -1.7647 -0.2786 W -3.3608 -2.4241 -4.4169 -5.8244 -1.8362 -3.5158 -5.1805 -5.5302 -0.5828 -1.8102 -0.6108 -4.5788 -0.2121 3.4611 -4.9373 -3.7640 -3.0713 17.1345 4.4030 -2.5976 Y -2.2628 -1.3077 -1.4503 -3.7954 -1.0953 -1.5897 -3.0836 -4.4686 2.3457 -1.3629 -0.5675 -2.5953 -0.0476 4.8558 -3.3579 -2.2121 -1.7647 4.4030 9.9157 -1.3575 V 0.0738 -3.2493 -4.0178 -5.6126 0.0833 -2.7734 -3.5406 -4.9756 -3.3143 4.3142 2.3156 -3.4403 1.3271 0.5970 -2.6059 -2.2408 -0.2786 -2.5976 -1.3575 5.4257