# MMLSUM Exp_Change = 0.7 log odds matrix (in 1/4-bit units) # Default Gap-open = 19.3514 # Default Gap-extn = 2.1146 # Notes: Matrix derived from MMLSUM (t = 140) 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 6.9070 -1.9699 -2.4584 -3.3241 -0.3981 -0.8509 -1.0771 -0.1276 -2.9589 -2.1154 -1.9544 -1.4559 -1.2840 -3.5745 -1.2401 1.1324 -0.6395 -4.9474 -3.5743 -0.2001 R -1.9699 10.0646 -0.5002 -1.7270 -4.9431 1.9001 0.4786 -4.1220 0.9096 -4.8524 -3.7603 4.3833 -2.5296 -5.4198 -3.0067 -1.1560 -1.5493 -3.5270 -2.1420 -4.9691 N -2.4584 -0.5002 10.1634 3.3551 -4.8360 0.4730 -0.1044 -0.2029 0.8034 -6.3330 -6.7317 0.6901 -4.2690 -5.8976 -2.1152 1.3691 -0.1071 -6.3381 -2.1627 -5.8997 D -3.3241 -1.7270 3.3551 10.5031 -7.8364 0.1730 3.4459 -1.2920 -1.5010 -9.1856 -8.6007 -0.0295 -6.6186 -8.5259 -1.9865 0.2062 -1.1846 -8.0044 -5.6201 -8.2716 C -0.3981 -4.9431 -4.8360 -7.8364 18.9060 -5.8592 -7.7172 -5.9295 -3.9553 -1.8867 -1.3196 -6.8721 -1.3914 -1.2710 -6.6799 -0.9838 -2.2768 -3.2078 -2.1877 -0.7343 Q -0.8509 1.9001 0.4730 0.1730 -5.8592 9.2041 3.1899 -3.8587 1.4504 -5.0804 -3.7992 2.3420 -1.1764 -5.3409 -1.8163 -0.1510 -0.4549 -5.0793 -2.4979 -4.1931 E -1.0771 0.4786 -0.1044 3.4459 -7.7172 3.1899 8.7512 -3.8725 -1.1877 -6.5088 -6.0708 1.8775 -4.1276 -7.4179 -1.5816 -0.4839 -0.8811 -7.3512 -4.6288 -5.0882 G -0.1276 -4.1220 -0.2029 -1.2920 -5.9295 -3.8587 -3.8725 10.9591 -3.6157 -8.3501 -7.7228 -3.5535 -5.8863 -6.5637 -2.7065 -0.1900 -3.0117 -7.5095 -6.4131 -7.1569 H -2.9589 0.9096 0.8034 -1.5010 -3.9553 1.4504 -1.1877 -3.6157 14.2999 -5.4829 -4.1418 -0.3630 -3.2978 -2.0165 -3.6615 -1.4867 -2.2116 -1.5507 2.4070 -5.0269 I -2.1154 -4.8524 -6.3330 -9.1856 -1.8867 -5.0804 -6.5088 -8.3501 -5.4829 8.1940 3.5528 -5.1740 2.5499 0.8680 -5.2133 -4.7657 -2.1382 -3.3311 -2.8580 4.9654 L -1.9544 -3.7603 -6.7317 -8.6007 -1.3196 -3.7992 -6.0708 -7.7228 -4.1418 3.5528 7.6418 -5.0677 3.8185 2.2187 -5.6744 -5.1500 -3.1637 -1.7593 -1.7609 1.9661 K -1.4559 4.3833 0.6901 -0.0295 -6.8721 2.3420 1.8775 -3.5535 -0.3630 -5.1740 -5.0677 8.5728 -2.9720 -6.8199 -1.4469 -0.4874 -0.5721 -6.6542 -4.0566 -5.2181 M -1.2840 -2.5296 -4.2690 -6.6186 -1.3914 -1.1764 -4.1276 -5.8863 -3.2978 2.5499 3.8185 -2.9720 11.7466 1.1284 -5.5884 -2.7772 -1.7483 -1.0478 -0.7370 0.7020 F -3.5745 -5.4198 -5.8976 -8.5259 -1.2710 -5.3409 -7.4179 -6.5637 -2.0165 0.8680 2.2187 -6.8199 1.1284 11.4137 -5.3887 -4.7500 -3.6332 3.0708 5.2187 -0.2568 P -1.2401 -3.0067 -2.1152 -1.9865 -6.6799 -1.8163 -1.5816 -2.7065 -3.6615 -5.2133 -5.6744 -1.4469 -5.5884 -5.3887 13.4656 -0.7676 -1.9468 -6.9009 -4.9359 -3.8408 S 1.1324 -1.1560 1.3691 0.2062 -0.9838 -0.1510 -0.4839 -0.1900 -1.4867 -4.7657 -5.1500 -0.4874 -2.7772 -4.7500 -0.7676 7.0899 2.7565 -5.3867 -3.4072 -3.5588 T -0.6395 -1.5493 -0.1071 -1.1846 -2.2768 -0.4549 -0.8811 -3.0117 -2.2116 -2.1382 -3.1637 -0.5721 -1.7483 -3.6332 -1.9468 2.7565 8.0365 -4.5065 -2.8314 -0.6030 W -4.9474 -3.5270 -6.3381 -8.0044 -3.2078 -5.0793 -7.3512 -7.5095 -1.5507 -3.3311 -1.7593 -6.6542 -1.0478 3.0708 -6.9009 -5.3867 -4.5065 19.1650 4.1671 -4.4264 Y -3.5743 -2.1420 -2.1627 -5.6201 -2.1877 -2.4979 -4.6288 -6.4131 2.4070 -2.8580 -1.7609 -4.0566 -0.7370 5.2187 -4.9359 -3.4072 -2.8314 4.1671 12.4542 -2.5890 V -0.2001 -4.9691 -5.8997 -8.2716 -0.7343 -4.1931 -5.0882 -7.1569 -5.0269 4.9654 1.9661 -5.2181 0.7020 -0.2568 -3.8408 -3.5588 -0.6030 -4.4264 -2.5890 7.5209