INFERNAL1/a [1.1.4 | Dec 2020] NAME GP_knot1 ACC RF01073 DESC Gag/pol translational readthrough site STATES 190 NODES 53 CLEN 62 W 77 ALPH RNA RF no CONS yes MAP yes DATE Wed Sep 14 16:32:59 2022 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/14.9/3Dfams/RF01073_Gag-pol_translational_readthrough_site/CM PBEGIN 0.05 PEND 0.05 WBETA 1e-07 QDBBETA1 1e-07 QDBBETA2 1e-15 N2OMEGA 1.52588e-05 N3OMEGA 1.52588e-05 ELSELF -0.08926734 NSEQ 8 EFFN 2.800781 CKSUM 239607544 NULL 0.000 0.000 0.000 0.000 GA 67.70 TC 67.70 NC 67.60 EFP7GF -11.3476 0.71908 ECMLC 0.61393 -8.13528 2.22654 1600000 694860 0.001727 ECMGC 0.37375 -22.09691 -6.39302 1600000 141596 0.002825 ECMLI 0.62551 -5.47554 3.85595 1600000 411274 0.002918 ECMGI 0.41002 -16.42044 -3.23115 1600000 89261 0.004481 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 77 96 -7.267 -7.474 -0.155 -3.476 IL 1 1 2 1 4 1 21 81 101 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 21 80 100 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - U - - - ML 3 2 3 5 3 1 20 77 96 -8.160 -0.018 -6.814 -1.855 -1.788 -2.605 1.709 D 4 2 3 5 3 0 16 75 95 -7.007 -2.520 -0.290 IL 5 5 3 5 3 1 20 79 99 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - A - - - ML 6 5 3 8 3 1 19 76 95 -8.160 -0.018 -6.814 1.792 -2.769 -2.361 -2.351 D 7 5 3 8 3 0 16 74 94 -7.007 -2.520 -0.290 IL 8 8 3 8 3 1 19 78 98 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - G - - - ML 9 8 3 11 3 1 18 75 94 -8.160 -0.018 -6.814 -1.993 -3.273 1.802 -2.660 D 10 8 3 11 3 0 15 74 93 -7.007 -0.706 -1.399 IL 11 11 3 11 3 1 18 77 97 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 17 74 93 -8.263 -0.017 -6.917 -2.203 -3.509 1.832 -2.894 D 13 11 3 14 3 0 14 73 92 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 17 76 96 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - G - - - ML 15 14 3 17 3 1 16 73 92 -8.263 -0.017 -6.917 -0.656 -2.406 1.535 -1.839 D 16 14 3 17 3 0 13 71 91 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 16 75 94 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - g - - - ML 18 17 3 20 3 1 15 72 91 -8.263 -0.017 -6.917 0.430 -1.779 0.946 -1.201 D 19 17 3 20 3 0 13 70 90 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 15 74 93 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - a - - - ML 21 20 3 23 3 1 14 71 90 -8.635 -0.247 -2.690 0.681 -1.140 0.123 -0.229 D 22 20 3 23 3 0 12 70 89 -5.620 -0.734 -1.403 IL 23 23 3 23 3 1 15 72 91 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 63 - A - - MR 24 23 3 26 3 1 14 70 89 -8.406 -0.018 -6.724 1.742 -2.483 -2.104 -2.036 D 25 23 3 26 3 0 10 68 88 -7.704 -0.447 -1.934 IR 26 26 3 26 3 1 14 71 90 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 62 - C - - MR 27 26 3 29 3 1 14 69 88 -8.635 -0.015 -6.953 -0.024 1.002 -1.625 -0.536 D 28 26 3 29 3 0 8 67 86 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 13 70 89 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 61 - G - - MR 30 29 3 32 3 1 13 68 87 -8.635 -0.015 -6.953 -2.203 -3.509 1.832 -2.894 D 31 29 3 32 3 0 7 66 85 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 12 69 88 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 60 - G - - MR 33 32 3 35 3 1 12 67 86 -8.635 -0.015 -6.953 -2.203 -3.509 1.832 -2.894 D 34 32 3 35 3 0 6 65 84 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 11 68 87 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 59 - G - - MR 36 35 3 38 3 1 11 66 85 -8.635 -0.015 -6.953 -0.695 -2.433 1.547 -1.865 D 37 35 3 38 3 0 5 64 83 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 10 67 86 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 58 - G - - MR 39 38 3 41 3 1 10 65 84 -8.635 -0.015 -6.953 -2.203 -3.509 1.832 -2.894 D 40 38 3 41 3 0 4 63 82 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 9 66 85 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 57 - g - - MR 42 41 3 44 3 1 10 64 83 -8.635 -0.015 -6.953 0.490 -1.756 0.893 -1.178 D 43 41 3 44 3 0 3 62 81 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 8 64 84 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 56 - G - - MR 45 44 3 47 3 1 9 63 82 -8.635 -0.015 -6.953 -2.203 -3.509 1.832 -2.894 D 46 44 3 47 3 0 3 61 80 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 7 63 83 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 55 - a - - MR 48 47 3 50 3 1 8 62 81 -8.635 -0.015 -6.953 0.410 -0.653 0.149 -0.109 D 49 47 3 50 3 0 2 60 79 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 7 62 82 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 54 - U - - MR 51 50 3 53 3 1 7 61 80 -8.635 -0.015 -6.953 -2.052 -1.952 -2.809 1.748 D 52 50 3 53 3 0 1 59 78 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 6 61 81 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 53 - G - - MR 54 53 3 56 3 1 7 60 79 -8.635 -0.015 -6.953 -0.656 -2.406 1.535 -1.839 D 55 53 3 56 3 0 1 58 77 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 5 60 80 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 52 - a - - MR 57 56 3 59 3 1 6 59 78 -8.635 -0.015 -6.953 0.576 -0.928 -0.568 0.389 D 58 56 3 59 3 0 0 57 76 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 4 59 79 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 51 - a - - MR 60 59 3 62 3 1 5 58 77 -8.635 -0.015 -6.953 0.923 0.049 -1.311 -0.585 D 61 59 3 62 3 0 0 56 75 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 4 58 78 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 50 - a - - MR 63 62 3 65 3 1 5 57 76 -8.635 -0.015 -6.953 0.832 -1.023 -0.606 0.099 D 64 62 3 65 3 0 0 55 74 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 3 57 77 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 49 - a - - MR 66 65 3 68 3 1 4 56 75 -8.635 -0.015 -6.953 0.202 -0.325 0.123 -0.056 D 67 65 3 68 3 0 0 54 73 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 2 56 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 48 - U - - MR 69 68 3 71 3 1 4 55 74 -8.635 -0.015 -6.953 -2.052 -1.952 -2.809 1.748 D 70 68 3 71 3 0 0 53 72 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 2 55 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 47 - c - - MR 72 71 3 74 3 1 3 54 73 -8.635 -0.015 -6.953 -1.011 0.841 -1.840 0.519 D 73 71 3 74 3 0 0 52 71 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 1 54 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 46 - u - - MR 75 74 3 77 3 1 3 53 72 -8.635 -0.015 -6.953 -0.283 0.166 -1.353 0.735 D 76 74 3 77 3 0 0 51 70 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 1 53 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 45 - C - - MR 78 77 3 80 3 1 2 52 71 -8.635 -0.015 -6.953 -2.473 1.774 -3.302 -1.744 D 79 77 3 80 3 0 0 50 69 -6.390 -1.568 -0.620 IR 80 80 3 80 3 1 1 52 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 44 - A - - MR 81 80 3 83 3 1 2 51 70 -8.635 -0.015 -6.953 1.822 -2.976 -2.549 -2.581 D 82 80 3 83 3 0 0 49 68 -6.390 -1.568 -0.620 IR 83 83 3 83 3 1 1 51 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 43 - A - - MR 84 83 3 86 5 1 1 50 69 -7.357 -0.032 -7.173 -7.385 -8.276 1.822 -2.976 -2.549 -2.581 D 85 83 3 86 5 0 0 48 67 -5.352 -0.707 -2.978 -4.409 -2.404 IR 86 86 3 86 5 1 1 50 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 8 42 G U - - MP 87 86 3 91 6 2 2 49 68 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -4.001 -2.680 -4.191 0.866 -5.211 -5.981 -0.757 -4.175 -3.775 0.834 -4.323 3.394 -1.098 -5.069 -2.694 -2.829 ML 88 86 3 91 6 1 1 47 67 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 89 86 3 91 6 1 1 47 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 3 91 6 0 0 45 64 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 48 67 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 92 92 6 92 5 1 1 48 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 9 41 u a - - MP 93 92 6 97 6 2 2 47 66 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -1.768 -1.945 -0.790 1.041 -1.872 -2.799 1.499 -2.256 -2.014 0.977 -2.581 -0.534 1.875 -0.828 0.691 -1.185 ML 94 92 6 97 6 1 1 46 65 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 6 1 1 46 65 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 96 92 6 97 6 0 0 44 63 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 6 1 1 46 66 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 98 98 6 98 5 1 1 46 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 10 40 C G - - MP 99 98 6 103 4 2 2 45 64 -7.267 -7.474 -0.042 -5.888 -5.212 -5.173 -4.785 -1.358 -3.374 -5.109 3.713 -4.250 -4.864 -1.195 -5.046 -3.137 0.063 -5.235 -1.104 -3.684 ML 100 98 6 103 4 1 1 45 65 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 101 98 6 103 4 1 1 45 64 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 102 98 6 103 4 0 0 44 63 -4.568 -4.250 -2.265 -0.520 IL 103 103 5 103 4 1 1 47 66 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 104 104 6 104 3 1 1 46 65 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 11 - A - - - ML 105 104 6 107 3 1 1 42 61 -8.635 -0.015 -6.953 1.016 -1.672 0.264 -1.112 D 106 104 6 107 3 0 0 41 60 -5.620 -0.734 -1.403 IL 107 107 3 107 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 33 ] - 39 - G - - MR 108 107 3 110 3 1 1 41 60 -8.635 -0.015 -6.953 -2.203 -3.509 1.832 -2.894 D 109 107 3 110 3 0 0 39 58 -6.390 -1.568 -0.620 IR 110 110 3 110 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 34 ] - 38 - A - - MR 111 110 3 113 5 1 1 40 59 -7.357 -0.032 -7.173 -7.385 -8.276 1.441 -1.005 -1.587 -1.140 D 112 110 3 113 5 0 0 39 58 -5.352 -0.707 -2.978 -4.409 -2.404 IR 113 113 3 113 5 1 1 40 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 12 37 G C - - MP 114 113 3 118 6 2 2 39 58 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -4.343 -2.895 -4.365 0.564 -5.211 -4.741 -0.523 -4.764 -4.200 3.391 -4.570 1.000 -0.795 -4.237 -2.523 -3.251 ML 115 113 3 118 6 1 1 38 56 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 116 113 3 118 6 1 1 37 56 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 117 113 3 118 6 0 0 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 118 118 5 118 6 1 1 39 58 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 36 ] 13 36 G C - - MP 120 119 6 124 6 2 2 37 56 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -5.325 -3.377 -5.503 -0.203 -6.048 -4.913 -1.267 -5.770 -4.687 3.751 -4.987 -1.105 -1.638 -4.844 -3.339 -4.371 ML 121 119 6 124 6 1 1 36 54 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 122 119 6 124 6 1 1 35 54 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 123 119 6 124 6 0 0 33 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 37 56 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 36 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 37 ] 14 35 G C - - MP 126 125 6 130 6 2 2 35 54 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -5.325 -3.377 -5.503 -0.203 -6.048 -4.913 -1.267 -5.770 -4.687 3.751 -4.987 -1.105 -1.638 -4.844 -3.339 -4.371 ML 127 125 6 130 6 1 1 34 53 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 128 125 6 130 6 1 1 34 52 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 129 125 6 130 6 0 0 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 35 54 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 131 131 6 131 5 1 1 34 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 38 ] 15 34 c g - - MP 132 131 6 136 4 2 2 33 52 -3.542 -8.405 -0.190 -4.859 -3.733 -3.691 -3.661 0.074 -2.651 -4.289 2.699 -3.340 -3.654 0.263 -4.078 -1.664 2.142 -3.903 0.684 -2.531 ML 133 131 6 136 4 1 1 32 51 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 134 131 6 136 4 1 1 32 51 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 135 131 6 136 4 0 0 30 49 -12.737 -14.007 -2.036 -0.404 IL 136 136 5 136 4 1 1 32 51 -3.238 -4.741 -0.431 -3.120 0.000 0.000 0.000 0.000 IR 137 137 6 137 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 39 ] - 33 - A - - MR 138 137 6 140 5 1 1 31 50 -7.357 -0.032 -7.173 -7.385 -8.276 1.822 -2.976 -2.549 -2.581 D 139 137 6 140 5 0 0 29 48 -5.352 -0.707 -2.978 -4.409 -2.404 IR 140 140 3 140 5 1 1 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 40 ] 17 32 c g - - MP 141 140 3 145 6 2 2 30 49 -9.238 -9.177 -0.074 -4.616 -8.233 -8.628 -4.187 -4.200 -3.954 -0.448 -2.724 -4.416 2.976 -3.499 -3.982 -0.278 -4.310 -2.243 0.847 -4.276 1.924 -2.839 ML 142 140 3 145 6 1 1 28 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 143 140 3 145 6 1 1 28 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 144 140 3 145 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 145 145 5 145 6 1 1 30 48 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 146 146 6 146 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 41 ] 18 31 a u - - MP 147 146 6 151 6 2 2 28 47 -9.184 -9.123 -0.020 -7.899 -8.179 -8.574 -1.880 -1.898 -2.065 1.829 -2.022 -0.223 1.389 -0.830 -2.114 1.279 -2.647 -0.364 1.180 -2.187 -0.165 -1.278 ML 148 146 6 151 6 1 1 27 46 -6.868 -7.214 -0.710 -1.623 -7.064 -4.593 -0.221 -0.517 -0.845 0.916 MR 149 146 6 151 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 150 146 6 151 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 151 151 5 151 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 152 152 6 152 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 19 30 G C - - MP 153 152 6 157 6 2 2 26 45 -9.238 -9.177 -0.019 -7.953 -8.233 -8.628 -4.491 -0.491 -4.520 0.384 -5.270 -4.633 -0.624 -4.973 -4.305 3.536 -4.634 -0.690 -0.902 -4.227 -2.614 -3.460 ML 154 152 6 157 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 155 152 6 157 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 156 152 6 157 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 157 157 5 157 6 1 1 26 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 158 158 6 158 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 20 29 G C - - MP 159 158 6 163 4 2 2 24 43 -7.267 -7.474 -0.042 -5.888 -5.325 -3.377 -5.503 -0.203 -6.048 -4.913 -1.267 -5.770 -4.687 3.751 -4.987 -1.105 -1.638 -4.844 -3.339 -4.371 ML 160 158 6 163 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 161 158 6 163 4 1 1 24 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 162 158 6 163 4 0 0 23 42 -4.568 -4.250 -2.265 -0.520 IL 163 163 5 163 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 164 164 6 164 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 44 ] 21 - A - - - ML 165 164 6 167 3 1 1 21 40 -8.263 -0.017 -6.917 1.822 -2.976 -2.549 -2.581 D 166 164 6 167 3 0 0 20 39 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 45 ] 22 - g - - - ML 168 167 3 170 3 1 1 20 38 -8.263 -0.017 -6.917 -0.538 0.341 0.426 -0.513 D 169 167 3 170 3 0 0 19 38 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 23 - C - - - ML 171 170 3 173 3 1 1 19 37 -8.263 -0.017 -6.917 -2.473 1.774 -3.302 -1.744 D 172 170 3 173 3 0 0 18 37 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 24 - C - - - ML 174 173 3 176 3 1 1 17 36 -8.263 -0.017 -6.917 -2.473 1.774 -3.302 -1.744 D 175 173 3 176 3 0 0 17 36 -6.174 -1.687 -0.566 IL 176 176 3 176 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 48 ] 25 - C - - - ML 177 176 3 179 3 1 1 16 35 -8.263 -0.017 -6.917 -2.473 1.774 -3.302 -1.744 D 178 176 3 179 3 0 0 16 34 -6.174 -1.687 -0.566 IL 179 179 3 179 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 49 ] 26 - C - - - ML 180 179 3 182 3 1 1 15 33 -8.263 -0.017 -6.917 -2.473 1.774 -3.302 -1.744 D 181 179 3 182 3 0 0 15 33 -6.174 -1.687 -0.566 IL 182 182 3 182 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 50 ] 27 - c - - - ML 183 182 3 185 3 1 1 13 31 -8.263 -0.017 -6.917 -1.010 0.837 -1.838 0.524 D 184 182 3 185 3 0 0 13 32 -6.174 -1.687 -0.566 IL 185 185 3 185 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 51 ] 28 - C - - - ML 186 185 3 188 2 1 1 1 1 * 0.000 -2.473 1.774 -3.302 -1.744 D 187 185 3 188 2 0 0 0 0 * 0.000 IL 188 188 3 188 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 52 ] - - - - - - E 189 188 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME GP_knot1 ACC RF01073 DESC Gag/pol translational readthrough site LENG 62 MAXL 142 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Sep 14 16:32:59 2022 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED NSEQ 8 EFFN 3.464844 CKSUM 239607544 STATS LOCAL MSV -8.2833 0.71908 STATS LOCAL VITERBI -8.8626 0.71908 STATS LOCAL FORWARD -3.3070 0.71908 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.49946 1.31982 1.09906 1.73510 1.38629 1.38629 1.38629 1.38629 0.11232 4.14400 2.40369 1.46634 0.26236 0.00000 * 1 2.91594 2.82891 3.44389 0.15685 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.03487 4.06655 4.06655 1.46634 0.26236 2.04111 0.13913 2 0.10976 3.56096 3.25472 3.29836 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.03487 4.06655 4.06655 1.46634 0.26236 2.04111 0.13913 3 3.02326 3.94130 0.10300 3.51310 3 G - - : 1.38629 1.38629 1.38629 1.38629 0.03487 4.06655 4.06655 1.46634 0.26236 0.30079 1.34796 4 3.17045 4.10426 0.08766 3.67147 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 5 1.91784 3.23550 0.27948 2.85495 5 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 6 1.08061 2.76597 0.68363 2.37605 6 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 7 0.89566 2.24459 1.27899 1.57323 7 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 8 2.15242 3.36223 0.21317 3.19117 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 9 1.61919 1.56807 1.69592 0.89145 9 u - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 10 3.69822 0.14571 3.52802 2.50758 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 11 0.64501 2.69297 1.17467 2.31523 11 A - - - 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 12 2.33566 3.16003 0.20852 3.01511 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 13 2.89835 3.71022 0.11157 3.65016 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 14 2.89759 3.70915 0.11169 3.64870 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 15 2.60641 0.83685 2.37619 0.91573 15 c - - < 1.38629 1.38629 1.38629 1.38629 0.12556 2.28143 4.14400 0.28601 1.39131 1.09861 0.40547 16 3.01516 0.64223 2.82907 1.00573 17 C - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 17 1.28363 1.30275 1.56130 1.42162 18 a - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 18 2.05781 3.21271 0.24127 3.07066 19 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 19 2.86607 3.66513 0.11669 3.58941 20 G - - < 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 20 0.09345 3.71324 3.39383 3.46612 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 21 1.86145 1.10413 1.03665 1.84256 22 g - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 22 3.41450 0.11566 3.97628 2.85476 23 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 23 3.41450 0.11566 3.97628 2.85476 24 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 24 3.41450 0.11566 3.97628 2.85476 25 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 25 3.41450 0.11566 3.97628 2.85476 26 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 26 2.21857 0.75405 2.80905 1.02022 27 c - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 27 3.41450 0.11566 3.97628 2.85476 28 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 28 3.80876 0.13514 3.54743 2.58453 29 C - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 29 3.34372 0.21382 3.08034 2.19594 30 C - - > 1.38629 1.38629 1.38629 1.38629 0.12556 4.14400 2.28143 1.46634 0.26236 1.09861 0.40547 30 1.70662 1.43351 1.45051 1.06247 31 u - - > 1.38629 1.38629 1.38629 1.38629 0.03533 4.05377 4.05377 1.46634 0.26236 0.27044 1.43987 31 2.18213 3.00225 0.25263 2.80070 32 G - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 32 0.09345 3.71324 3.39383 3.46612 33 A - - - 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 33 1.19578 2.54767 0.64207 2.37443 34 G - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 34 3.83239 0.13380 3.55888 2.58891 35 C - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 35 3.84100 0.13331 3.56302 2.59048 36 C - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 36 3.25496 0.37423 2.98244 1.50091 37 C - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 37 0.34200 2.12063 2.62925 2.32728 38 A - - - 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 38 3.17045 4.10426 0.08766 3.67147 39 G - - - 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 39 2.79131 3.69723 0.12476 3.46859 40 G - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 40 1.24361 1.71502 1.11857 1.58497 41 g - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 41 3.40735 2.29305 3.15844 0.19429 42 U - - > 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 42 0.09345 3.71324 3.39383 3.46612 43 A - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 43 0.09345 3.71324 3.39383 3.46612 44 A - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 44 3.41450 0.11566 3.97628 2.85476 45 C - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 45 1.61941 1.24194 2.40553 0.86052 46 u - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 46 2.21974 0.75096 2.81049 1.02367 47 c - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 47 3.06335 2.95265 3.59526 0.13512 48 U - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 48 1.25391 1.60573 1.27573 1.44968 49 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 49 0.78253 2.15821 1.82710 1.32299 50 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 50 0.70658 1.32538 2.40296 1.89367 51 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 51 0.96901 2.08657 1.79473 1.10788 52 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 52 1.91784 3.23550 0.27948 2.85495 53 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 53 3.06335 2.95265 3.59526 0.13512 54 U - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 54 1.09870 1.85640 1.25854 1.48549 55 a - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 55 3.17045 4.10426 0.08766 3.67147 56 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 56 1.03472 2.74938 0.72116 2.35894 57 g - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 57 3.17045 4.10426 0.08766 3.67147 58 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 58 1.94820 3.25610 0.27111 2.87533 59 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 59 3.17045 4.10426 0.08766 3.67147 60 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 60 3.17045 4.10426 0.08766 3.67147 61 G - - : 1.38629 1.38629 1.38629 1.38629 0.03223 4.14400 4.14400 1.46634 0.26236 1.09861 0.40547 61 1.42908 0.62605 2.65729 1.86027 62 C - - : 1.38629 1.38629 1.38629 1.38629 0.22320 4.14400 1.69179 1.46634 0.26236 1.09861 0.40547 62 0.13801 3.34649 3.06017 3.06148 63 A - - : 1.38629 1.38629 1.38629 1.38629 0.11742 2.20011 * 1.39569 0.28457 0.00000 * //