INFERNAL1/a [1.1.5 | Sep 2023] NAME SAM-II ACC RF01726 DESC SAM-II riboswitch aptamer (SAM-II long loop) STATES 184 NODES 54 CLEN 60 W 135 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 9 02:45:43 2024 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/15/rescan/families/RF01726/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 126 EFFN 5.102600 CKSUM 3138906500 NULL 0.000 0.000 0.000 0.000 GA 44.00 TC 44.00 NC 43.90 EFP7GF -13.1795 0.71910 ECMLC 0.60008 -7.58645 2.32116 1600000 458353 0.002618 ECMGC 0.35840 -18.13061 -2.84200 1600000 95878 0.004172 ECMLI 0.56516 -5.87796 3.32342 1600000 217581 0.005515 ECMGI 0.39422 -13.79245 -0.41653 1600000 78004 0.005128 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 135 235 -7.875 -8.082 -0.028 -6.496 IL 1 1 2 1 4 1 23 137 237 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 23 137 237 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - a - - - ML 3 2 3 5 3 1 22 135 235 -8.841 -0.011 -7.495 0.420 -0.242 -0.632 0.228 D 4 2 3 5 3 0 18 133 233 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 22 136 236 -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 21 134 234 -8.841 -0.023 -6.219 0.496 -0.502 -0.616 0.300 D 7 5 3 8 3 0 17 132 232 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 21 135 235 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - a - - - ML 9 8 3 11 3 1 21 133 233 -8.830 -0.059 -4.728 0.862 -0.746 -0.870 0.056 D 10 8 3 11 3 0 16 131 231 -6.355 -1.868 -0.486 IL 11 11 3 11 3 1 20 134 234 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - a - - - ML 12 11 3 14 3 1 20 132 232 -8.783 -0.012 -7.437 0.737 -0.806 -0.856 0.273 D 13 11 3 14 3 0 16 131 231 -6.919 -0.765 -1.310 IL 14 14 3 14 3 1 19 133 233 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - a - - - ML 15 14 3 17 3 1 19 131 231 -4.946 -0.056 -7.506 0.656 -0.184 -0.956 0.040 D 16 14 3 17 3 0 14 130 230 -5.620 -0.734 -1.403 IL 17 17 3 17 3 1 18 132 232 -2.163 -0.455 -4.401 0.000 0.000 0.000 0.000 [ MATR 6 ] - 109 - u - - MR 18 17 3 20 3 1 18 130 230 -9.188 -0.010 -7.506 -0.202 -0.338 -0.571 0.736 D 19 17 3 20 3 0 12 128 228 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 17 131 231 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 108 - u - - MR 21 20 3 23 3 1 18 129 229 -9.188 -0.010 -7.506 -0.452 0.105 -1.175 0.808 D 22 20 3 23 3 0 11 127 227 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 16 130 230 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 107 - u - - MR 24 23 3 26 3 1 17 128 228 -9.188 -0.010 -7.506 0.236 -0.354 -0.749 0.531 D 25 23 3 26 3 0 10 126 226 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 15 129 229 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 106 - a - - MR 27 26 3 29 3 1 16 127 227 -9.188 -0.010 -7.506 0.558 -0.759 -0.405 0.240 D 28 26 3 29 3 0 10 125 225 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 15 128 228 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 105 - u - - MR 30 29 3 32 3 1 15 126 226 -9.188 -0.010 -7.506 0.202 -0.753 -0.688 0.710 D 31 29 3 32 3 0 9 124 224 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 14 127 227 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 104 - G - - MR 33 32 3 35 3 1 14 125 225 -9.188 -0.010 -7.506 -0.423 -1.180 1.094 -0.562 D 34 32 3 35 3 0 8 123 223 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 13 126 226 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 103 - A - - MR 36 35 3 38 3 1 14 124 224 -9.188 -0.010 -7.506 1.373 -1.048 -1.443 -0.842 D 37 35 3 38 3 0 7 122 222 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 12 125 225 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 102 - C - - MR 39 38 3 41 3 1 13 123 223 -9.188 -0.010 -7.506 -0.653 1.257 -2.075 -0.441 D 40 38 3 41 3 0 6 121 221 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 11 124 224 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 101 - g - - MR 42 41 3 44 3 1 12 122 222 -9.188 -0.010 -7.506 0.566 -1.666 0.780 -1.037 D 43 41 3 44 3 0 5 120 220 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 10 123 223 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 100 - A - - MR 45 44 3 47 3 1 11 121 221 -9.188 -0.010 -7.506 1.861 -3.347 -3.104 -2.711 D 46 44 3 47 3 0 5 119 219 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 10 122 222 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 99 - A - - MR 48 47 3 50 3 1 10 120 220 -9.188 -0.010 -7.506 1.920 -4.074 -3.562 -3.776 D 49 47 3 50 3 0 4 118 218 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 9 121 221 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 98 - A - - MR 51 50 3 53 3 1 9 119 219 -9.188 -0.010 -7.506 1.920 -4.074 -3.562 -3.776 D 52 50 3 53 3 0 3 117 217 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 8 120 220 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 97 - U - - MR 54 53 3 56 3 1 9 118 219 -9.188 -0.010 -7.506 -3.120 -2.858 -3.901 1.880 D 55 53 3 56 3 0 3 116 216 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 7 119 219 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 96 - C - - MR 57 56 3 59 3 1 8 117 218 -7.039 -0.019 -7.506 -3.724 1.902 -4.453 -2.819 D 58 56 3 59 3 0 2 115 215 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 7 118 218 -1.974 -0.532 -4.212 0.000 0.000 0.000 0.000 [ MATR 20 ] - 94 - G - - MR 60 59 3 62 3 1 7 116 217 -9.188 -0.010 -7.506 -3.235 -4.646 1.922 -3.977 D 61 59 3 62 3 0 1 114 214 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 6 117 217 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 93 - U - - MR 63 62 3 65 3 1 6 115 216 -9.188 -0.010 -7.506 -1.147 -1.441 -2.413 1.581 D 64 62 3 65 3 0 1 113 213 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 5 116 216 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 92 - A - - MR 66 65 3 68 3 1 5 114 215 -9.188 -0.010 -7.506 1.012 -1.226 -0.641 -0.128 D 67 65 3 68 3 0 0 112 212 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 4 115 215 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 91 - A - - MR 69 68 3 71 3 1 4 113 214 -9.188 -0.010 -7.506 1.920 -4.074 -3.562 -3.776 D 70 68 3 71 3 0 0 111 211 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 4 114 214 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 90 - A - - MR 72 71 3 74 3 1 4 112 213 -9.188 -0.010 -7.506 1.920 -4.074 -3.562 -3.776 D 73 71 3 74 3 0 0 110 210 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 3 113 213 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 89 - A - - MR 75 74 3 77 3 1 3 111 212 -9.188 -0.065 -4.569 1.828 -3.086 -2.928 -2.327 D 76 74 3 77 3 0 0 110 210 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 2 112 212 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 88 - A - - MR 78 77 3 80 3 1 2 111 211 -9.134 -0.066 -4.547 1.874 -3.464 -3.149 -2.929 D 79 77 3 80 3 0 0 109 209 -7.016 -2.194 -0.370 IR 80 80 3 80 3 1 2 111 211 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 87 - A - - MR 81 80 3 83 3 1 1 110 210 -9.080 -0.429 -1.968 1.710 -1.944 -2.342 -1.877 D 82 80 3 83 3 0 0 109 209 -7.443 -2.620 -0.266 IR 83 83 3 83 3 1 2 110 210 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 86 - A - - MR 84 83 3 86 3 1 1 108 208 -3.450 -0.224 -4.264 1.830 -3.040 -2.607 -2.651 D 85 83 3 86 3 0 0 109 209 -3.046 -0.394 -3.083 IR 86 86 3 86 3 1 2 120 220 -0.266 -2.633 -7.173 0.000 0.000 0.000 0.000 [ MATR 29 ] - 60 - a - - MR 87 86 3 89 3 1 1 56 86 -9.143 -0.011 -7.461 0.858 -1.001 -0.868 0.189 D 88 86 3 89 3 0 0 55 85 -6.932 -0.876 -1.162 IR 89 89 3 89 3 1 1 57 87 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 30 ] - 59 - u - - MR 90 89 3 92 5 1 1 55 85 -7.884 -0.075 -4.828 -6.819 -8.804 0.248 -0.522 -0.459 0.474 D 91 89 3 92 5 0 0 54 84 -5.352 -0.707 -2.978 -4.409 -2.404 IR 92 92 3 92 5 1 1 56 86 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 7 58 a u - - MP 93 92 3 97 6 2 2 54 84 -9.503 -9.442 -0.016 -8.219 -8.498 -8.893 -0.505 -1.423 -0.680 1.617 -1.694 -2.693 1.543 -1.242 -1.555 0.822 -2.482 -0.492 1.413 -1.747 -0.019 -1.041 ML 94 92 3 97 6 1 1 53 83 -6.661 -7.007 -0.860 -1.416 -6.857 -4.386 0.921 -0.791 -0.527 -0.262 MR 95 92 3 97 6 1 1 53 83 -7.050 -5.779 -1.503 -5.757 -0.891 -3.971 0.549 -0.510 -0.217 -0.038 D 96 92 3 97 6 0 0 50 80 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 6 1 1 54 84 -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 54 84 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 32 ] 8 57 G C - - MP 99 98 6 103 6 2 2 52 82 -9.534 -9.473 -0.016 -8.250 -8.529 -8.924 -5.969 -3.769 -6.260 -0.230 -7.128 -5.273 -2.122 -6.579 -5.134 3.815 -5.412 -1.519 -2.430 -5.314 -4.241 -5.119 ML 100 98 6 103 6 1 1 51 81 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 101 98 6 103 6 1 1 51 81 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 102 98 6 103 6 0 0 48 78 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 103 103 5 103 6 1 1 52 82 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 104 104 6 104 5 1 1 52 82 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 33 ] 9 56 a u - - MP 105 104 6 109 6 2 2 50 80 -9.534 -9.473 -0.016 -8.250 -8.529 -8.924 -3.431 -2.981 -3.534 2.503 -3.391 -4.497 0.812 -3.644 -3.520 1.162 -4.055 -0.207 2.033 -3.748 -1.135 -2.485 ML 106 104 6 109 6 1 1 49 79 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 107 104 6 109 6 1 1 49 79 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 108 104 6 109 6 0 0 46 76 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 109 109 5 109 6 1 1 50 80 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 110 110 6 110 5 1 1 50 80 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 10 55 G C - - MP 111 110 6 115 6 2 2 48 79 -9.534 -9.473 -0.016 -8.250 -8.529 -8.924 -6.379 -3.909 -6.864 -0.984 -7.459 -5.298 -2.423 -7.064 -5.260 3.868 -5.514 -1.710 -2.784 -5.493 -4.588 -5.720 ML 112 110 6 115 6 1 1 47 77 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 113 110 6 115 6 1 1 47 77 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 114 110 6 115 6 0 0 45 75 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 115 115 5 115 6 1 1 48 78 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 116 116 6 116 5 1 1 48 78 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 11 54 G C - - MP 117 116 6 121 4 2 2 46 77 -7.875 -4.117 -0.109 -6.496 -6.379 -3.909 -6.864 -0.984 -7.459 -5.298 -2.423 -7.064 -5.260 3.868 -5.514 -1.710 -2.784 -5.493 -4.588 -5.720 ML 118 116 6 121 4 1 1 46 76 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 119 116 6 121 4 1 1 45 75 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 120 116 6 121 4 0 0 44 74 -4.568 -4.250 -2.265 -0.520 IL 121 121 5 121 4 1 1 47 77 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 122 122 6 122 3 1 1 46 76 -1.730 -0.617 -4.430 0.000 0.000 0.000 0.000 [ MATL 36 ] 12 - A - - - ML 123 122 6 125 3 1 1 44 74 -8.841 -0.021 -6.311 1.920 -4.074 -3.562 -3.776 D 124 122 6 125 3 0 0 42 72 -6.174 -1.687 -0.566 IL 125 125 3 125 3 1 1 45 75 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 13 - a - - - ML 126 125 3 128 3 1 1 43 73 -8.831 -0.011 -7.485 0.885 -0.714 -0.612 -0.168 D 127 125 3 128 3 0 0 42 72 -6.337 -1.380 -0.729 IL 128 128 3 128 3 1 1 44 74 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 14 - a - - - ML 129 128 3 131 3 1 1 42 72 -8.841 -0.011 -7.495 0.589 -0.797 0.220 -0.406 D 130 128 3 131 3 0 0 41 71 -6.174 -1.687 -0.566 IL 131 131 3 131 3 1 1 43 73 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 39 ] 15 - G - - - ML 132 131 3 134 3 1 1 41 71 -9.188 -0.010 -7.506 -0.851 -3.106 1.661 -2.589 D 133 131 3 134 3 0 0 40 70 -5.620 -0.734 -1.403 IL 134 134 3 134 3 1 1 42 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 40 ] - 52 - A - - MR 135 134 3 137 3 1 1 40 70 -5.553 -0.039 -7.506 1.882 -3.662 -2.839 -3.393 D 136 134 3 137 3 0 0 38 68 -6.390 -1.568 -0.620 IR 137 137 3 137 3 1 1 41 71 -2.081 -0.487 -4.320 0.000 0.000 0.000 0.000 [ MATR 41 ] - 50 - A - - MR 138 137 3 140 3 1 1 39 69 -9.188 -0.010 -7.506 1.828 -3.287 -2.172 -3.005 D 139 137 3 140 3 0 0 37 67 -6.390 -1.568 -0.620 IR 140 140 3 140 3 1 1 40 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 42 ] - 49 - C - - MR 141 140 3 143 3 1 1 38 68 -9.188 -0.010 -7.506 -3.724 1.902 -4.453 -2.819 D 142 140 3 143 3 0 0 36 66 -6.390 -1.568 -0.620 IR 143 143 3 143 3 1 1 39 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 43 ] - 48 - G - - MR 144 143 3 146 3 1 1 37 67 -9.188 -0.010 -7.506 -3.235 -4.646 1.922 -3.977 D 145 143 3 146 3 0 0 35 66 -6.390 -1.568 -0.620 IR 146 146 3 146 3 1 1 38 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 44 ] - 47 - U - - MR 147 146 3 149 5 1 1 36 66 -7.884 -0.022 -7.700 -7.912 -8.804 -3.120 -2.858 -3.901 1.880 D 148 146 3 149 5 0 0 35 65 -5.352 -0.707 -2.978 -4.409 -2.404 IR 149 149 3 149 5 1 1 36 66 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 16 46 A U - - MP 150 149 3 154 6 2 2 35 65 -9.534 -9.473 -0.016 -8.250 -8.529 -8.924 -5.459 -4.205 -5.168 3.842 -6.562 -7.861 -2.171 -5.106 -5.226 -0.750 -5.841 -1.506 -2.547 -6.663 -4.091 -4.062 ML 151 149 3 154 6 1 1 34 64 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 152 149 3 154 6 1 1 33 63 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 153 149 3 154 6 0 0 31 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 154 154 5 154 6 1 1 35 65 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 155 155 6 155 5 1 1 34 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 46 ] 17 45 U A - - MP 156 155 6 160 6 2 2 33 63 -9.534 -9.473 -0.016 -8.250 -8.529 -8.924 -4.107 -4.118 -4.029 -0.612 -3.124 -4.627 1.065 -3.797 -4.062 -0.494 -4.467 -2.266 3.031 1.579 -0.890 -3.019 ML 157 155 6 160 6 1 1 32 62 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 158 155 6 160 6 1 1 31 61 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 159 155 6 160 6 0 0 29 59 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 160 160 5 160 6 1 1 33 63 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 161 161 6 161 5 1 1 32 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 47 ] 18 44 U G - - MP 162 161 6 166 4 2 2 31 61 -7.875 -2.225 -0.376 -6.496 -5.423 -5.340 -4.926 -1.601 -3.462 -5.229 0.836 -4.294 -4.970 -1.605 -5.179 -3.277 -0.122 -5.437 3.564 -1.401 ML 163 161 6 166 4 1 1 29 59 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 164 161 6 166 4 1 1 29 59 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 165 161 6 166 4 0 0 28 58 -4.568 -4.250 -2.265 -0.520 IL 166 166 5 166 4 1 1 31 62 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 167 167 6 167 3 1 1 32 62 -0.885 -1.181 -5.846 0.000 0.000 0.000 0.000 [ MATL 48 ] 19 - U - - - ML 168 167 6 170 3 1 1 17 35 -8.841 -0.011 -7.495 -3.120 -2.858 -3.901 1.880 D 169 167 6 170 3 0 0 17 35 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 49 ] 20 - G - - - ML 171 170 3 173 3 1 1 16 34 -8.841 -0.011 -7.495 -3.235 -4.646 1.922 -3.977 D 172 170 3 173 3 0 0 16 34 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 50 ] 21 - A - - - ML 174 173 3 176 3 1 1 14 33 -8.841 -0.011 -7.495 1.374 -1.513 -1.073 -0.781 D 175 173 3 176 3 0 0 15 33 -6.174 -1.687 -0.566 IL 176 176 3 176 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 51 ] 22 - C - - - ML 177 176 3 179 3 1 1 12 31 -8.841 -0.011 -7.495 -0.605 1.059 -0.782 -0.562 D 178 176 3 179 3 0 0 13 32 -6.174 -1.687 -0.566 IL 179 179 3 179 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 52 ] 23 - U - - - ML 180 179 3 182 2 1 1 1 1 * 0.000 -1.321 -0.914 -2.367 1.524 D 181 179 3 182 2 0 0 0 0 * 0.000 IL 182 182 3 182 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 53 ] - - - - - - E 183 182 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SAM-II ACC RF01726 DESC SAM-II riboswitch aptamer (SAM-II long loop) LENG 60 MAXL 208 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 9 02:45:43 2024 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/15/rescan/families/RF01726/CM NSEQ 126 EFFN 6.317688 CKSUM 3138906500 STATS LOCAL MSV -7.7822 0.71910 STATS LOCAL VITERBI -8.6596 0.71910 STATS LOCAL FORWARD -4.1265 0.71910 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.02097 1.70798 1.53572 1.41378 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 0.00000 * 1 1.08583 1.55093 1.83816 1.23369 1 a - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 2 1.03027 1.74858 1.82699 1.17709 2 a - - : 1.38629 1.38629 1.38629 1.38629 0.02850 4.62214 4.00287 1.46634 0.26236 1.09861 0.40547 3 0.76452 1.93271 2.02278 1.35712 3 a - - : 1.38629 1.38629 1.38629 1.38629 0.05578 4.61367 3.11601 1.46634 0.26236 1.35004 0.30007 4 0.85335 1.98437 2.01162 1.19476 4 a - - : 1.38629 1.38629 1.38629 1.38629 0.02075 4.57865 4.57865 1.46634 0.26236 0.31869 1.29866 5 0.91323 1.50506 2.08794 1.37504 5 a - - : 1.38629 1.38629 1.38629 1.38629 0.06105 3.12448 4.18218 0.39962 1.11041 1.09861 0.40547 6 1.14411 1.45771 1.71686 1.31270 7 a - - < 1.38629 1.38629 1.38629 1.38629 0.01997 4.61669 4.61669 1.46634 0.26236 0.82773 0.57454 7 2.84378 4.10855 0.09781 3.98780 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 8 0.89744 2.29333 1.69294 1.17934 9 a - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 9 3.39763 4.36326 0.06149 4.30908 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 10 3.40837 4.38073 0.06054 4.33262 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 11 0.04226 4.48288 4.11482 4.28686 12 A - - - 1.38629 1.38629 1.38629 1.38629 0.02758 4.62214 4.05276 1.46634 0.26236 1.09861 0.40547 12 0.74872 1.90305 1.82656 1.52809 13 a - - - 1.38629 1.38629 1.38629 1.38629 0.02001 4.61457 4.61457 1.46634 0.26236 0.75694 0.63318 13 0.96425 1.96156 1.20988 1.71558 14 a - - - 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 14 2.02114 3.72818 0.21148 3.37920 15 G - - - 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 15 0.07851 4.36109 3.04077 4.20322 16 A - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 16 3.33489 2.13635 3.16049 0.21829 17 U - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 17 3.80341 2.27426 3.68083 0.16295 18 U - - < 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 18 3.81567 3.60187 4.36181 0.06406 19 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 19 3.86872 4.87115 0.04192 4.38154 20 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 20 0.39792 2.52796 2.18473 1.99541 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 21 1.87683 0.60118 1.94199 1.86213 22 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 22 2.42199 2.07159 3.20708 0.29465 23 U - - _ 1.38629 1.38629 1.38629 1.38629 0.26895 1.48727 4.62214 0.98081 0.47002 1.09861 0.40547 23 2.87445 3.88320 0.13514 3.00834 44 G - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 24 0.56394 1.39787 1.97426 3.10003 45 A - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 25 4.45046 3.45879 4.18267 0.06017 46 U - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 26 3.81567 3.60187 4.36181 0.06406 47 U - - - 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 27 3.86872 4.87115 0.04192 4.38154 48 G - - - 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 28 4.24271 0.05204 4.70550 3.60097 49 C - - - 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 29 0.10043 3.87701 2.98820 3.71077 50 A - - - 1.38629 1.38629 1.38629 1.38629 0.04230 3.45518 4.62214 0.53719 0.87801 1.09861 0.40547 30 0.06589 4.15765 3.51657 3.99420 52 A - - - 1.38629 1.38629 1.38629 1.38629 0.07811 2.72866 4.62214 0.27793 1.41615 1.09861 0.40547 31 4.44959 0.07347 4.26828 3.09786 54 C - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 32 4.44573 0.07358 4.26616 3.09715 55 C - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 33 1.25005 2.00046 2.12073 0.78025 56 u - - > 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 34 4.24546 0.10716 4.06644 2.65708 57 C - - > 1.38629 1.38629 1.38629 1.38629 0.05632 4.62214 3.10270 1.46634 0.26236 1.09861 0.40547 35 1.37215 1.85267 1.23048 1.21245 58 u - - > 1.38629 1.38629 1.38629 1.38629 0.02059 4.58641 4.58641 1.46634 0.26236 0.36302 1.18931 36 1.21289 1.76645 1.70649 1.04919 59 u - - : 1.38629 1.38629 1.38629 1.38629 0.05529 4.62214 3.12448 1.46634 0.26236 1.09861 0.40547 37 0.76601 2.13760 2.02262 1.25566 60 a - - : 1.38629 1.38629 1.38629 1.38629 0.58173 2.02338 1.17486 2.36920 0.09823 0.36970 1.17422 38 0.08891 3.76065 3.43734 3.51818 86 A - - : 1.38629 1.38629 1.38629 1.38629 0.08402 4.28177 2.70649 1.46634 0.26236 0.21816 1.62962 39 0.17512 2.80742 3.18683 2.83061 87 A - - : 1.38629 1.38629 1.38629 1.38629 0.02161 4.53839 4.53839 1.46634 0.26236 0.79703 0.59905 40 0.07018 4.00846 3.79919 3.60359 88 A - - : 1.38629 1.38629 1.38629 1.38629 0.02071 4.58062 4.58062 1.46634 0.26236 0.32883 1.27212 41 0.09944 3.72048 3.63053 3.12522 89 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 42 0.04226 4.48288 4.11482 4.28686 90 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 43 0.04226 4.48288 4.11482 4.28686 91 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 44 0.65569 2.31177 1.85123 1.49261 92 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 45 2.26783 2.49399 3.24244 0.25513 93 U - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 46 3.86872 4.87115 0.04192 4.38154 94 G - - : 1.38629 1.38629 1.38629 1.38629 0.02655 4.11214 4.62214 0.94805 0.49020 1.09861 0.40547 47 4.24271 0.05204 4.70550 3.60097 96 C - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 48 3.81567 3.60187 4.36181 0.06406 97 U - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 49 0.04226 4.48288 4.11482 4.28686 98 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 50 0.04226 4.48288 4.11482 4.28686 99 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 51 0.07896 3.91378 3.76082 3.42059 100 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 52 0.98655 2.65300 0.80370 2.21614 101 g - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 53 1.89009 0.47134 2.96457 1.75335 102 C - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 54 0.39716 2.15289 2.48153 2.05565 103 A - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 55 1.73793 2.25953 0.57990 1.83405 104 G - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 56 1.24400 1.94787 1.87611 0.87705 105 u - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 57 0.98513 1.94596 1.66944 1.21940 106 a - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 58 1.21994 1.63946 1.92345 1.00905 107 u - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 59 1.74465 1.29428 2.24404 0.80930 108 u - - : 1.38629 1.38629 1.38629 1.38629 0.01986 4.62214 4.62214 1.46634 0.26236 1.09861 0.40547 60 1.55213 1.62644 1.78244 0.85956 109 u - - : 1.38629 1.38629 1.38629 1.38629 0.00998 4.61226 * 1.46634 0.26236 0.00000 * //