INFERNAL1/a [1.1.5 | Sep 2023] NAME nadA ACC RF03013 DESC nadA riboswitch STATES 190 NODES 41 CLEN 62 W 177 ALPH RNA RF no CONS yes MAP yes DATE Mon Jul 8 00:15:16 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /homes/nancyontiveros/3D_families/3D_release15/RF03013/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 186 EFFN 21.907562 CKSUM 190925323 NULL 0.000 0.000 0.000 0.000 GA 37.50 TC 37.50 NC 37.30 EFP7GF -16.1680 0.72244 ECMLC 0.67088 -5.41550 3.14874 1600000 375380 0.003197 ECMGC 0.45232 -16.66927 -3.51864 1600000 153242 0.002610 ECMLI 0.67689 -4.49353 3.81680 1600000 332780 0.003606 ECMGI 0.49555 -10.87482 0.22091 1600000 97733 0.004093 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 177 298 -10.770 -10.709 -0.020 -9.485 -7.873 -7.108 IL 1 1 2 1 6 1 5 178 300 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 2 2 3 2 5 1 5 178 300 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 128 G C - - MP 3 2 3 7 6 2 9 177 299 -10.756 -10.695 -0.007 -9.472 -9.751 -10.146 -3.489 -1.148 -4.743 0.376 -3.138 -5.339 -0.937 -5.430 -5.179 3.527 -5.427 -0.338 -0.668 -4.598 -2.011 -2.734 ML 4 2 3 7 6 1 3 175 296 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 5 2 3 7 6 1 3 174 296 -7.143 -5.872 -1.346 -5.850 -0.984 -4.064 0.161 0.097 -0.513 0.153 D 6 2 3 7 6 0 0 171 293 -9.473 -8.171 -1.651 -4.650 -4.668 -0.743 IL 7 7 5 7 6 1 4 176 298 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 8 8 6 8 5 1 4 176 298 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 127 g c - - MP 9 8 6 13 6 2 8 175 297 -10.770 -10.709 -0.021 -9.485 -6.484 -10.160 -5.031 -3.944 -4.922 0.006 -5.046 -4.007 2.648 -5.202 -2.985 2.768 -5.495 -0.739 -0.682 -4.861 -2.398 -3.796 ML 10 8 6 13 6 1 3 173 294 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 11 8 6 13 6 1 3 172 294 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 12 8 6 13 6 0 0 168 290 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 6 1 4 174 296 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 4 174 296 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 126 u g - - MP 15 14 6 19 6 2 9 173 295 -10.755 -10.694 -0.012 -7.610 -9.751 -10.146 -7.357 -7.555 -6.743 -3.715 -5.129 -6.932 2.536 -6.028 -6.826 -3.641 -6.978 -5.779 1.749 -7.230 2.711 -5.620 ML 16 14 6 19 6 1 3 171 293 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 17 14 6 19 6 1 2 170 292 -7.438 -6.167 -1.220 -6.145 -1.279 -3.000 0.059 -0.464 -0.201 0.447 D 18 14 6 19 6 0 0 166 288 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 4 172 294 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 4 172 294 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 125 U A - - MP 21 20 6 25 6 2 8 171 293 -10.760 -10.699 -0.011 -7.850 -9.756 -10.151 -10.204 -11.907 -12.126 -10.628 -10.363 -12.034 -9.475 -11.792 -9.496 -10.701 -12.326 -11.367 3.995 -10.423 -5.670 -5.413 ML 22 20 6 25 6 1 2 169 291 -6.457 -6.803 -1.050 -1.212 -6.653 -4.183 0.122 -0.374 -0.466 0.502 MR 23 20 6 25 6 1 2 168 290 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 6 25 6 0 0 165 287 -9.254 -7.952 -2.274 -4.431 -4.449 -0.524 IL 25 25 5 25 6 1 3 170 292 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 3 170 292 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 5 124 u a - - MP 27 26 6 31 6 2 8 169 291 -7.165 -10.705 -0.016 -9.481 -9.761 -10.156 -3.735 -3.744 -3.872 -0.183 -3.516 -4.709 0.528 -2.333 -3.898 1.889 -4.443 -1.946 2.661 -2.407 1.151 -1.625 ML 28 26 6 31 6 1 2 167 289 -6.417 -6.763 -1.094 -1.172 -6.613 -4.142 0.163 -0.367 -0.422 0.442 MR 29 26 6 31 6 1 2 166 288 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 30 26 6 31 6 0 0 163 285 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 3 168 290 -2.840 -3.103 -0.604 -4.758 -5.534 -5.195 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 3 168 290 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 7 123 C G - - MP 33 32 6 37 6 2 7 167 289 -10.770 -10.709 -0.007 -9.485 -9.765 -10.160 -9.622 -9.845 -7.842 -6.215 -6.130 -7.571 3.986 -8.348 -9.169 -6.182 -7.608 -8.249 -4.170 -9.550 -5.147 -7.968 ML 34 32 6 37 6 1 2 165 287 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 6 1 2 165 286 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 36 32 6 37 6 0 0 162 284 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 2 166 288 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 38 38 6 38 5 1 2 166 288 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 8 122 A U - - MP 39 38 6 43 4 2 6 165 287 -9.687 -9.894 -0.008 -8.308 -8.340 -7.128 -6.025 3.978 -9.854 -10.729 -5.778 -5.873 -8.143 -3.778 -8.727 -4.199 -5.956 -9.623 -7.568 -5.702 ML 40 38 6 43 4 1 1 164 286 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 1 163 285 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 42 38 6 43 4 0 0 161 283 -4.568 -4.250 -2.265 -0.520 IL 43 43 5 43 4 1 2 165 287 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 2 164 286 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 9 - A - - - ML 45 44 6 47 3 1 5 163 285 -10.612 -0.003 -9.266 1.986 -6.644 -6.007 -6.198 D 46 44 6 47 3 0 0 160 282 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 163 285 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 10 - C - - - ML 48 47 3 50 3 1 4 162 284 -10.612 -0.003 -9.266 -5.958 1.979 -6.414 -5.065 D 49 47 3 50 3 0 0 159 281 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 162 284 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 11 - A - - - ML 51 50 3 53 3 1 4 161 283 -10.612 -0.003 -9.266 1.986 -6.644 -6.007 -6.198 D 52 50 3 53 3 0 0 158 280 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 161 283 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 12 - U - - - ML 54 53 3 56 3 1 3 160 282 -10.612 -0.003 -9.266 -0.858 -2.633 -3.049 1.663 D 55 53 3 56 3 0 0 157 279 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 160 282 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 13 - C - - - ML 57 56 3 59 3 1 3 159 281 -10.612 -0.003 -9.266 -5.958 1.979 -6.414 -5.065 D 58 56 3 59 3 0 0 156 278 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 159 281 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 14 - C - - - ML 60 59 3 62 3 1 3 158 280 -10.612 -0.003 -9.266 -3.951 1.932 -5.349 -3.402 D 61 59 3 62 3 0 0 155 277 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 158 280 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 15 - C - - - ML 63 62 3 65 3 1 2 157 279 -10.612 -0.003 -9.266 -5.958 1.979 -6.414 -5.065 D 64 62 3 65 3 0 0 154 276 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 157 279 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 16 - C - - - ML 66 65 3 68 5 1 2 156 278 -9.578 -0.007 -9.394 -9.606 -10.497 -5.532 1.957 -5.952 -3.630 D 67 65 3 68 5 0 0 154 275 -4.959 -0.803 -4.221 -2.596 -2.508 IL 68 68 3 68 5 1 1 156 278 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 17 121 G C - - MP 69 68 3 73 6 2 2 155 277 -10.770 -10.709 -0.007 -9.485 -9.765 -10.160 -8.575 -5.339 -10.375 -2.760 -10.142 -6.539 -4.576 -10.023 -6.697 3.963 -6.903 -3.248 -4.941 -6.988 -6.980 -9.280 ML 70 68 3 73 6 1 1 153 274 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 3 73 6 1 1 152 274 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 3 73 6 0 0 147 269 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 154 276 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 74 74 6 74 5 1 1 154 276 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 18 120 U A - - MP 75 74 6 79 6 2 2 153 275 -10.770 -10.709 -0.007 -9.485 -9.765 -10.160 -6.373 -6.275 -6.122 -2.246 -1.724 -6.614 1.923 -5.553 -6.095 -2.061 -6.438 -4.062 3.065 -6.441 1.452 -2.476 ML 76 74 6 79 6 1 1 151 272 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 77 74 6 79 6 1 1 150 272 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 78 74 6 79 6 0 0 146 267 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 152 274 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 80 80 6 80 5 1 1 152 274 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 19 119 c g - - MP 81 80 6 85 6 2 2 151 273 -10.770 -10.709 -0.011 -7.896 -9.765 -10.160 -3.004 -3.152 -1.699 1.056 -3.033 -4.031 1.891 -3.437 -3.232 1.793 -3.132 -1.645 1.811 -2.735 0.618 -2.372 ML 82 80 6 85 6 1 1 149 270 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 6 1 1 149 270 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 84 80 6 85 6 0 0 144 266 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 1 150 272 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 86 86 6 86 5 1 1 150 272 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 20 118 g c - - MP 87 86 6 91 6 2 2 149 271 -10.766 -10.705 -0.040 -9.481 -5.388 -10.156 -5.023 -4.324 -4.976 0.126 -4.370 -5.728 2.421 -4.851 -5.023 2.612 -5.464 -0.734 0.988 -5.036 -1.059 -3.715 ML 88 86 6 91 6 1 1 146 268 -6.411 -6.757 -1.471 -1.166 -6.607 -2.623 0.177 0.066 -0.493 0.153 MR 89 86 6 91 6 1 1 147 269 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 6 91 6 0 0 143 264 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 148 270 -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 1 148 270 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 21 117 c g - - MP 93 92 6 97 6 2 2 147 269 -10.732 -5.862 -0.035 -9.448 -9.728 -7.998 -3.022 -1.551 -3.199 1.015 -2.615 -4.001 2.113 -3.490 -2.758 1.550 -3.787 1.674 0.508 -2.723 -0.597 -2.388 ML 94 92 6 97 6 1 1 145 267 -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 1 145 267 -7.859 -3.612 -0.839 -6.566 -1.700 -4.779 1.304 -1.256 -0.992 -0.714 D 96 92 6 97 6 0 0 141 263 -9.251 -7.949 -3.746 -2.498 -4.446 -0.521 IL 97 97 5 97 6 1 1 146 268 -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 1 146 268 -2.865 -0.437 -4.033 -4.544 -5.649 0.000 0.000 0.000 0.000 [ MATP 21 ] 22 115 u a - - MP 99 98 6 103 6 2 2 145 267 -10.756 -10.695 -0.073 -9.472 -4.455 -10.147 -1.406 -2.629 -2.220 1.296 -2.274 -2.851 1.390 -2.586 -2.325 1.529 -2.754 -0.559 2.197 -2.753 -0.637 -1.446 ML 100 98 6 103 6 1 1 143 265 -6.593 -6.939 -1.196 -1.348 -6.789 -2.805 0.493 -0.218 -0.513 0.045 MR 101 98 6 103 6 1 1 143 265 -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 0 140 262 -9.260 -7.958 -3.755 -4.437 -4.455 -0.271 IL 103 103 5 103 6 1 1 144 266 -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 1 144 266 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 23 114 u a - - MP 105 104 6 109 4 2 2 143 265 -1.574 -10.654 -0.672 -4.792 -1.814 -2.228 -1.889 0.604 -2.560 -2.721 1.642 -2.520 -1.925 1.814 -2.261 -0.454 2.052 -2.710 -0.438 -1.557 ML 106 104 6 109 4 1 1 141 263 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 107 104 6 109 4 1 1 142 264 -0.909 -14.729 -1.945 -2.267 0.277 -0.992 0.523 -0.237 D 108 104 6 109 4 0 0 139 261 -14.025 -15.294 -1.366 -0.709 IL 109 109 5 109 4 1 1 142 264 -1.793 -7.895 -0.592 -4.510 0.000 0.000 0.000 0.000 IR 110 110 6 110 3 1 1 142 264 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 113 - G - - MR 111 110 6 113 5 1 1 141 263 -9.492 -0.111 -9.307 -4.430 -5.343 -1.644 -2.402 1.537 -0.762 D 112 110 6 113 5 0 0 138 260 -6.744 -1.563 -2.514 -5.801 -1.123 IR 113 113 3 113 5 1 1 141 263 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 24 ] 26 112 g u - - MP 114 113 3 118 4 2 2 140 262 -9.507 -9.714 -0.015 -6.981 -2.016 -0.033 -2.536 0.449 -1.918 -1.477 0.805 -1.730 -1.049 0.961 -0.572 2.389 -0.030 -1.756 -0.831 -1.365 ML 115 113 3 118 4 1 1 139 261 -4.148 -4.330 -0.370 -3.060 0.079 -0.567 0.172 0.192 MR 116 113 3 118 4 1 1 138 259 -6.124 -5.153 -0.850 -1.312 0.354 0.159 -0.868 0.081 D 117 113 3 118 4 0 0 135 257 -6.356 -6.038 -1.860 -0.521 IL 118 118 5 118 4 1 1 140 261 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 119 119 6 119 3 1 1 139 261 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 27 - G - - - ML 120 119 6 122 3 1 1 138 260 -6.540 -0.092 -4.297 -1.341 -0.482 1.341 -1.492 D 121 119 6 122 3 0 0 134 256 -7.224 -2.048 -0.412 IL 122 122 3 122 3 1 1 137 259 -2.171 -0.801 -2.294 0.000 0.000 0.000 0.000 [ MATR 26 ] - 111 - G - - MR 123 122 3 125 3 1 1 137 259 -10.754 -0.027 -5.774 -1.937 -0.619 1.347 -0.880 D 124 122 3 125 3 0 0 132 254 -9.068 -4.245 -0.081 IR 125 125 3 125 3 1 1 137 259 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 110 - A - - MR 126 125 3 128 5 1 1 136 258 -4.397 -0.135 -5.306 -7.199 -6.707 1.085 -0.935 -0.222 -1.003 D 127 125 3 128 5 0 0 132 254 -7.499 -1.338 -2.116 -6.557 -1.483 IR 128 128 3 128 5 1 1 136 258 -3.116 -0.283 -6.627 -4.795 -5.901 0.000 0.000 0.000 0.000 [ MATP 28 ] 29 108 G C - - MP 129 128 3 133 6 2 2 135 257 -10.625 -10.564 -0.068 -6.143 -9.620 -5.100 -4.725 -3.465 -4.575 0.804 -3.599 -5.191 0.479 -5.196 -2.131 3.242 -5.248 0.478 -0.089 -4.453 -1.420 -3.546 ML 130 128 3 133 6 1 1 133 255 -7.758 -8.105 -0.759 -1.417 -7.954 -5.484 0.547 -1.196 0.527 -0.597 MR 131 128 3 133 6 1 1 133 255 -7.180 -5.909 -1.291 -5.887 -1.021 -4.101 0.110 -0.376 -0.480 0.519 D 132 128 3 133 6 0 0 123 245 -10.884 -9.583 -5.380 -3.378 -6.079 -0.212 IL 133 133 5 133 6 1 1 134 256 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 134 134 6 134 5 1 1 134 256 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 30 107 c g - - MP 135 134 6 139 6 2 2 133 255 -10.620 -10.560 -0.180 -4.092 -7.647 -4.250 -1.755 -1.247 -0.950 1.256 -1.564 -3.362 2.325 -1.606 -2.205 0.512 -2.264 -0.391 1.397 -2.651 -0.305 -1.373 ML 136 134 6 139 6 1 1 130 252 -7.435 -7.782 -1.850 -0.875 -7.631 -2.626 0.402 -0.055 -0.799 0.191 MR 137 134 6 139 6 1 1 131 253 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 138 134 6 139 6 0 0 120 242 -11.265 -9.963 -5.760 -6.442 -6.460 -0.063 IL 139 139 5 139 6 1 1 133 255 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 140 140 6 140 5 1 1 133 255 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 31 106 g c - - MP 141 140 6 145 6 2 2 132 254 -10.458 -10.397 -0.054 -6.199 -9.454 -5.613 -2.597 -2.393 -3.608 0.529 -2.830 -4.374 1.436 -3.988 -2.345 2.899 -4.245 -0.007 0.833 -3.655 -1.172 -2.727 ML 142 140 6 145 6 1 1 129 250 -8.216 -8.562 -3.277 -0.198 -8.412 -5.942 0.499 -0.844 0.277 -0.289 MR 143 140 6 145 6 1 1 130 251 -7.154 -5.883 -1.330 -5.861 -0.995 -4.075 0.139 -0.371 -0.448 0.478 D 144 140 6 145 6 0 0 118 240 -11.961 -10.659 -6.456 -4.836 -7.156 -0.081 IL 145 145 5 145 6 1 1 131 253 -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 1 131 253 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 32 105 c g - - MP 147 146 6 151 6 2 2 130 252 -10.418 -10.358 -0.151 -5.905 -6.320 -3.862 -1.189 -2.057 -1.507 0.917 -1.378 -1.866 2.317 -1.886 -2.440 1.172 -2.604 -0.923 1.212 -2.085 0.014 -1.065 ML 148 146 6 151 6 1 1 127 249 -8.412 -8.758 -2.272 -0.574 -8.608 -3.138 0.976 -0.573 -1.141 -0.140 MR 149 146 6 151 6 1 1 128 250 -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 0 117 239 -12.076 -10.774 -6.571 -7.253 -7.271 -0.036 IL 151 151 5 151 6 1 1 129 251 -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 1 129 251 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 32 ] 33 104 c g - - MP 153 152 6 157 6 2 2 128 250 -6.350 -3.951 -0.360 -4.741 -6.122 -3.443 -2.097 -1.622 -0.548 0.922 -1.684 -1.702 1.546 -2.648 -1.734 1.499 -1.170 0.106 1.110 -1.188 0.365 -0.663 ML 154 152 6 157 6 1 1 126 248 -8.250 -8.596 -0.881 -1.875 -8.446 -2.509 0.353 -0.853 0.404 -0.241 MR 155 152 6 157 6 1 1 126 248 -7.385 -2.642 -2.022 -6.092 -0.937 -4.305 0.369 -0.021 -0.589 0.081 D 156 152 6 157 6 0 0 116 238 -12.580 -11.278 -4.760 -5.718 -7.775 -0.091 IL 157 157 5 157 6 1 1 128 250 -2.910 -1.663 -1.091 -4.828 -5.604 -5.265 0.000 0.000 0.000 0.000 IR 158 158 6 158 5 1 1 128 249 -3.496 -0.422 -7.007 -2.791 -6.281 0.000 0.000 0.000 0.000 [ MATP 33 ] 35 102 g c - - MP 159 158 6 163 6 2 2 127 249 -10.177 -10.116 -0.093 -4.123 -9.172 -9.567 -1.219 -2.235 -1.124 0.884 -2.211 -2.142 1.358 -1.760 0.181 1.707 -1.246 -0.327 1.304 -2.359 0.085 -1.279 ML 160 158 6 163 6 1 1 124 246 -7.736 -8.082 -0.948 -1.163 -7.932 -5.461 0.009 -0.569 0.174 0.252 MR 161 158 6 163 6 1 1 123 245 -7.946 -6.675 -2.584 -6.653 -0.492 -3.345 -0.374 0.679 -1.116 0.222 D 162 158 6 163 6 0 0 115 237 -12.992 -11.690 -5.723 -8.170 -8.187 -0.038 IL 163 163 5 163 6 1 1 126 248 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 164 164 6 164 5 1 1 126 248 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 36 101 c g - - MP 165 164 6 169 6 2 2 125 247 -10.159 -10.099 -0.160 -8.875 -9.155 -3.333 -0.706 -1.176 -0.645 1.090 -1.506 -2.209 1.775 -2.558 -2.274 1.557 -2.295 -0.774 1.034 -1.474 0.261 -1.080 ML 166 164 6 169 6 1 1 120 242 -7.970 -8.316 -1.737 -1.959 -8.166 -1.210 0.810 -0.681 -0.681 -0.002 MR 167 164 6 169 6 1 1 122 244 -7.851 -6.580 -1.459 -2.559 -1.268 -4.771 -0.018 -0.294 0.037 0.227 D 168 164 6 169 6 0 0 114 236 -12.990 -11.688 -5.968 -8.167 -4.311 -0.105 IL 169 169 5 169 6 1 1 125 246 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 170 170 6 170 5 1 1 125 246 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 37 100 c g - - MP 171 170 6 175 4 2 2 124 246 -0.230 -5.463 -3.072 -7.375 -0.939 -1.211 -2.155 0.792 -0.478 -2.440 1.818 -2.026 -1.008 1.389 -1.831 -0.870 1.248 -2.296 0.561 -1.254 ML 172 170 6 175 4 1 1 118 240 -1.373 -4.533 -1.100 -3.263 -0.198 0.437 -0.915 0.315 MR 173 170 6 175 4 1 1 119 241 -1.118 -4.677 -2.544 -1.605 -0.042 -0.589 0.035 0.422 D 174 170 6 175 4 0 0 114 235 -2.315 -1.835 -1.056 -4.724 IL 175 175 5 175 4 1 1 123 245 -0.260 -2.664 -7.176 -11.593 0.000 0.000 0.000 0.000 IR 176 176 6 176 3 1 1 111 232 -0.218 -2.853 -8.862 0.000 0.000 0.000 0.000 [ MATL 36 ] 53 - g - - - ML 177 176 6 179 3 1 1 14 33 -10.601 -0.016 -6.607 0.225 -0.238 0.288 -0.392 D 178 176 6 179 3 0 0 15 34 -6.693 -1.481 -0.662 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 37 ] 54 - a - - - ML 180 179 3 182 3 1 1 13 31 -10.594 -0.036 -5.367 0.301 -0.020 -0.456 0.074 D 181 179 3 182 3 0 0 14 32 -6.962 -2.475 -0.300 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 38 ] 55 - a - - - ML 183 182 3 185 3 1 1 11 30 -10.561 -0.158 -3.280 0.573 -0.450 -0.588 0.157 D 184 182 3 185 3 0 0 12 31 -7.768 -3.281 -0.164 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 39 ] 56 - a - - - ML 186 185 3 188 2 1 1 1 1 * 0.000 0.480 -0.669 -0.177 0.127 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 40 ] - - - - - - E 189 188 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME nadA ACC RF03013 DESC nadA riboswitch LENG 62 MAXL 185 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jul 8 00:15:16 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /homes/nancyontiveros/3D_families/3D_release15/RF03013/CM NSEQ 186 EFFN 186.000000 CKSUM 190925323 STATS LOCAL MSV -8.2126 0.72244 STATS LOCAL VITERBI -8.8765 0.72244 STATS LOCAL FORWARD -2.9041 0.72244 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.57072 1.20648 1.24034 1.59175 1.38629 1.38629 1.38629 1.38629 0.00947 7.53603 4.72294 1.46634 0.26236 0.00000 * 1 2.59220 4.19851 0.14185 3.16120 1 G - - < 1.38629 1.38629 1.38629 1.38629 0.00108 7.52764 7.52764 1.46634 0.26236 0.11336 2.23331 2 3.94010 0.70451 0.72631 5.98674 2 c - - < 1.38629 1.38629 1.38629 1.38629 0.01419 7.54009 4.30068 1.46634 0.26236 1.09861 0.40547 3 7.09678 1.03066 7.06070 0.44388 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.00108 7.52698 7.52698 1.46634 0.26236 0.39432 1.12127 4 4.45129 5.41671 4.52212 0.02734 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.00107 7.53638 7.53638 1.46634 0.26236 0.22396 1.60617 5 4.50484 3.99973 1.32222 0.35086 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.00943 4.72700 7.54009 0.11600 2.21164 1.09861 0.40547 6 7.10521 0.00226 7.23098 7.24297 7 C - - < 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 7 0.00453 6.51670 6.44831 6.53081 8 A - - < 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 8 0.00136 8.05417 7.52454 7.60092 9 A - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 9 7.97626 0.00136 8.37907 7.14631 10 C - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 10 0.00136 8.05417 7.52454 7.60092 11 A - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 11 1.92751 3.83987 3.94427 0.20625 12 U - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 12 7.97626 0.00136 8.37907 7.14631 13 C - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 13 4.43934 0.02980 6.94493 4.09866 14 C - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 14 7.97626 0.00136 8.37907 7.14631 15 C - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 15 7.34196 0.01590 7.60954 4.22494 16 C - - - 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 16 6.38120 7.50783 0.00276 7.56693 17 G - - < 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 17 7.19696 1.43885 7.12264 0.27280 18 U - - < 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 18 1.97523 1.42135 1.32984 1.03462 19 u - - < 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 19 3.22818 0.98668 0.76702 2.09424 20 g - - < 1.38629 1.38629 1.38629 1.38629 0.03477 7.54009 3.39214 1.46634 0.26236 1.09861 0.40547 20 2.02060 1.13407 0.74919 2.61790 21 g - - < 1.38629 1.38629 1.38629 1.38629 0.00506 7.50642 5.40405 1.46634 0.26236 0.03110 3.48590 21 1.69261 1.80708 1.36137 0.92756 22 u - - < 1.38629 1.38629 1.38629 1.38629 0.02452 7.53626 3.74283 1.46634 0.26236 2.32097 0.10334 22 2.50504 1.53929 1.06439 1.02484 23 u - - < 1.38629 1.38629 1.38629 1.38629 0.47020 1.06220 3.52583 0.25556 1.48936 0.95177 0.48786 23 2.32625 2.12885 0.36506 2.41674 26 G - - < 1.38629 1.38629 1.38629 1.38629 0.02437 7.49454 3.74999 1.46634 0.26236 2.12147 0.12767 24 2.66662 1.60289 0.41466 2.67891 27 G - - - 1.38629 1.38629 1.38629 1.38629 0.02798 4.46978 4.12628 0.09612 2.38986 1.94872 0.15368 25 2.33786 2.50535 0.28073 2.70928 29 G - - < 1.38629 1.38629 1.38629 1.38629 0.03737 7.47006 3.32105 1.46634 0.26236 1.70039 0.20164 26 1.45595 0.80044 2.19316 1.57927 30 c - - < 1.38629 1.38629 1.38629 1.38629 0.08661 7.44725 2.49635 1.46634 0.26236 5.13502 0.00590 27 2.38465 1.73722 0.48122 2.17294 31 G - - < 1.38629 1.38629 1.38629 1.38629 0.02581 7.36190 3.69491 1.46634 0.26236 2.77745 0.06422 28 1.56626 0.80657 1.90628 1.62885 32 c - - < 1.38629 1.38629 1.38629 1.38629 0.12313 7.34922 2.16103 1.46634 0.26236 5.79913 0.00303 29 1.69836 1.59040 0.98937 1.42147 33 g - - < 1.38629 1.38629 1.38629 1.38629 0.21258 4.16570 1.73736 0.09111 2.44092 3.02430 0.04981 30 1.98220 1.82275 0.71368 1.55678 35 g - - < 1.38629 1.38629 1.38629 1.38629 0.00173 7.05551 7.05551 1.46634 0.26236 4.21641 0.01486 31 1.23266 1.33820 1.38335 1.63256 36 a - - < 1.38629 1.38629 1.38629 1.38629 0.13656 7.06385 2.06520 1.46634 0.26236 1.33247 0.30629 32 2.10249 1.00031 1.33407 1.39967 37 c - - < 1.38629 1.38629 1.38629 1.38629 2.86564 0.05951 7.09808 1.82613 0.17559 0.01337 4.32166 33 1.24094 1.50988 1.08514 1.88322 53 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01486 7.53638 4.25353 1.46634 0.26236 0.22396 1.60617 34 1.17340 1.33311 1.70696 1.40399 54 a - - _ 1.38629 1.38629 1.38629 1.38629 0.02532 7.52637 3.71060 1.46634 0.26236 3.35521 0.03553 35 0.93179 1.71608 1.83716 1.32008 55 a - - _ 1.38629 1.38629 1.38629 1.38629 0.03953 7.50215 3.26471 1.46634 0.26236 1.00847 0.45378 36 1.00978 1.93742 1.45473 1.35417 56 a - - _ 1.38629 1.38629 1.38629 1.38629 2.47459 0.31549 1.68002 2.05192 0.13753 4.75050 0.00868 37 1.32083 1.43656 0.91721 2.34642 100 g - - > 1.38629 1.38629 1.38629 1.38629 0.38862 7.27282 1.13534 1.46634 0.26236 1.36674 0.29429 38 1.90018 1.17390 0.93634 1.90220 101 g - - > 1.38629 1.38629 1.38629 1.38629 0.07242 6.99486 2.67445 1.46634 0.26236 2.07149 0.13467 39 1.28323 1.11856 1.39330 1.91152 102 c - - > 1.38629 1.38629 1.38629 1.38629 0.28135 2.00325 2.20421 0.01323 4.33153 1.22261 0.34879 40 2.02429 1.20723 1.00803 1.58987 104 g - - > 1.38629 1.38629 1.38629 1.38629 0.02699 7.10595 3.65721 1.46634 0.26236 1.42366 0.27553 41 1.75195 1.69364 0.67745 2.00393 105 G - - > 1.38629 1.38629 1.38629 1.38629 0.00148 7.20644 7.20644 1.46634 0.26236 2.14364 0.12469 42 2.05983 0.55615 1.64157 2.24963 106 C - - > 1.38629 1.38629 1.38629 1.38629 0.01086 7.25137 4.59631 1.46634 0.26236 0.66464 0.72249 43 1.62409 2.47823 0.70205 1.49857 107 g - - > 1.38629 1.38629 1.38629 1.38629 0.04980 7.40255 3.03714 1.46634 0.26236 0.98080 0.47002 44 2.64127 0.42055 2.28268 1.77178 108 C - - > 1.38629 1.38629 1.38629 1.38629 0.10714 2.98784 2.97200 0.02383 3.74856 1.36968 0.29328 45 0.54600 2.13233 1.48893 2.56964 110 A - - - 1.38629 1.38629 1.38629 1.38629 0.00123 7.39482 7.39482 1.46634 0.26236 2.11606 0.12841 46 3.75930 1.71799 0.40347 2.04583 111 G - - - 1.38629 1.38629 1.38629 1.38629 0.01596 7.41311 4.18421 1.46634 0.26236 0.79537 0.60041 47 2.28903 1.41830 1.98086 0.65670 112 U - - > 1.38629 1.38629 1.38629 1.38629 0.01312 7.45875 4.38520 1.46634 0.26236 1.11135 0.39916 48 2.97908 3.40376 0.27200 1.87045 113 G - - - 1.38629 1.38629 1.38629 1.38629 0.00504 7.47462 5.41366 1.46634 0.26236 0.07810 2.58855 49 1.06697 1.26716 1.31579 2.24379 114 a - - > 1.38629 1.38629 1.38629 1.38629 0.00107 7.53260 7.53260 1.46634 0.26236 2.83551 0.06048 50 0.91748 1.51432 1.73870 1.58587 115 a - - > 1.38629 1.38629 1.38629 1.38629 0.02305 3.80524 7.53260 0.04744 3.07198 0.73314 0.65469 51 2.56419 1.59013 1.09818 0.95285 117 u - - > 1.38629 1.38629 1.38629 1.38629 0.00107 7.53644 7.53644 1.46634 0.26236 2.28783 0.10701 52 2.27474 0.83538 0.93700 2.63576 118 c - - > 1.38629 1.38629 1.38629 1.38629 0.00107 7.53644 7.53644 1.46634 0.26236 0.22687 1.59468 53 1.42720 1.33335 0.98016 2.11050 119 g - - > 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 54 0.53386 7.24637 0.91243 4.47383 120 A - - > 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 55 7.57190 0.00355 7.41461 6.01961 121 C - - > 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 56 7.61656 7.26126 6.59521 0.00256 122 U - - > 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 57 6.68925 7.43732 0.00225 7.78525 123 G - - > 1.38629 1.38629 1.38629 1.38629 0.00504 7.54009 5.40400 1.46634 0.26236 1.09861 0.40547 58 0.69686 1.27715 1.71185 3.15843 124 a - - > 1.38629 1.38629 1.38629 1.38629 0.01004 7.53612 4.66111 1.46634 0.26236 0.21207 1.65501 59 0.02197 6.56609 5.32302 4.17056 125 A - - > 1.38629 1.38629 1.38629 1.38629 0.00107 7.53116 7.53116 1.46634 0.26236 0.10691 2.28876 60 1.56675 6.04364 0.24719 4.83883 126 G - - > 1.38629 1.38629 1.38629 1.38629 0.00106 7.54009 7.54009 1.46634 0.26236 1.09861 0.40547 61 4.50153 0.79218 0.71162 3.09664 127 g - - > 1.38629 1.38629 1.38629 1.38629 0.00943 7.54009 4.72700 1.46634 0.26236 1.09861 0.40547 62 3.28369 0.14648 3.98396 2.52383 128 C - - > 1.38629 1.38629 1.38629 1.38629 0.00054 7.53120 * 1.46634 0.26236 0.00000 * //