INFERNAL1/a [1.1.5 | Sep 2023] NAME Hammerhead_3 ACC RF00008 DESC Hammerhead ribozyme (type III) STATES 176 NODES 47 CLEN 54 W 218 ALPH RNA RF no CONS yes MAP yes DATE Fri Aug 16 17:25:07 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/15/3Dupdates/RF00008/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 85 EFFN 10.056915 CKSUM 2174881899 NULL 0.000 0.000 0.000 0.000 GA 48.50 TC 48.50 NC 48.40 EFP7GF -18.8598 0.71958 ECMLC 0.67677 -4.46784 3.78094 1600000 318882 0.003763 ECMGC 0.42136 -17.83942 -4.45649 1600000 112479 0.003556 ECMLI 0.65191 -3.95526 4.41290 1600000 280797 0.004274 ECMGI 0.44164 -14.79201 -2.69659 1600000 83554 0.004787 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 0 1 218 437 -10.019 -9.958 -0.242 -8.735 -4.649 -3.179 IL 1 1 2 1 6 2 18 220 438 -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 2 19 220 438 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 85 c g - - MP 3 2 3 7 6 4 22 219 437 -9.790 -9.729 -0.013 -8.505 -8.785 -9.180 -1.792 -1.114 -1.362 0.985 -1.112 -1.547 1.967 -2.342 -1.389 1.180 -1.780 -0.208 1.018 -1.192 0.309 -1.108 ML 4 2 3 7 6 1 16 216 435 -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 2 16 214 433 -7.855 -6.584 -2.492 -6.562 -0.395 -4.775 0.270 0.289 -0.809 0.002 D 6 2 3 7 6 0 13 213 432 -11.209 -9.907 -1.175 -6.386 -3.102 -1.227 IL 7 7 5 7 6 2 17 218 436 -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 2 18 218 436 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 84 a u - - MP 9 8 6 13 6 4 22 217 435 -9.887 -9.826 -0.012 -8.603 -8.882 -9.277 -2.358 -2.507 -2.536 2.399 -0.336 -3.383 1.380 -1.368 -2.588 0.571 -3.151 -0.413 1.388 -2.679 -0.482 -1.731 ML 10 8 6 13 6 1 16 214 433 -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 2 16 212 431 -8.087 -6.816 -2.725 -6.794 -0.329 -5.008 0.556 -0.401 -0.225 -0.126 D 12 8 6 13 6 0 12 208 426 -10.124 -8.823 -4.620 -5.302 -5.319 -0.143 IL 13 13 5 13 6 2 17 216 434 -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 2 17 216 434 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 83 a u - - MP 15 14 6 19 6 4 21 215 433 -9.887 -9.826 -0.012 -8.603 -8.882 -9.277 -2.488 -2.568 -2.654 2.073 -2.513 -3.495 1.623 -2.909 -2.712 1.024 -3.268 -0.309 1.733 -2.320 -0.558 -0.977 ML 16 14 6 19 6 1 15 212 431 -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 15 211 429 -8.087 -6.816 -2.725 -6.794 -0.329 -5.008 -0.079 -0.293 0.034 0.279 D 18 14 6 19 6 0 12 207 426 -10.124 -8.823 -4.620 -5.302 -2.067 -0.531 IL 19 19 5 19 6 1 16 214 432 -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 2 17 214 432 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 82 g c - - MP 21 20 6 25 6 4 20 213 432 -9.887 -9.826 -0.012 -8.603 -8.882 -9.277 -4.180 -3.332 -4.143 2.083 -4.082 -4.911 2.091 -4.312 -4.270 2.324 -4.690 -1.009 0.065 -4.204 -1.588 -3.031 ML 22 20 6 25 6 1 15 211 429 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 6 1 15 209 428 -8.280 -7.009 -2.918 -6.988 -0.283 -5.201 -0.256 -0.680 0.849 -0.439 D 24 20 6 25 6 0 11 206 424 -9.778 -8.476 -4.273 -4.955 -4.972 -0.184 IL 25 25 5 25 6 1 16 212 430 -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 16 212 430 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 5 81 A U - - MP 27 26 6 31 6 4 18 211 430 -9.887 -9.826 -0.012 -8.603 -8.882 -9.277 -4.390 -4.012 -4.381 3.044 -3.705 -5.164 1.519 -4.223 -4.367 0.384 -4.833 -1.784 1.232 -4.612 -1.349 -3.245 ML 28 26 6 31 6 1 15 209 427 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 29 26 6 31 6 1 14 208 426 -8.280 -7.009 -2.918 -6.988 -0.283 -5.201 0.797 -1.122 0.155 -0.535 D 30 26 6 31 6 0 11 205 423 -9.778 -8.476 -4.273 -4.955 -4.972 -0.184 IL 31 31 5 31 6 1 16 210 429 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 16 210 428 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 6 80 G C - - MP 33 32 6 37 6 4 16 209 428 -9.887 -9.826 -0.012 -8.603 -8.882 -9.277 -6.774 -4.269 -7.308 -0.406 -8.166 -5.682 -2.995 -7.539 -5.630 3.867 -5.889 -2.063 -3.297 -5.886 -5.185 -6.148 ML 34 32 6 37 6 1 14 207 426 -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 13 206 425 -8.280 -7.009 -2.918 -6.988 -0.283 -5.201 -0.574 0.848 -1.343 0.181 D 36 32 6 37 6 0 11 204 423 -9.778 -8.476 -4.273 -4.955 -4.972 -0.184 IL 37 37 5 37 6 1 15 208 427 -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 15 208 427 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 7 79 U A - - MP 39 38 6 43 4 3 14 207 426 -8.473 -8.680 -0.018 -7.094 -8.046 -7.930 -7.508 -4.221 -5.985 -7.771 -1.729 -6.845 -7.440 -4.272 -7.738 -5.875 3.945 -7.900 -3.474 -5.131 ML 40 38 6 43 4 1 13 206 425 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 12 205 424 -6.227 -5.256 -3.123 -0.242 1.533 -1.727 -1.423 -1.213 D 42 38 6 43 4 0 11 204 423 -5.259 -4.940 -2.956 -0.300 IL 43 43 5 43 4 1 14 207 425 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 13 206 425 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - C - - - ML 45 44 6 47 3 1 12 205 424 -6.860 -0.018 -8.067 -1.700 1.752 -3.791 -1.995 D 46 44 6 47 3 0 11 204 422 -7.321 -0.189 -3.104 IL 47 47 3 47 3 1 12 205 424 -2.015 -0.514 -4.253 0.000 0.000 0.000 0.000 [ MATR 9 ] - 78 - A - - MR 48 47 3 50 3 1 11 204 423 -9.941 -0.006 -8.259 1.966 -5.307 -4.744 -5.002 D 49 47 3 50 3 0 9 202 421 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 11 204 423 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 77 - A - - MR 51 50 3 53 3 1 10 203 422 -9.941 -0.006 -8.259 1.934 -4.667 -3.423 -4.463 D 52 50 3 53 3 0 9 201 420 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 10 203 422 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 76 - G - - MR 54 53 3 56 2 1 9 202 421 -10.194 -0.001 -1.895 -4.068 1.831 -3.142 D 55 53 3 56 2 0 8 201 420 -4.432 -0.068 IR 56 56 3 56 2 1 10 202 421 -1.823 -0.479 0.000 0.000 0.000 0.000 [ BIF 12 ] - - - - - - B 57 56 3 112 58 0 8 201 420 [ BEGR 32 ] - - - - - - S 58 57 1 59 3 0 0 180 398 -9.616 -0.007 -8.271 IL 59 59 2 59 3 1 1 181 400 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 35 - A - - - ML 60 59 2 62 5 1 1 180 398 -8.615 -0.013 -8.430 -8.642 -9.534 1.966 -5.307 -4.744 -5.002 D 61 59 2 62 5 0 0 177 396 -4.959 -0.803 -4.221 -2.596 -2.508 IL 62 62 3 62 5 1 1 180 398 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 36 75 G C - - MP 63 62 3 67 6 2 2 179 397 -10.019 -9.958 -0.011 -8.735 -9.014 -9.409 -7.088 -2.382 -7.734 -1.589 -8.516 -5.765 -3.238 -8.000 -5.808 3.889 -6.042 -1.493 -3.538 -6.014 -5.466 -6.620 ML 64 62 3 67 6 1 1 176 395 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 65 62 3 67 6 1 1 176 394 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 3 67 6 0 0 171 389 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 178 396 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 68 68 6 68 5 1 1 178 396 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 37 74 u a - - MP 69 68 6 73 6 2 2 177 395 -10.019 -9.958 -0.011 -8.735 -9.014 -9.409 -4.379 -4.217 -4.389 -0.257 -3.412 -5.169 2.170 -4.051 -4.314 0.924 -3.229 -1.983 2.865 -4.582 -0.785 -3.131 ML 70 68 6 73 6 1 1 174 393 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 6 73 6 1 1 174 392 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 6 73 6 0 0 169 388 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 176 394 -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 1 176 394 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 36 ] 38 73 C G - - MP 75 74 6 79 6 2 2 175 393 -10.019 -9.958 -0.011 -8.735 -9.014 -9.409 -6.275 -6.418 -5.712 -2.539 -4.129 -5.936 3.715 -5.015 -5.781 -2.440 -5.956 -4.544 0.687 -6.178 -0.679 -4.571 ML 76 74 6 79 6 1 1 173 391 -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 1 171 390 -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 0 168 387 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 174 392 -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 1 174 392 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 37 ] 39 72 c g - - MP 81 80 6 85 4 2 2 173 391 -8.674 -8.881 -0.016 -7.295 -4.148 -2.665 -4.187 -0.004 -3.346 -5.007 2.396 -3.934 -4.129 1.766 -4.640 -1.677 2.249 -4.347 -0.906 -2.949 ML 82 80 6 85 4 1 1 171 390 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 4 1 1 169 387 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 84 80 6 85 4 0 0 167 385 -4.568 -4.250 -2.265 -0.520 IL 85 85 5 85 4 1 1 172 391 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 86 86 6 86 3 1 1 172 391 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 40 - c - - - ML 87 86 6 89 3 1 1 171 389 -9.616 -0.007 -8.271 -0.386 0.443 0.008 -0.201 D 88 86 6 89 3 0 0 164 383 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 171 390 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 39 ] 41 - U - - - ML 90 89 3 92 3 1 1 170 389 -9.616 -0.449 -1.910 -0.262 -2.416 -2.938 1.510 D 91 89 3 92 3 0 0 160 379 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 173 392 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 40 ] 42 - G - - - ML 93 92 3 95 3 1 1 172 391 -9.177 -0.009 -7.831 -2.015 -4.197 1.855 -3.636 D 94 92 3 95 3 0 0 136 354 -9.285 -4.798 -0.055 IL 95 95 3 95 3 1 1 172 391 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 41 ] 43 - A - - - ML 96 95 3 98 3 1 1 171 390 -3.069 -0.253 -4.578 1.363 -1.496 -0.386 -1.704 D 97 95 3 98 3 0 0 119 338 -9.285 -4.798 -0.055 IL 98 98 3 98 3 1 1 196 414 -0.122 -3.695 -8.109 0.000 0.000 0.000 0.000 [ MATL 42 ] 68 - a - - - ML 99 98 3 101 3 1 1 15 34 -9.121 -0.009 -7.775 0.716 -0.730 0.361 -1.090 D 100 98 3 101 3 0 0 14 32 -9.413 -3.019 -0.192 IL 101 101 3 101 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 43 ] 69 - A - - - ML 102 101 3 104 3 1 1 14 32 -9.180 -0.009 -7.834 1.897 -3.799 -3.582 -3.055 D 103 101 3 104 3 0 0 13 31 -9.276 -0.239 -2.727 IL 104 104 3 104 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 44 ] 70 - u - - - ML 105 104 3 107 3 1 1 12 30 -9.585 -0.007 -8.239 0.112 -0.668 -1.108 0.869 D 106 104 3 107 3 0 0 13 31 -6.871 -2.384 -0.322 IL 107 107 3 107 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 45 ] 71 - A - - - ML 108 107 3 110 2 1 1 1 1 * 0.000 1.212 -3.564 0.575 -3.199 D 109 107 3 110 2 0 0 0 0 * 0.000 IL 110 110 3 110 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 46 ] - - - - - - E 111 110 3 -1 0 0 0 0 0 [ BEGL 13 ] - - - - - - S 112 57 1 113 1 0 0 80 154 0.000 [ BIF 14 ] - - - - - - B 113 112 1 114 155 0 0 80 154 [ BEGL 15 ] - - - - - - S 114 113 1 115 4 0 0 74 148 -0.177 -7.948 -3.215 -7.996 [ MATP 16 ] 10 28 u a - - MP 115 114 1 119 6 2 2 74 148 -9.885 -9.825 -0.012 -8.601 -8.881 -9.276 -3.710 -3.325 -3.783 0.893 -3.465 -4.629 0.848 -3.850 -2.125 2.044 -4.318 -1.174 2.674 -3.922 -1.153 -2.725 ML 116 114 1 119 6 1 1 72 146 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 117 114 1 119 6 1 1 73 147 -8.534 -7.263 -0.380 -7.241 -2.375 -5.454 1.030 -0.998 -1.043 -0.041 D 118 114 1 119 6 0 0 68 141 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 119 119 5 119 6 1 1 73 147 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 120 120 6 120 5 1 1 73 147 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 11 27 G C - - MP 121 120 6 125 6 2 2 72 146 -10.019 -9.958 -0.011 -8.735 -9.014 -9.409 -4.428 -2.461 -4.267 1.169 -5.337 -4.837 0.674 -4.922 -4.637 3.292 -4.900 -0.073 -0.706 -4.121 -2.446 -3.225 ML 122 120 6 125 6 1 1 70 144 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 123 120 6 125 6 1 1 70 144 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 124 120 6 125 6 0 0 66 140 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 125 125 5 125 6 1 1 71 145 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 126 126 6 126 5 1 1 71 145 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 12 26 g c - - MP 127 126 6 131 6 2 2 70 144 -10.019 -9.958 -0.030 -6.027 -9.014 -9.409 -3.912 -3.202 -3.902 0.999 -3.834 -4.635 1.411 -4.118 -4.060 2.445 -4.488 0.557 1.733 -3.920 -1.396 -2.842 ML 128 126 6 131 6 1 1 68 142 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 129 126 6 131 6 1 1 68 142 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 130 126 6 131 6 0 0 64 138 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 131 131 5 131 6 1 1 70 143 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 132 132 6 132 5 1 1 69 143 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 13 25 G C - - MP 133 132 6 137 6 2 2 68 142 -10.000 -9.939 -0.011 -8.716 -8.995 -9.391 -4.429 -1.629 -4.274 1.671 -5.361 -4.858 -0.467 -4.923 -4.632 3.242 -4.902 -0.703 0.117 -4.138 -2.473 -3.229 ML 134 132 6 137 6 1 1 67 141 -6.656 -7.002 -0.864 -1.411 -6.852 -4.381 0.079 -0.801 0.618 -0.261 MR 135 132 6 137 6 1 1 66 139 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 136 132 6 137 6 0 0 63 137 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 137 137 5 137 6 1 1 68 141 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 138 138 6 138 5 1 1 67 141 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 14 24 c g - - MP 139 138 6 143 4 2 2 66 140 -8.674 -8.881 -0.016 -7.295 -4.171 -3.898 -4.201 0.642 -3.395 -5.005 2.945 -3.972 -4.159 1.731 -3.304 -1.665 0.708 -4.353 -0.374 -2.978 ML 140 138 6 143 4 1 1 65 139 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 141 138 6 143 4 1 1 63 137 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 142 138 6 143 4 0 0 62 136 -4.568 -4.250 -2.265 -0.520 IL 143 143 5 143 4 1 1 66 140 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 144 144 6 144 3 1 1 66 140 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 15 - u - - - ML 145 144 6 147 3 1 1 64 138 -9.616 -0.007 -8.271 -0.119 -0.806 -0.656 0.905 D 146 144 6 147 3 0 0 59 133 -6.174 -1.687 -0.566 IL 147 147 3 147 3 1 1 65 138 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 16 - U - - - ML 148 147 3 150 3 1 1 63 137 -1.319 -0.746 -8.271 0.336 -1.331 -2.083 1.073 D 149 147 3 150 3 0 0 49 123 -6.174 -1.687 -0.566 IL 150 150 3 150 3 1 1 66 140 -0.360 -2.201 -8.146 0.000 0.000 0.000 0.000 [ MATL 23 ] 23 - a - - - ML 151 150 3 153 2 1 1 1 1 * 0.000 0.967 -0.510 -0.906 -0.306 D 152 150 3 153 2 0 0 0 0 * 0.000 IL 153 153 3 153 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 24 ] - - - - - - E 154 153 3 -1 0 0 0 0 0 [ BEGR 25 ] - - - - - - S 155 113 1 156 5 0 0 18 37 -8.615 -0.013 -8.430 -8.642 -9.534 IL 156 156 2 156 5 1 1 20 39 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 29 34 C G - - MP 157 156 2 161 4 2 2 18 37 -8.674 -8.881 -0.016 -7.295 -7.950 -8.124 -6.921 -4.376 -5.265 -6.888 3.956 -6.618 -7.423 -4.354 -6.929 -6.369 -2.427 -7.843 -3.419 -6.227 ML 158 156 2 161 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 159 156 2 161 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 160 156 2 161 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 161 161 5 161 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 162 162 6 162 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 27 ] 30 - U - - - ML 163 162 6 165 3 1 1 15 33 -9.616 -0.007 -8.271 -4.340 -3.954 -5.144 1.948 D 164 162 6 165 3 0 0 16 34 -6.174 -1.687 -0.566 IL 165 165 3 165 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 28 ] 31 - G - - - ML 166 165 3 168 3 1 1 14 32 -9.616 -0.007 -8.271 -3.645 -3.842 1.926 -4.300 D 167 165 3 168 3 0 0 15 33 -6.174 -1.687 -0.566 IL 168 168 3 168 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 29 ] 32 - A - - - ML 169 168 3 171 3 1 1 12 30 -9.616 -0.007 -8.271 1.966 -5.307 -4.744 -5.002 D 170 168 3 171 3 0 0 13 32 -6.174 -1.687 -0.566 IL 171 171 3 171 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 33 - U - - - ML 172 171 3 174 2 1 1 1 1 * 0.000 -2.895 -0.479 -3.676 1.618 D 173 171 3 174 2 0 0 0 0 * 0.000 IL 174 174 3 174 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 31 ] - - - - - - E 175 174 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME Hammerhead_3 ACC RF00008 DESC Hammerhead ribozyme (type III) LENG 54 MAXL 370 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Aug 16 17:25:07 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/15/3Dupdates/RF00008/CM NSEQ 85 EFFN 63.140411 CKSUM 2174881899 STATS LOCAL MSV -7.5428 0.71958 STATS LOCAL VITERBI -8.1364 0.71958 STATS LOCAL FORWARD -4.4157 0.71958 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.28142 1.46796 1.30659 1.50861 1.38629 1.38629 1.38629 1.38629 0.25138 6.73546 1.50920 1.46634 0.26236 0.00000 * 1 1.91864 0.89946 1.36865 1.65050 1 c - - ( 1.38629 1.38629 1.38629 1.38629 0.00305 6.48713 6.48713 1.46634 0.26236 0.75738 0.63279 2 0.50398 1.54880 2.99402 2.01523 2 A - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 3 0.91050 1.73786 2.09350 1.20890 3 a - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 4 1.04733 1.09335 1.18216 4.90323 4 a - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 5 0.34207 2.02453 3.51361 2.05686 5 A - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 6 3.16475 6.16920 0.04763 6.12240 6 G - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 7 6.92325 6.83345 7.17972 0.00283 7 U - - ( 1.38629 1.38629 1.38629 1.38629 0.00269 6.61181 6.61181 1.46634 0.26236 4.61412 0.00996 8 2.57245 0.10523 5.70795 3.90121 8 C - - , 1.38629 1.38629 1.38629 1.38629 0.17623 4.56847 1.88917 0.24166 1.53862 0.22293 1.61031 9 2.43110 5.61066 1.18056 0.50867 10 U - - < 1.38629 1.38629 1.38629 1.38629 0.00270 6.60985 6.60985 1.46634 0.26236 0.01519 4.19440 10 2.10084 2.22665 0.28146 4.19477 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 11 2.28404 1.89798 0.72710 1.32823 12 g - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 12 1.44178 4.73340 0.37068 2.74217 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 13 2.61311 0.45825 1.40788 3.00294 14 C - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 14 1.61707 2.17856 1.89733 0.61925 15 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 15 1.07162 2.92114 4.82348 0.51812 16 U - - _ 1.38629 1.38629 1.38629 1.38629 0.62319 0.77085 6.77079 1.64108 0.21539 1.09861 0.40547 16 0.57721 1.75949 2.20035 1.86022 23 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 17 4.12508 1.44474 0.39640 2.58642 24 G - - > 1.38629 1.38629 1.38629 1.38629 0.02444 6.77079 3.77241 1.46634 0.26236 1.09861 0.40547 18 2.76835 0.35013 4.58631 1.50307 25 C - - > 1.38629 1.38629 1.38629 1.38629 0.00235 6.74870 6.74870 1.46634 0.26236 0.09507 2.40030 19 1.34901 1.00328 1.86661 1.51786 26 c - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 20 4.32648 0.33736 2.19635 1.82060 27 C - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 21 0.45862 1.38755 4.66969 2.21842 28 A - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 22 7.47512 0.00234 7.39524 6.76547 29 C - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 23 7.17589 6.56795 7.91697 0.00254 30 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 24 5.94009 4.19008 0.01957 6.43300 31 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 25 0.00360 7.05924 6.54919 6.64038 32 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 26 5.54539 1.65075 6.07959 0.22077 33 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 27 6.50920 7.48543 0.00244 7.85269 34 G - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 28 0.00360 7.05924 6.54919 6.64038 35 A - - , 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 29 3.97891 6.50921 0.02185 6.55816 36 G - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 30 4.97787 1.34764 2.18103 0.47750 37 U - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 31 6.13029 0.11983 6.06265 2.22173 38 C - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 32 3.84098 1.03028 1.36789 1.00245 39 u - - < 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 33 1.97811 0.89240 1.25132 1.79654 40 c - - _ 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 34 1.45768 5.14028 5.76027 0.27678 41 U - - _ 1.38629 1.38629 1.38629 1.38629 0.36524 6.77079 1.18803 1.46634 0.26236 1.09861 0.40547 35 2.98986 6.46313 0.05611 5.90985 42 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00330 6.40885 6.40885 1.46634 0.26236 5.59026 0.00374 36 0.31967 2.73023 1.60908 4.78710 43 A - - _ 1.38629 1.38629 1.38629 1.38629 0.21410 1.92928 3.04750 3.13727 0.04437 5.59026 0.00374 37 0.76889 1.91482 0.97627 4.39062 68 a - - _ 1.38629 1.38629 1.38629 1.38629 0.00346 6.36194 6.36194 1.46634 0.26236 2.26743 0.10934 38 0.02534 5.94514 5.83049 3.93910 69 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00329 6.41180 6.41180 1.46634 0.26236 0.09267 2.42468 39 1.33580 2.01698 2.49057 0.65175 70 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00235 6.74577 6.74577 1.46634 0.26236 3.20046 0.04160 40 0.51933 6.10378 0.91519 6.02921 71 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00235 6.74577 6.74577 1.46634 0.26236 0.08500 2.50731 41 1.01829 1.33823 1.01616 4.23383 72 g - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 42 2.51384 6.19571 0.08963 5.90261 73 G - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 43 0.49687 2.26219 1.27793 4.72915 74 A - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 44 6.61121 0.02410 6.43600 3.86995 75 C - - > 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 45 2.87691 5.98728 0.07658 4.20597 76 G - - , 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 46 0.01786 6.68321 4.21369 6.40104 77 A - - , 1.38629 1.38629 1.38629 1.38629 0.00230 6.77079 6.77079 1.46634 0.26236 1.09861 0.40547 47 0.00360 7.05924 6.54919 6.64038 78 A - - , 1.38629 1.38629 1.38629 1.38629 0.00238 6.73546 6.73546 1.46634 0.26236 1.09861 0.40547 48 0.00621 6.93100 5.86941 6.03500 79 A - - ) 1.38629 1.38629 1.38629 1.38629 0.00238 6.73546 6.73546 1.46634 0.26236 1.09861 0.40547 49 5.24276 0.07085 5.61359 2.82242 80 C - - ) 1.38629 1.38629 1.38629 1.38629 0.00238 6.73546 6.73546 1.46634 0.26236 1.09861 0.40547 50 1.79431 3.58054 1.86687 0.42880 81 U - - ) 1.38629 1.38629 1.38629 1.38629 0.00238 6.73546 6.73546 1.46634 0.26236 1.09861 0.40547 51 4.51571 1.25226 0.97483 1.12100 82 g - - ) 1.38629 1.38629 1.38629 1.38629 0.02739 6.73546 3.65629 1.46634 0.26236 1.09861 0.40547 52 1.42420 2.36846 1.61290 0.76279 83 u - - ) 1.38629 1.38629 1.38629 1.38629 0.00244 6.71051 6.71051 1.46634 0.26236 3.16718 0.04304 53 1.42255 3.75849 2.35228 0.44561 84 U - - ) 1.38629 1.38629 1.38629 1.38629 0.14489 6.71051 2.01239 1.46634 0.26236 3.16718 0.04304 54 1.98305 1.28325 0.83063 1.90085 85 g - - ) 1.38629 1.38629 1.38629 1.38629 0.00141 6.56702 * 1.46634 0.26236 0.00000 * //