INFERNAL1/a [1.1.5 | Sep 2023] NAME Hammerhead_II ACC RF02276 DESC Hammerhead ribozyme (type II) STATES 207 NODES 55 CLEN 66 W 120 ALPH RNA RF no CONS yes MAP yes DATE Sun Jul 7 18:48:07 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/rescan/families/RF02276/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 24 EFFN 6.793945 CKSUM 4291876430 NULL 0.000 0.000 0.000 0.000 GA 37.00 TC 37.00 NC 36.90 EFP7GF -13.2599 0.71899 ECMLC 0.63038 -6.54657 2.56130 1600000 373814 0.003210 ECMGC 0.38596 -18.32526 -4.74363 1600000 75620 0.005290 ECMLI 0.60341 -5.47487 3.55393 1600000 278774 0.004305 ECMGI 0.41626 -14.41836 -2.24716 1600000 63439 0.006305 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 0 1 120 185 -8.200 -8.407 -0.022 -6.821 IL 1 1 2 1 4 3 29 122 187 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 2 28 122 187 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - A - - - ML 3 2 3 5 3 3 28 120 185 -9.491 -0.008 -7.809 1.119 -0.900 -0.702 -0.561 D 4 2 3 5 3 0 23 119 183 -5.620 -0.734 -1.403 IL 5 5 3 5 3 2 27 121 185 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 81 - g - - MR 6 5 3 8 3 3 27 119 184 -9.491 -0.008 -7.809 0.292 -0.328 0.343 -0.495 D 7 5 3 8 3 0 21 117 182 -6.390 -1.568 -0.620 IR 8 8 3 8 3 2 26 120 184 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 80 - A - - MR 9 8 3 11 3 3 26 118 183 -9.491 -0.008 -7.809 1.002 -0.997 0.114 -1.273 D 10 8 3 11 3 0 20 116 181 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 25 119 183 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 79 - A - - MR 12 11 3 14 3 2 25 117 182 -9.491 -0.008 -7.809 1.329 -0.930 -1.080 -1.030 D 13 11 3 14 3 0 20 115 180 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 24 118 182 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 78 - a - - MR 15 14 3 17 3 2 24 116 181 -9.491 -0.008 -7.809 0.675 -0.256 -0.180 -0.550 D 16 14 3 17 3 0 19 114 179 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 23 117 181 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 77 - C - - MR 18 17 3 20 3 2 23 115 180 -9.491 -0.008 -7.809 -0.886 1.149 -1.571 -0.145 D 19 17 3 20 3 0 18 113 178 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 23 116 180 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 76 - C - - MR 21 20 3 23 3 2 23 114 179 -9.491 -0.008 -7.809 -0.432 1.468 -2.922 -1.474 D 22 20 3 23 3 0 17 112 177 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 22 115 179 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 75 - G - - MR 24 23 3 26 3 2 22 113 178 -9.491 -0.008 -7.809 -1.976 -4.150 1.851 -3.592 D 25 23 3 26 3 0 16 111 176 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 21 114 178 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 74 - A - - MR 27 26 3 29 5 1 21 112 177 -8.177 -0.018 -7.993 -8.205 -9.096 1.944 -4.600 -4.064 -4.319 D 28 26 3 29 5 0 15 111 175 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 5 1 19 112 177 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 2 73 g c - - MP 30 29 3 34 6 2 20 111 176 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -2.875 1.135 -3.005 0.711 -3.190 -1.520 0.439 -3.395 -3.093 2.287 -3.557 -0.571 0.236 1.263 -1.188 -2.161 ML 31 29 3 34 6 1 17 110 174 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 32 29 3 34 6 1 15 109 174 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 3 34 6 0 12 106 171 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 18 111 175 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 35 35 6 35 5 1 18 110 175 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 3 72 G G - - MP 36 35 6 40 4 2 18 109 174 -8.200 -1.815 -0.507 -6.821 -5.903 -5.864 -5.327 -2.117 -3.791 -5.576 2.060 -4.648 -5.384 -2.149 3.314 -3.841 -0.491 -5.868 -1.489 -4.208 ML 37 35 6 40 4 1 15 108 173 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 38 35 6 40 4 1 13 107 172 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 39 35 6 40 4 0 12 106 170 -4.568 -4.250 -2.265 -0.520 IL 40 40 5 40 4 1 17 109 174 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 41 41 6 41 3 1 17 108 173 -1.396 -0.729 -5.885 0.000 0.000 0.000 0.000 [ MATL 12 ] 4 - C - - - ML 42 41 6 44 3 1 16 107 171 -9.155 -0.009 -7.809 -4.247 1.931 -4.894 -3.319 D 43 41 6 44 3 0 12 104 169 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 15 107 172 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 5 - G - - - ML 45 44 3 47 3 1 15 106 170 -9.155 -0.009 -7.809 -3.696 -5.155 1.944 -4.434 D 46 44 3 47 3 0 11 104 168 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 15 106 171 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 6 - A - - - ML 48 47 3 50 3 1 14 105 169 -9.155 -0.009 -7.809 1.944 -4.600 -4.064 -4.319 D 49 47 3 50 3 0 10 103 167 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 14 105 170 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 7 - A - - - ML 51 50 3 53 3 1 13 104 168 -9.491 -0.008 -7.809 1.944 -4.600 -4.064 -4.319 D 52 50 3 53 3 0 10 102 167 -5.620 -0.734 -1.403 IL 53 53 3 53 3 1 13 104 169 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 69 - A - - MR 54 53 3 56 3 1 12 103 167 -9.491 -0.008 -7.809 1.944 -4.600 -4.064 -4.319 D 55 53 3 56 3 0 8 101 165 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 12 103 168 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 68 - G - - MR 57 56 3 59 3 1 11 102 166 -9.491 -0.008 -7.809 -3.696 -5.155 1.944 -4.434 D 58 56 3 59 3 0 8 100 164 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 11 102 167 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 67 - U - - MR 60 59 3 62 3 1 10 101 165 -9.491 -0.008 -7.809 -2.058 0.169 -2.886 1.322 D 61 59 3 62 3 0 7 99 163 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 10 101 166 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 66 - A - - MR 63 62 3 65 3 1 9 100 164 -9.491 -0.008 -7.809 1.944 -4.600 -4.064 -4.319 D 64 62 3 65 3 0 6 98 162 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 9 100 165 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 65 - G - - MR 66 65 3 68 3 1 8 99 163 -9.491 -0.008 -7.809 -3.696 -5.155 1.944 -4.434 D 67 65 3 68 3 0 6 97 162 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 8 99 164 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 64 - U - - MR 69 68 3 71 3 1 7 98 162 -9.491 -0.008 -7.809 -3.635 -3.313 -4.425 1.915 D 70 68 3 71 3 0 5 96 161 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 7 98 163 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 63 - C - - MR 72 71 3 74 2 1 6 97 161 -9.702 -0.002 -4.247 1.931 -4.894 -3.319 D 73 71 3 74 2 0 5 96 161 -4.432 -0.068 IR 74 74 3 74 2 1 6 97 162 -1.823 -0.479 0.000 0.000 0.000 0.000 [ BIF 23 ] - - - - - - B 75 74 3 76 135 0 5 96 160 [ BEGL 24 ] - - - - - - S 76 75 1 77 4 0 0 73 137 -0.026 -7.597 -7.004 -7.644 [ MATP 25 ] 8 37 A U - - MP 77 76 1 81 6 2 2 73 137 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -5.136 -0.196 -5.186 3.733 -6.943 -7.943 -2.511 -5.225 -4.923 -0.393 -5.569 -1.158 -2.595 -6.410 -4.370 -3.899 ML 78 76 1 81 6 1 1 71 135 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 79 76 1 81 6 1 1 70 135 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 80 76 1 81 6 0 0 66 131 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 81 81 5 81 6 1 1 72 137 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 82 82 6 82 5 1 1 72 136 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 9 36 C G - - MP 83 82 6 87 6 2 2 71 135 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -5.762 -5.841 -5.258 -1.996 -3.739 -5.524 3.711 -0.204 -5.323 -1.905 -5.513 -3.903 -0.325 -5.716 -1.430 -4.129 ML 84 82 6 87 6 1 1 69 133 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 85 82 6 87 6 1 1 68 133 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 86 82 6 87 6 0 0 64 129 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 87 87 5 87 6 1 1 70 135 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 88 88 6 88 5 1 1 70 134 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 10 35 g c - - MP 89 88 6 93 6 2 2 69 133 -9.718 -4.755 -0.067 -8.434 -8.714 -9.109 -3.871 -3.037 -3.842 1.206 -3.842 -4.586 2.169 -4.062 -3.994 2.533 -4.411 -0.001 0.330 -3.866 -1.347 -2.751 ML 90 88 6 93 6 1 1 67 131 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 91 88 6 93 6 1 1 66 131 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 92 88 6 93 6 0 0 63 127 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 93 93 5 93 6 1 1 68 133 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 94 94 6 94 5 1 1 68 132 -2.815 -0.358 -6.326 -4.494 -5.600 0.000 0.000 0.000 0.000 [ MATP 28 ] 11 33 c g - - MP 95 94 6 99 6 2 2 67 131 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -3.349 -3.034 -3.431 0.510 -3.133 -4.233 2.514 -3.538 -3.482 2.113 -0.924 -0.209 0.737 -3.538 -0.861 -2.417 ML 96 94 6 99 6 1 1 65 130 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 97 94 6 99 6 1 1 64 129 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 98 94 6 99 6 0 0 61 126 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 99 99 5 99 6 1 1 66 131 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 100 100 6 100 5 1 1 66 130 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 12 32 c g - - MP 101 100 6 105 6 2 2 65 129 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -2.555 -2.674 -2.719 0.867 -1.379 -1.066 2.448 -2.887 -2.749 1.011 -3.309 -1.049 1.607 -2.867 0.047 -1.844 ML 102 100 6 105 6 1 1 63 128 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 103 100 6 105 6 1 1 63 127 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 104 100 6 105 6 0 0 60 125 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 105 105 5 105 6 1 1 64 129 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 106 106 6 106 5 1 1 64 129 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 13 31 C G - - MP 107 106 6 111 4 2 2 63 127 -8.200 -8.407 -0.022 -6.821 -4.365 -4.238 -4.295 -0.452 -3.316 -1.451 3.298 -3.989 -4.290 1.240 -4.716 -2.148 0.492 -4.522 -0.964 -3.149 ML 108 106 6 111 4 1 1 62 126 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 109 106 6 111 4 1 1 61 125 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 110 106 6 111 4 0 0 59 124 -4.568 -4.250 -2.265 -0.520 IL 111 111 5 111 4 1 1 63 127 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 112 112 6 112 3 1 1 62 127 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 14 - c - - - ML 113 112 6 115 3 1 1 61 125 -9.155 -0.009 -7.809 -1.164 0.934 -0.340 -0.228 D 114 112 6 115 3 0 0 58 122 -6.174 -1.687 -0.566 IL 115 115 3 115 3 1 1 61 126 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 15 - c - - - ML 116 115 3 118 3 1 1 60 124 -9.155 -0.066 -4.548 0.068 0.300 -0.618 0.096 D 117 115 3 118 3 0 0 56 121 -6.174 -1.687 -0.566 IL 118 118 3 118 3 1 1 60 125 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 16 - g - - - ML 119 118 3 121 3 1 1 59 124 -9.099 -0.009 -7.753 -0.128 0.157 0.266 -0.381 D 120 118 3 121 3 0 0 52 117 -7.029 -2.542 -0.285 IL 121 121 3 121 3 1 1 59 124 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 17 - c - - - ML 122 121 3 124 3 1 1 58 123 -1.313 -1.201 -2.621 0.111 0.412 -0.799 0.021 D 123 121 3 124 3 0 0 43 108 -7.029 -2.542 -0.285 IL 124 124 3 124 3 1 1 60 125 -0.411 -2.044 -7.574 0.000 0.000 0.000 0.000 [ MATL 35 ] 28 - u - - - ML 125 124 3 127 3 1 1 14 33 -8.851 -0.011 -7.505 -0.039 0.091 -0.233 0.151 D 126 124 3 127 3 0 0 13 32 -8.500 -0.213 -2.892 IL 127 127 3 127 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 29 - g - - - ML 128 127 3 130 3 1 1 12 31 -9.155 -0.009 -7.809 -0.073 -1.119 0.667 0.001 D 129 127 3 130 3 0 0 13 32 -6.174 -1.687 -0.566 IL 130 130 3 130 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 30 - g - - - ML 131 130 3 133 2 1 1 1 1 * 0.000 -0.334 -0.583 0.927 -0.648 D 132 130 3 133 2 0 0 0 0 * 0.000 IL 133 133 3 133 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 38 ] - - - - - - E 134 133 3 -1 0 0 0 0 0 [ BEGR 39 ] - - - - - - S 135 75 1 136 3 0 0 36 55 -9.155 -0.009 -7.809 IL 136 136 2 136 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 40 ] 38 - C - - - ML 137 136 2 139 5 1 1 36 55 -8.177 -0.136 -7.993 -3.625 -9.096 -3.240 1.795 -4.063 -1.459 D 138 136 2 139 5 0 0 35 53 -4.959 -0.803 -4.221 -2.596 -2.508 IL 139 139 3 139 5 1 1 36 55 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 41 ] 39 62 u a - - MP 140 139 3 144 6 2 2 35 54 -9.643 -9.582 -0.015 -8.359 -8.639 -9.034 -2.613 -2.659 -2.766 1.478 -2.509 -3.608 1.520 -2.940 -0.816 1.213 -3.356 -0.952 2.278 -2.907 -0.449 -1.879 ML 141 139 3 144 6 1 1 34 52 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 142 139 3 144 6 1 1 34 52 -7.910 -6.639 -0.636 -6.617 -1.751 -4.831 0.317 0.259 -0.817 -0.015 D 143 139 3 144 6 0 0 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 144 144 5 144 6 1 1 35 53 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 145 145 6 145 5 1 1 34 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 40 61 g c - - MP 146 145 6 150 6 2 2 33 52 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -1.922 -1.999 -2.119 1.609 -2.132 -2.928 1.071 -1.003 -2.176 1.632 -1.157 0.504 1.099 -1.397 0.201 -1.367 ML 147 145 6 150 6 1 1 32 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 148 145 6 150 6 1 1 32 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 149 145 6 150 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 150 150 5 150 6 1 1 33 51 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 151 151 6 151 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 41 60 C G - - MP 152 151 6 156 6 2 2 31 50 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -5.015 -5.048 -4.765 -1.253 -3.493 -5.216 3.377 -4.279 -4.787 -1.124 -1.131 -3.078 0.090 -5.097 1.424 -3.634 ML 153 151 6 156 6 1 1 30 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 154 151 6 156 6 1 1 30 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 155 151 6 156 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 156 156 5 156 6 1 1 31 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 157 157 6 157 5 1 1 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 44 ] 42 59 C G - - MP 158 157 6 162 6 2 2 29 48 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -4.082 -4.026 -4.077 -0.243 -3.163 -1.495 3.227 -3.811 -4.050 0.405 -4.519 -1.968 1.155 -4.288 -0.028 -2.934 ML 159 157 6 162 6 1 1 28 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 160 157 6 162 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 161 157 6 162 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 162 162 5 162 6 1 1 29 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 163 163 6 163 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 43 58 g c - - MP 164 163 6 168 6 2 2 27 46 -9.718 -5.364 -0.048 -8.434 -8.714 -9.109 -2.580 -2.454 -0.915 0.786 -2.712 -2.022 1.992 -3.037 -2.816 2.320 -3.341 -0.288 0.725 -2.810 -0.365 -1.879 ML 165 163 6 168 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 166 163 6 168 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 167 163 6 168 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 168 168 5 168 6 1 1 27 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 169 169 6 169 5 1 1 26 45 -2.683 -0.397 -6.194 -4.362 -5.468 0.000 0.000 0.000 0.000 [ MATP 46 ] 44 56 g c - - MP 170 169 6 174 6 2 2 25 44 -9.718 -9.658 -0.065 -8.434 -4.751 -9.109 -2.958 -2.437 -3.031 1.197 -3.349 -0.030 0.423 -1.069 -3.212 2.733 -3.661 0.424 0.229 -1.384 -1.251 -2.170 ML 171 169 6 174 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 172 169 6 174 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 173 169 6 174 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 174 174 5 174 6 1 1 25 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 175 175 6 175 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 47 ] 45 55 G C - - MP 176 175 6 180 4 2 2 23 42 -1.884 -9.208 -0.499 -5.662 -4.760 -3.234 -4.679 0.864 -5.593 -4.941 -0.013 -5.221 -4.702 3.530 -4.985 -0.895 -1.032 -4.428 -2.759 -3.609 ML 177 175 6 180 4 1 1 22 41 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 178 175 6 180 4 1 1 22 40 -5.346 -13.773 -0.152 -3.730 -0.315 0.804 -1.041 -0.053 D 179 175 6 180 4 0 0 20 39 -12.737 -14.007 -2.036 -0.404 IL 180 180 5 180 4 1 1 22 40 -4.404 -5.907 -0.177 -4.285 0.000 0.000 0.000 0.000 IR 181 181 6 181 3 1 1 23 41 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 48 ] - 54 - G - - MR 182 181 6 184 5 1 1 21 39 -8.177 -0.018 -7.993 -8.205 -9.096 -0.649 -1.590 1.331 -0.961 D 183 181 6 184 5 0 0 20 38 -5.352 -0.707 -2.978 -4.409 -2.404 IR 184 184 3 184 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 49 ] 47 53 c g - - MP 185 184 3 189 6 2 2 20 38 -9.718 -9.658 -0.014 -8.434 -8.714 -9.109 -1.866 -1.154 -1.253 0.852 -2.024 -2.911 2.157 -1.481 -2.124 1.252 -1.402 -0.717 1.058 -2.201 0.637 -1.315 ML 186 184 3 189 6 1 1 20 39 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 187 184 3 189 6 1 1 20 38 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 188 184 3 189 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 189 189 5 189 6 1 1 20 38 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 190 190 6 190 5 1 1 19 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 50 ] 48 52 g u - - MP 191 190 6 195 4 2 2 18 36 -8.200 -8.407 -0.022 -6.821 -4.204 -2.968 -4.271 1.587 -5.183 -5.116 -0.665 -1.015 -4.241 2.354 -4.627 2.464 -0.916 -4.408 -2.593 -3.127 ML 192 190 6 195 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 193 190 6 195 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 194 190 6 195 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 195 195 5 195 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 196 196 6 196 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 51 ] 49 - U - - - ML 197 196 6 199 3 1 1 14 32 -9.155 -0.009 -7.809 -2.577 -1.302 -3.325 1.734 D 198 196 6 199 3 0 0 15 33 -6.174 -1.687 -0.566 IL 199 199 3 199 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 52 ] 50 - G - - - ML 200 199 3 202 3 1 1 12 31 -9.155 -0.009 -7.809 -0.996 -1.858 1.584 -2.152 D 201 199 3 202 3 0 0 13 32 -6.174 -1.687 -0.566 IL 202 202 3 202 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 53 ] 51 - G - - - ML 203 202 3 205 2 1 1 1 1 * 0.000 -1.078 -3.560 1.732 -3.055 D 204 202 3 205 2 0 0 0 0 * 0.000 IL 205 205 3 205 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 54 ] - - - - - - E 206 205 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME Hammerhead_II ACC RF02276 DESC Hammerhead ribozyme (type II) LENG 66 MAXL 145 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sun Jul 7 18:48:07 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/rescan/families/RF02276/CM NSEQ 24 EFFN 13.637695 CKSUM 4291876430 STATS LOCAL MSV -7.9137 0.71899 STATS LOCAL VITERBI -8.7630 0.71899 STATS LOCAL FORWARD -3.3897 0.71899 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.53530 1.27350 1.10235 1.75638 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 0.00000 * 1 0.52421 2.10238 1.92562 1.96591 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 2 1.22664 2.79169 1.07666 1.18851 2 g - - ( 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 3 4.59021 1.39999 0.35241 3.21249 3 G - - ( 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 4 5.05988 0.02296 5.40151 4.43627 4 C - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 5 4.65098 5.76385 0.01860 5.16083 5 G - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 6 0.01657 5.43761 5.03088 5.19359 6 A - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 7 0.01657 5.43761 5.03088 5.19359 7 A - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 8 0.06638 4.93977 3.06550 4.56201 8 A - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 9 4.64965 0.06397 4.55526 3.17266 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 10 1.89563 1.12815 0.77813 2.70486 10 g - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 11 2.74352 0.81559 0.90019 2.44431 11 c - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 12 2.17250 0.74379 1.92299 1.32943 12 c - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 13 3.99819 0.25662 1.88811 2.87122 13 C - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 14 2.77447 0.60475 1.57004 1.69626 14 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 15 1.37348 1.09053 1.83951 1.37895 15 c - - _ 1.38629 1.38629 1.38629 1.38629 0.05727 4.90526 3.03128 1.46634 0.26236 1.09861 0.40547 16 1.57491 1.17708 1.11368 1.85505 16 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01557 4.86356 4.86356 1.46634 0.26236 2.14173 0.12494 17 1.33072 1.00196 2.00380 1.45359 17 c - - _ 1.38629 1.38629 1.38629 1.38629 0.94900 0.82961 1.73356 1.56673 0.23411 2.14173 0.12494 18 1.48676 1.24714 1.50822 1.32702 28 c - - _ 1.38629 1.38629 1.38629 1.38629 0.01876 4.67851 4.67851 1.46634 0.26236 0.06808 2.72090 19 1.50632 2.35109 0.82131 1.41405 29 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 20 1.75804 1.78287 0.62885 2.06945 30 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 21 3.14216 1.72980 0.27967 3.75273 31 G - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 22 1.48023 1.77833 0.75254 2.02248 32 g - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 23 2.67108 1.17847 0.68521 2.12788 33 G - - > 1.38629 1.38629 1.38629 1.38629 0.08008 2.66566 4.90526 0.20088 1.70380 1.09861 0.40547 24 2.95082 0.91505 1.09166 1.55331 35 c - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 25 3.47318 4.67911 0.12311 2.58320 36 G - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 26 4.66829 2.36449 4.65285 0.11982 37 U - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 27 4.39258 0.09950 4.87499 2.59423 38 C - - , 1.38629 1.38629 1.38629 1.38629 0.10861 4.90526 2.34848 1.46634 0.26236 1.09861 0.40547 28 1.57294 1.78266 1.58735 0.86772 39 u - - < 1.38629 1.38629 1.38629 1.38629 0.01638 4.81303 4.81303 1.46634 0.26236 0.14419 2.00782 29 1.40437 1.87576 0.98646 1.47690 40 g - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 30 4.50252 0.32210 3.08774 1.52011 41 C - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 31 3.45277 0.32160 2.61819 1.76950 42 C - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 32 2.00363 1.16716 0.84140 2.09722 43 g - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 33 1.94177 1.71410 0.52969 2.43453 44 G - - < 1.38629 1.38629 1.38629 1.38629 0.07811 4.90526 2.69220 1.46634 0.26236 1.09861 0.40547 34 2.23018 2.84856 0.21432 3.59463 45 G - - < 1.38629 1.38629 1.38629 1.38629 0.36096 1.22041 4.84304 0.05259 2.97133 0.19781 1.71772 35 1.81725 0.99076 1.50142 1.41297 47 c - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 36 1.65232 2.89786 0.31076 3.89403 48 G - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 37 3.83124 2.38449 4.34281 0.13561 49 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 38 2.24622 2.75106 0.22781 3.37955 50 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 39 2.21121 4.53179 0.14582 4.17615 51 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 40 4.12898 1.22370 3.94583 0.39984 52 U - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 41 1.97896 1.59939 0.69637 1.82402 53 g - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 42 2.00241 2.68809 0.37143 2.23276 54 G - - - 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 43 3.62796 0.24434 2.76548 2.06148 55 C - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 44 3.03527 0.48319 2.74645 1.30574 56 C - - > 1.38629 1.38629 1.38629 1.38629 0.05638 3.04881 4.90526 0.28764 1.38642 1.09861 0.40547 45 2.47248 0.90373 0.99778 1.95283 58 c - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 46 2.14169 2.35807 0.29225 3.18540 59 G - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 47 3.32214 4.38832 0.06700 4.11612 60 G - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 48 1.91825 1.33674 1.52928 0.98418 61 u - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 49 0.86383 1.80714 1.67240 1.48484 62 a - - > 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 50 5.05988 0.02296 5.40151 4.43627 63 C - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 51 4.79417 4.49414 5.36343 0.02443 64 U - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 52 4.65098 5.76385 0.01860 5.16083 65 G - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 53 0.01657 5.43761 5.03088 5.19359 66 A - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 54 3.61295 1.22445 4.21150 0.40904 67 U - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 55 4.65098 5.76385 0.01860 5.16083 68 G - - , 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 56 0.01657 5.43761 5.03088 5.19359 69 A - - , 1.38629 1.38629 1.38629 1.38629 0.36434 1.21086 4.90526 0.51074 0.91642 1.09861 0.40547 57 3.52775 4.67900 0.05309 4.33899 72 G - - ) 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 58 3.70778 0.13696 3.36560 2.67480 73 C - - ) 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 59 0.01657 5.43761 5.03088 5.19359 74 A - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 60 2.92839 5.00134 0.07312 4.57559 75 G - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 61 1.71072 0.26798 4.30070 3.19961 76 C - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 62 2.23127 0.48026 2.64409 1.59497 77 C - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 63 0.86450 1.51658 1.48175 2.02468 78 a - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 64 0.37289 2.09804 2.27013 2.46203 79 A - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 65 0.60390 2.17352 1.24536 2.96208 80 A - - : 1.38629 1.38629 1.38629 1.38629 0.01493 4.90526 4.90526 1.46634 0.26236 1.09861 0.40547 66 1.18369 1.57598 1.06284 1.95494 81 g - - : 1.38629 1.38629 1.38629 1.38629 0.00749 4.89783 * 1.46634 0.26236 0.00000 * //