INFERNAL1/a [1.1.4 | Dec 2020] NAME Hammerhead_II ACC RF02276 DESC Hammerhead ribozyme (type II) STATES 210 NODES 56 CLEN 67 W 124 ALPH RNA RF no CONS yes MAP yes DATE Thu Feb 20 19:56:18 2014 COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi 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 6.688477 CKSUM 4291876430 NULL 0.000 0.000 0.000 0.000 GA 37.00 TC 37.20 NC 36.90 EFP7GF -13.8733 0.71896 ECMLC 0.62082 -6.61527 2.51165 1600000 346727 0.003461 ECMGC 0.39165 -17.92510 -4.69636 1600000 71150 0.005622 ECMLI 0.59885 -5.46981 3.52027 1600000 261397 0.004591 ECMGI 0.40082 -14.89113 -2.31008 1600000 61958 0.006456 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 0 1 124 193 -8.182 -8.389 -0.022 -6.803 IL 1 1 2 1 4 3 29 126 195 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 3 29 126 195 -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 29 124 193 -9.474 -0.009 -7.792 1.126 -0.944 -0.736 -0.519 D 4 2 3 5 3 0 24 122 191 -5.620 -0.734 -1.403 IL 5 5 3 5 3 2 27 124 193 -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 28 123 192 -9.474 -0.009 -7.792 0.250 -0.263 0.358 -0.523 D 7 5 3 8 3 0 22 121 190 -6.390 -1.568 -0.620 IR 8 8 3 8 3 2 27 123 192 -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 27 122 191 -9.474 -0.009 -7.792 0.946 -0.837 0.098 -1.173 D 10 8 3 11 3 0 21 120 189 -6.390 -1.568 -0.620 IR 11 11 3 11 3 2 26 122 191 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 79 - A - - MR 12 11 3 14 3 3 26 121 190 -9.474 -0.009 -7.792 1.395 -1.066 -1.183 -1.147 D 13 11 3 14 3 0 20 119 188 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 25 121 190 -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 25 120 189 -9.474 -0.009 -7.792 0.695 -0.286 -0.177 -0.564 D 16 14 3 17 3 0 19 118 187 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 24 120 189 -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 24 119 188 -9.474 -0.009 -7.792 -0.986 1.194 -1.687 -0.157 D 19 17 3 20 3 0 18 117 186 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 23 119 188 -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 23 118 187 -9.474 -0.009 -7.792 -0.429 1.463 -2.895 -1.452 D 22 20 3 23 3 0 18 116 185 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 22 118 187 -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 22 117 186 -9.474 -0.009 -7.792 -2.018 -4.161 1.854 -3.600 D 25 23 3 26 3 0 17 115 184 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 21 117 186 -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 21 116 185 -8.161 -0.019 -7.976 -8.188 -9.080 1.943 -4.572 -4.036 -4.290 D 28 26 3 29 5 0 16 114 183 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 5 1 19 116 185 -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 20 115 184 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -2.873 1.113 -3.001 0.720 -3.187 -1.694 0.446 -3.393 -3.093 2.292 -3.559 -0.568 0.244 1.280 -1.183 -2.157 ML 31 29 3 34 6 1 17 113 182 -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 16 113 182 -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 13 110 179 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 18 114 183 -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 18 114 183 -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 19 113 182 -8.182 -1.837 -0.499 -6.803 -5.880 -5.839 -5.307 -2.092 -3.773 -5.557 2.064 -4.630 -5.363 -2.122 3.309 -3.814 -0.472 -5.847 -1.471 -4.187 ML 37 35 6 40 4 1 16 112 181 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 38 35 6 40 4 1 14 111 180 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 39 35 6 40 4 0 13 110 178 -4.568 -4.250 -2.265 -0.520 IL 40 40 5 40 4 1 17 113 182 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 41 41 6 41 3 1 18 112 181 -1.389 -0.735 -5.862 0.000 0.000 0.000 0.000 [ MATL 12 ] 4 - C - - - ML 42 41 6 44 3 1 16 111 179 -9.137 -0.009 -7.791 -4.221 1.930 -4.871 -3.293 D 43 41 6 44 3 0 12 108 177 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 16 111 180 -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 15 110 178 -9.137 -0.009 -7.791 -3.671 -5.128 1.943 -4.410 D 46 44 3 47 3 0 11 107 176 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 15 110 179 -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 15 109 177 -9.137 -0.009 -7.791 1.943 -4.572 -4.036 -4.290 D 49 47 3 50 3 0 11 107 175 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 14 109 178 -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 14 108 176 -9.474 -0.009 -7.792 1.943 -4.572 -4.036 -4.290 D 52 50 3 53 3 0 10 106 175 -5.620 -0.734 -1.403 IL 53 53 3 53 3 1 13 108 177 -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 13 107 175 -9.474 -0.009 -7.792 1.943 -4.572 -4.036 -4.290 D 55 53 3 56 3 0 9 104 173 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 12 107 176 -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 12 106 174 -9.474 -0.009 -7.792 -3.671 -5.128 1.943 -4.410 D 58 56 3 59 3 0 8 103 172 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 11 106 175 -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 11 105 173 -9.474 -0.009 -7.792 -2.042 0.145 -2.867 1.330 D 61 59 3 62 3 0 8 102 171 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 11 105 174 -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 10 104 172 -9.474 -0.009 -7.792 1.943 -4.572 -4.036 -4.290 D 64 62 3 65 3 0 7 102 170 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 10 104 173 -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 9 103 171 -9.474 -0.009 -7.792 -3.671 -5.128 1.943 -4.410 D 67 65 3 68 3 0 6 101 170 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 9 103 172 -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 8 102 170 -9.474 -0.009 -7.792 -3.607 -3.287 -4.397 1.914 D 70 68 3 71 3 0 6 100 169 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 8 102 171 -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 7 101 169 -9.683 -0.002 -4.221 1.930 -4.871 -3.293 D 73 71 3 74 2 0 6 100 169 -4.432 -0.068 IR 74 74 3 74 2 1 7 101 170 -1.823 -0.479 0.000 0.000 0.000 0.000 [ BIF 23 ] - - - - - - B 75 74 3 76 138 0 6 100 168 [ BEGL 24 ] - - - - - - S 76 75 1 77 4 0 0 77 145 -0.026 -7.584 -6.992 -7.632 [ MATP 25 ] 8 37 A U - - MP 77 76 1 81 6 2 2 77 145 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -5.223 -0.503 -5.208 3.762 -7.017 -8.009 -2.589 -5.236 -5.012 -0.479 -5.657 -1.246 -2.676 -6.491 -4.448 -3.961 ML 78 76 1 81 6 1 1 74 143 -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 74 143 -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 70 139 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 81 81 5 81 6 1 1 76 145 -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 76 144 -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 75 143 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -5.794 -5.869 -5.288 -2.023 -3.770 -5.552 3.732 -0.472 -5.359 -1.929 -5.539 -3.926 -0.360 -5.751 -1.469 -4.165 ML 84 82 6 87 6 1 1 73 141 -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 72 141 -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 68 137 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 87 87 5 87 6 1 1 74 143 -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 74 142 -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 73 141 -9.707 -4.620 -0.072 -8.423 -8.703 -9.098 -3.876 -3.043 -3.847 1.160 -3.828 -4.591 2.184 -4.056 -3.994 2.545 -4.412 -0.061 0.348 -3.872 -1.331 -2.750 ML 90 88 6 93 6 1 1 71 139 -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 70 139 -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 67 135 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 93 93 5 93 6 1 1 72 141 -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 72 140 -2.848 -0.349 -6.359 -4.526 -5.632 0.000 0.000 0.000 0.000 [ MATP 28 ] 11 33 c g - - MP 95 94 6 99 6 2 2 71 139 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -3.361 -3.032 -3.439 0.520 -3.140 -4.239 2.511 -3.545 -3.493 2.141 -1.123 -0.237 0.741 -3.544 -0.860 -2.421 ML 96 94 6 99 6 1 1 69 138 -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 68 137 -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 65 134 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 99 99 5 99 6 1 1 70 139 -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 70 138 -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 69 137 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -2.530 -2.652 -2.695 0.842 -1.309 -1.251 2.429 -2.868 -2.726 1.025 -3.287 -1.035 1.614 -2.843 0.157 -1.824 ML 102 100 6 105 6 1 1 67 136 -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 66 135 -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 64 133 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 105 105 5 105 6 1 1 68 137 -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 68 137 -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 67 135 -8.182 -8.389 -0.022 -6.803 -4.304 -4.178 -4.245 -0.405 -3.289 -1.391 3.276 -3.954 -4.240 1.269 -4.671 -2.095 0.520 -4.466 -0.941 -3.105 ML 108 106 6 111 4 1 1 66 134 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 109 106 6 111 4 1 1 64 133 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 110 106 6 111 4 0 0 63 132 -4.568 -4.250 -2.265 -0.520 IL 111 111 5 111 4 1 1 67 135 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 112 112 6 112 3 1 1 66 135 -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 65 133 -9.137 -0.009 -7.791 -1.176 0.964 -0.435 -0.207 D 114 112 6 115 3 0 0 62 130 -6.174 -1.687 -0.566 IL 115 115 3 115 3 1 1 65 134 -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 64 132 -9.137 -0.062 -4.635 0.067 0.278 -0.618 0.123 D 117 115 3 118 3 0 0 60 129 -6.174 -1.687 -0.566 IL 118 118 3 118 3 1 1 64 133 -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 63 132 -9.085 -0.009 -7.739 -0.152 0.201 0.268 -0.422 D 120 118 3 121 3 0 0 56 125 -6.977 -2.490 -0.297 IL 121 121 3 121 3 1 1 63 132 -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 62 131 -1.504 -1.782 -1.488 0.163 0.384 -0.825 0.015 D 123 121 3 124 3 0 0 47 115 -6.977 -2.490 -0.297 IL 124 124 3 124 3 1 1 65 134 -0.386 -2.125 -7.497 0.000 0.000 0.000 0.000 [ MATL 35 ] 27 - u - - - ML 125 124 3 127 3 1 1 16 34 -8.459 -0.015 -7.113 -0.244 -0.355 0.240 0.254 D 126 124 3 127 3 0 0 14 33 -9.315 -0.931 -1.077 IL 127 127 3 127 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 28 - u - - - ML 128 127 3 130 3 1 1 14 33 -8.872 -0.011 -7.526 -0.069 0.058 -0.135 0.132 D 129 127 3 130 3 0 0 13 32 -8.346 -0.240 -2.738 IL 130 130 3 130 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 29 - g - - - ML 131 130 3 133 3 1 1 12 31 -9.137 -0.009 -7.791 -0.092 -1.123 0.652 0.045 D 132 130 3 133 3 0 0 13 32 -6.174 -1.687 -0.566 IL 133 133 3 133 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 30 - g - - - ML 134 133 3 136 2 1 1 1 1 * 0.000 -0.247 -0.667 0.925 -0.670 D 135 133 3 136 2 0 0 0 0 * 0.000 IL 136 136 3 136 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 39 ] - - - - - - E 137 136 3 -1 0 0 0 0 0 [ BEGR 40 ] - - - - - - S 138 75 1 139 3 0 0 36 55 -9.137 -0.009 -7.791 IL 139 139 2 139 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 41 ] 38 - C - - - ML 140 139 2 142 5 1 1 36 55 -8.161 -0.123 -7.976 -3.782 -9.080 -3.310 1.812 -4.113 -1.600 D 141 139 2 142 5 0 0 35 53 -4.959 -0.803 -4.221 -2.596 -2.508 IL 142 142 3 142 5 1 1 36 55 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 39 62 u a - - MP 143 142 3 147 6 2 2 35 54 -9.641 -9.580 -0.015 -8.357 -8.636 -9.031 -2.621 -2.655 -2.772 1.527 -2.521 -3.613 1.500 -2.949 -0.990 1.268 -3.362 -0.938 2.255 -2.911 -0.459 -1.884 ML 144 142 3 147 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 145 142 3 147 6 1 1 34 52 -7.827 -6.556 -0.684 -6.535 -1.668 -4.748 0.317 0.226 -0.785 0.006 D 146 142 3 147 6 0 0 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 147 147 5 147 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 148 148 6 148 5 1 1 34 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 40 61 g c - - MP 149 148 6 153 6 2 2 33 52 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -1.908 -1.999 -2.104 1.597 -2.114 -2.919 1.086 -1.140 -2.163 1.605 -1.266 0.516 1.154 -1.467 0.258 -1.354 ML 150 148 6 153 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 151 148 6 153 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 152 148 6 153 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 153 153 5 153 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 154 154 6 154 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 44 ] 41 60 C G - - MP 155 154 6 159 6 2 2 31 50 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -4.993 -5.022 -4.745 -1.224 -3.475 -5.199 3.381 -4.260 -4.766 -1.092 -1.292 -3.046 0.114 -5.076 1.411 -3.612 ML 156 154 6 159 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 157 154 6 159 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 158 154 6 159 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 159 159 5 159 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 160 160 6 160 5 1 1 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 42 59 C G - - MP 161 160 6 165 6 2 2 29 48 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -4.084 -4.030 -4.076 -0.245 -3.156 -1.640 3.227 -3.806 -4.050 0.350 -4.517 -1.972 1.164 -4.288 0.079 -2.933 ML 162 160 6 165 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 163 160 6 165 6 1 1 28 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 164 160 6 165 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 165 165 5 165 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 166 166 6 166 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 46 ] 43 58 g c - - MP 167 166 6 171 6 2 2 27 46 -9.707 -5.150 -0.054 -8.423 -8.703 -9.098 -2.640 -2.486 -1.078 0.782 -2.760 -2.132 2.030 -3.084 -2.872 2.342 -3.393 -0.324 0.719 -2.860 -0.426 -1.921 ML 168 166 6 171 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 169 166 6 171 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 170 166 6 171 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 171 171 5 171 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 172 172 6 172 5 1 1 26 45 -2.722 -0.385 -6.234 -4.401 -5.507 0.000 0.000 0.000 0.000 [ MATP 47 ] 44 56 g c - - MP 173 172 6 177 6 2 2 25 44 -9.707 -9.647 -0.058 -8.423 -4.960 -9.098 -2.977 -2.435 -3.047 1.203 -3.376 -0.015 0.417 -1.252 -3.230 2.742 -3.675 0.467 0.220 -1.459 -1.265 -2.181 ML 174 172 6 177 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 175 172 6 177 6 1 1 24 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 176 172 6 177 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 177 177 5 177 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 178 178 6 178 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 48 ] 45 55 G C - - MP 179 178 6 183 4 2 2 23 42 -1.949 -9.203 -0.475 -5.656 -4.672 -3.183 -4.580 0.883 -5.462 -4.894 0.191 -5.121 -4.650 3.496 -4.935 -0.841 -0.920 -4.352 -2.641 -3.511 ML 180 178 6 183 4 1 1 22 41 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 181 178 6 183 4 1 1 22 40 -5.215 -13.642 -0.167 -3.598 -0.239 0.714 -0.957 -0.004 D 182 178 6 183 4 0 0 20 39 -12.737 -14.007 -2.036 -0.404 IL 183 183 5 183 4 1 1 22 40 -4.356 -5.859 -0.183 -4.238 0.000 0.000 0.000 0.000 IR 184 184 6 184 3 1 1 23 41 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 49 ] - 54 - G - - MR 185 184 6 187 5 1 1 21 39 -8.161 -0.019 -7.976 -8.188 -9.080 -0.683 -1.429 1.293 -0.848 D 186 184 6 187 5 0 0 20 38 -5.352 -0.707 -2.978 -4.409 -2.404 IR 187 187 3 187 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 50 ] 47 53 c g - - MP 188 187 3 192 6 2 2 20 38 -9.707 -9.647 -0.014 -8.423 -8.703 -9.098 -1.826 -1.039 -1.040 0.872 -1.994 -2.872 2.098 -1.257 -2.086 1.224 -1.184 -0.695 1.063 -2.162 0.561 -1.282 ML 189 187 3 192 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 190 187 3 192 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 191 187 3 192 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 192 192 5 192 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 193 193 6 193 5 1 1 19 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 51 ] 48 52 g c - - MP 194 193 6 198 4 2 2 18 36 -8.182 -8.389 -0.022 -6.803 -4.155 -2.941 -4.207 1.545 -5.090 -5.040 -0.585 -0.835 -4.210 2.419 -4.596 2.380 -0.835 -4.324 -2.509 -3.079 ML 195 193 6 198 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 196 193 6 198 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 197 193 6 198 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 198 198 5 198 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 199 199 6 199 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 52 ] 49 - U - - - ML 200 199 6 202 3 1 1 14 32 -9.137 -0.009 -7.791 -2.478 -1.076 -3.232 1.696 D 201 199 6 202 3 0 0 15 33 -6.174 -1.687 -0.566 IL 202 202 3 202 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 53 ] 50 - G - - - ML 203 202 3 205 3 1 1 12 31 -9.137 -0.009 -7.791 -0.976 -1.947 1.590 -2.166 D 204 202 3 205 3 0 0 13 32 -6.174 -1.687 -0.566 IL 205 205 3 205 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 54 ] 51 - G - - - ML 206 205 3 208 2 1 1 1 1 * 0.000 -1.130 -3.575 1.740 -3.067 D 207 205 3 208 2 0 0 0 0 * 0.000 IL 208 208 3 208 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 55 ] - - - - - - E 209 208 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Hammerhead_II ACC RF02276 DESC Hammerhead ribozyme (type II) LENG 67 MAXL 149 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Feb 20 19:56:18 2014 COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM NSEQ 24 EFFN 13.543945 CKSUM 4291876430 STATS LOCAL MSV -7.8588 0.71896 STATS LOCAL VITERBI -8.8049 0.71896 STATS LOCAL FORWARD -3.3776 0.71896 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.53648 1.27419 1.10332 1.75193 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 0.00000 * 1 0.51779 2.14969 1.95783 1.92087 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 2 1.23372 2.86506 1.07416 1.17045 2 g - - ( 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 3 4.58369 1.39888 0.35324 3.20648 3 G - - ( 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 4 5.05323 0.02311 5.39549 4.42941 4 C - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 5 4.64450 5.75634 0.01873 5.15426 5 G - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 6 0.01670 5.42928 5.02297 5.18612 6 A - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 7 0.01670 5.42928 5.02297 5.18612 7 A - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 8 0.06526 4.95123 3.08341 4.57572 8 A - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 9 4.64986 0.06387 4.55537 3.17480 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 10 1.93989 1.11484 0.77433 2.69858 10 g - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 11 2.73084 0.81634 0.90276 2.43792 11 c - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 12 2.19942 0.76308 1.90694 1.29328 12 c - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 13 3.97621 0.26249 1.86614 2.85791 13 C - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 14 2.78999 0.58298 1.64387 1.67604 14 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 15 1.37514 1.10748 1.84047 1.35455 15 c - - _ 1.38629 1.38629 1.38629 1.38629 0.05454 4.90265 3.08669 1.46634 0.26236 1.09861 0.40547 16 1.60089 1.13974 1.10872 1.90784 16 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01556 4.86368 4.86368 1.46634 0.26236 2.09765 0.13096 17 1.28466 1.02177 2.03221 1.45992 17 c - - _ 1.38629 1.38629 1.38629 1.38629 1.46510 0.95745 0.95432 1.64920 0.21345 2.09765 0.13096 18 1.71626 1.62868 1.10754 1.22518 27 g - - _ 1.38629 1.38629 1.38629 1.38629 0.02512 4.38990 4.38990 1.46634 0.26236 0.61583 0.77695 19 1.51923 1.27163 1.42697 1.34434 28 c - - _ 1.38629 1.38629 1.38629 1.38629 0.01828 4.70439 4.70439 1.46634 0.26236 0.07633 2.61064 20 1.52758 2.36346 0.82956 1.37593 29 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 21 1.67246 1.85807 0.62873 2.09580 30 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 22 3.12803 1.70239 0.28772 3.73061 31 G - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 23 1.46381 1.79778 0.74751 2.04456 32 g - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 24 2.66467 1.15470 0.69905 2.13564 33 g - - > 1.38629 1.38629 1.38629 1.38629 0.08752 2.57208 4.90265 0.18428 1.78203 1.09861 0.40547 25 2.94396 0.90215 1.07861 1.60157 35 c - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 26 3.47485 4.67916 0.11268 2.71338 36 G - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 27 4.68250 2.48451 4.66528 0.10763 37 U - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 28 4.44634 0.08887 4.90503 2.71953 38 C - - , 1.38629 1.38629 1.38629 1.38629 0.09845 4.90265 2.44952 1.46634 0.26236 1.09861 0.40547 29 1.52746 1.80501 1.58369 0.88377 39 u - - < 1.38629 1.38629 1.38629 1.38629 0.01626 4.82046 4.82046 1.46634 0.26236 0.15875 1.91873 30 1.41197 1.88327 1.01240 1.42338 40 g - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 31 4.49367 0.31616 3.16684 1.52444 41 C - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 32 3.46231 0.32484 2.68143 1.72860 42 C - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 33 2.05061 1.14113 0.83784 2.12659 43 g - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 34 1.93808 1.73588 0.52116 2.45408 44 G - - < 1.38629 1.38629 1.38629 1.38629 0.06920 4.90265 2.82286 1.46634 0.26236 1.09861 0.40547 35 2.22599 2.67341 0.23152 3.51674 45 G - - < 1.38629 1.38629 1.38629 1.38629 0.34344 1.26287 4.84924 0.05451 2.93659 0.22307 1.60972 36 1.74499 1.01522 1.48775 1.43906 47 c - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 37 1.68828 2.76886 0.31372 3.83009 48 G - - < 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 38 3.79604 2.19895 4.31136 0.15876 49 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 39 2.22541 2.83492 0.22371 3.38997 50 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 40 2.25526 4.55266 0.13981 4.19352 51 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 41 4.06878 1.16374 3.87401 0.43107 52 U - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 42 1.96744 1.59865 0.71740 1.77196 53 g - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 43 2.05847 2.54076 0.39109 2.14365 54 G - - - 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 44 3.57381 0.26288 2.59975 2.04929 55 C - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 45 3.03472 0.48166 2.74566 1.30952 56 C - - > 1.38629 1.38629 1.38629 1.38629 0.06395 2.90910 4.90265 0.25318 1.49756 1.09861 0.40547 46 2.48566 0.89872 0.99191 1.97494 58 c - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 47 2.13617 2.43801 0.28287 3.19563 59 G - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 48 3.31779 4.38460 0.06727 4.11340 60 G - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 49 1.85426 1.37282 1.50755 0.99808 61 u - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 50 0.88929 1.78542 1.68621 1.44347 62 a - - > 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 51 5.05323 0.02311 5.39549 4.42941 63 C - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 52 4.78480 4.48556 5.35375 0.02466 64 U - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 53 4.64450 5.75634 0.01873 5.15426 65 G - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 54 0.01670 5.42928 5.02297 5.18612 66 A - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 55 3.60942 1.24185 4.20502 0.40173 67 U - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 56 4.64450 5.75634 0.01873 5.15426 68 G - - , 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 57 0.01670 5.42928 5.02297 5.18612 69 A - - , 1.38629 1.38629 1.38629 1.38629 0.35908 1.22331 4.90265 0.51588 0.90876 1.09861 0.40547 58 3.52173 4.67249 0.05344 4.33237 72 G - - ) 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 59 3.70014 0.13807 3.35799 2.66739 73 C - - ) 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 60 0.01670 5.42928 5.02297 5.18612 74 A - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 61 2.96959 5.02019 0.07051 4.59033 75 G - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 62 1.71038 0.26874 4.29103 3.19012 76 C - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 63 2.32511 0.45172 2.74721 1.60152 77 C - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 64 0.84725 1.54111 1.47935 2.04422 78 a - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 65 0.32766 2.21587 2.36388 2.57341 79 A - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 66 0.64240 2.02512 1.25557 2.86334 80 A - - : 1.38629 1.38629 1.38629 1.38629 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547 67 1.22218 1.51879 1.04805 1.99647 81 g - - : 1.38629 1.38629 1.38629 1.38629 0.00751 4.89520 * 1.46634 0.26236 0.00000 * //