INFERNAL1/a [1.1.5 | Sep 2023] NAME HCV_SL8001 ACC RF04306 DESC Hepatitis C virus stem-loop SL8001 RNA STATES 178 NODES 43 CLEN 58 W 72 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 5 02:22:25 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/HCV_SL8001/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 57 EFFN 5.263733 CKSUM 1308032242 NULL 0.000 0.000 0.000 0.000 GA 41.00 TC 41.20 NC 35.40 EFP7GF -12.6372 0.71922 ECMLC 0.65780 -5.64712 3.14232 1600000 389154 0.003084 ECMGC 0.42438 -18.14810 -4.18615 1600000 149739 0.002671 ECMLI 0.63059 -4.61217 3.93397 1600000 262801 0.004566 ECMGI 0.45481 -14.21205 -1.77762 1600000 114315 0.003499 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 72 92 -7.909 -8.116 -0.027 -6.530 IL 1 1 2 1 4 1 12 77 96 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 12 76 95 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - C - - - ML 3 2 3 5 3 1 12 73 92 -8.874 -0.011 -7.528 -1.968 1.406 -2.900 -0.058 D 4 2 3 5 3 0 5 71 91 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 11 75 94 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - u - - - ML 6 5 3 8 3 1 11 71 91 -8.874 -0.011 -7.528 0.467 -1.409 -1.663 0.946 D 7 5 3 8 3 0 4 70 90 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 10 74 93 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - u - - - ML 9 8 3 11 3 1 10 70 90 -9.220 -0.010 -7.538 0.019 -0.599 -0.403 0.651 D 10 8 3 11 3 0 4 69 88 -5.620 -0.734 -1.403 IL 11 11 3 11 3 1 8 71 90 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 58 - A - - MR 12 11 3 14 3 1 9 69 89 -9.220 -0.010 -7.538 1.171 -0.978 -1.614 -0.130 D 13 11 3 14 3 0 2 68 87 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 7 70 89 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 57 - C - - MR 15 14 3 17 3 1 9 68 88 -9.220 -0.010 -7.538 -3.784 1.906 -4.505 -2.875 D 16 14 3 17 3 0 1 67 86 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 6 69 88 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 56 - A - - MR 18 17 3 20 3 1 8 67 87 -9.220 -0.010 -7.538 1.923 -4.131 -3.617 -3.836 D 19 17 3 20 3 0 1 66 85 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 5 68 87 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 55 - G - - MR 21 20 3 23 3 1 7 66 86 -9.220 -0.010 -7.538 -3.286 -4.702 1.925 -4.029 D 22 20 3 23 3 0 0 65 84 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 5 67 86 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 54 - A - - MR 24 23 3 26 5 1 7 65 85 -7.915 -0.022 -7.730 -7.943 -8.834 1.025 -1.412 -0.126 -0.574 D 25 23 3 26 5 0 0 64 83 -5.352 -0.707 -2.978 -4.409 -2.404 IR 26 26 3 26 5 1 3 66 85 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 4 53 u a - - MP 27 26 3 31 6 2 8 64 84 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -0.575 -2.351 -2.399 0.726 -2.273 -3.251 1.246 -2.661 1.226 0.883 -3.010 -0.822 2.106 -2.553 -0.379 -1.597 ML 28 26 3 31 6 1 2 63 82 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 29 26 3 31 6 1 2 63 82 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 30 26 3 31 6 0 0 60 80 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 2 64 83 -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 3 64 83 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 5 52 C G - - MP 33 32 6 37 6 2 7 62 82 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -2.149 -3.066 -2.019 0.078 -2.891 -2.245 3.374 -3.344 -3.134 -0.063 -3.662 -1.602 0.337 -3.225 -1.048 -2.285 ML 34 32 6 37 6 1 2 61 80 -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 1 61 80 -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 58 78 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 2 62 81 -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 62 81 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 6 51 C G - - MP 39 38 6 43 6 2 7 60 80 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -4.082 -4.047 -4.031 -0.273 -3.043 -4.685 3.206 -3.722 -0.900 -0.115 -4.455 -2.013 1.521 -4.267 -0.475 -2.896 ML 40 38 6 43 6 1 1 59 78 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 6 1 1 59 78 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 42 38 6 43 6 0 0 56 76 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 2 60 79 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 44 44 6 44 5 1 2 60 79 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 7 50 A U - - MP 45 44 6 49 6 2 7 58 78 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -3.893 -3.299 -3.957 3.340 -4.255 -5.175 -0.038 0.259 -3.961 0.402 -4.524 -0.158 -0.606 -4.366 -2.126 -2.959 ML 46 44 6 49 6 1 1 57 76 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 6 1 1 57 76 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 48 44 6 49 6 0 0 54 74 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 2 58 77 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 50 50 6 50 5 1 2 58 77 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 8 49 G C - - MP 51 50 6 55 6 2 6 56 76 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -3.499 -1.523 -3.443 1.220 -4.113 -1.602 0.230 -2.452 -3.752 3.071 -4.103 0.348 -0.010 -3.375 -1.637 -2.486 ML 52 50 6 55 6 1 1 55 74 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 6 1 1 55 74 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 54 50 6 55 6 0 0 52 72 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 2 56 75 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 56 56 6 56 5 1 2 56 75 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 9 48 c g - - MP 57 56 6 61 6 2 6 54 74 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -1.201 -1.899 -1.485 1.155 -1.876 -2.356 2.023 -1.940 -0.947 1.176 -2.527 -0.459 1.187 -2.029 0.072 -0.585 ML 58 56 6 61 6 1 1 53 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 6 1 1 53 72 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 60 56 6 61 6 0 0 51 70 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 6 1 1 54 73 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 62 62 6 62 5 1 1 54 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 10 47 A U - - MP 63 62 6 67 6 2 5 52 72 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -5.443 -4.161 -5.182 3.842 -7.051 -8.165 -2.615 -5.156 -5.222 -0.708 -5.860 -1.209 -2.791 -6.716 -4.505 -4.066 ML 64 62 6 67 6 1 1 51 70 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 6 1 1 51 70 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 6 67 6 0 0 49 68 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 52 71 -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 52 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 11 46 a u - - MP 69 68 6 73 6 2 4 50 70 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -3.938 1.192 -3.987 2.647 -4.784 -5.049 -0.527 -4.343 -4.006 2.069 -4.493 0.295 -0.729 -4.217 -2.372 -2.898 ML 70 68 6 73 6 1 1 50 69 -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 50 69 -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 48 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 50 69 -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 50 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 12 45 G C - - MP 75 74 6 79 4 2 3 48 67 -7.909 -8.116 -0.027 -6.530 -5.595 -0.046 -5.738 -0.425 -6.710 -5.173 -1.755 -6.186 -5.018 3.708 -5.297 -1.348 -2.033 -5.049 -3.830 -4.640 ML 76 74 6 79 4 1 1 49 69 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 77 74 6 79 4 1 1 49 68 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 78 74 6 79 4 0 0 48 67 -4.568 -4.250 -2.265 -0.520 IL 79 79 5 79 4 1 1 51 70 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 80 80 6 80 3 1 1 50 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 13 - G - - - ML 81 80 6 83 3 1 1 46 65 -9.220 -0.010 -7.538 -3.286 -4.702 1.925 -4.029 D 82 80 6 83 3 0 0 45 64 -5.620 -0.734 -1.403 IL 83 83 3 83 3 1 1 47 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 44 - A - - MR 84 83 3 86 5 1 1 45 64 -7.915 -0.022 -7.730 -7.943 -8.834 1.923 -4.131 -3.617 -3.836 D 85 83 3 86 5 0 0 44 63 -5.352 -0.707 -2.978 -4.409 -2.404 IR 86 86 3 86 5 1 1 45 64 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 14 43 C G - - MP 87 86 3 91 6 2 2 44 63 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -6.548 -6.624 -5.862 -2.804 -4.285 -6.011 3.884 -5.320 -6.066 -2.736 -6.018 -4.698 -1.072 -6.483 -2.132 -4.870 ML 88 86 3 91 6 1 1 44 63 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 89 86 3 91 6 1 1 43 63 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 3 91 6 0 0 42 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 44 63 -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 44 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 15 42 C G - - MP 93 92 6 97 4 2 2 42 61 -7.909 -8.116 -0.027 -6.530 -4.064 -4.163 -0.728 -0.661 1.654 -4.583 3.059 -3.759 -4.032 -0.595 -4.440 -2.409 0.437 -4.253 -0.835 -2.991 ML 94 92 6 97 4 1 1 43 62 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 4 1 1 43 62 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 96 92 6 97 4 0 0 42 61 -4.568 -4.250 -2.265 -0.520 IL 97 97 5 97 4 1 1 44 64 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 98 98 6 98 3 1 1 43 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 16 - a - - - ML 99 98 6 101 3 1 1 40 58 -8.874 -0.011 -7.528 0.736 -1.028 0.443 -1.047 D 100 98 6 101 3 0 0 39 58 -6.174 -1.687 -0.566 IL 101 101 3 101 3 1 1 42 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 17 - U - - - ML 102 101 3 104 3 1 1 38 57 -8.874 -0.011 -7.528 -2.382 -1.591 -3.129 1.749 D 103 101 3 104 3 0 0 38 57 -6.174 -1.687 -0.566 IL 104 104 3 104 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 18 - u - - - ML 105 104 3 107 3 1 1 37 56 -8.874 -0.011 -7.528 0.052 -0.687 -0.732 0.799 D 106 104 3 107 3 0 0 36 55 -6.174 -1.687 -0.566 IL 107 107 3 107 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 19 - A - - - ML 108 107 3 110 3 1 1 36 55 -8.874 -0.011 -7.528 1.152 -0.737 -1.134 -0.470 D 109 107 3 110 3 0 0 35 54 -6.174 -1.687 -0.566 IL 110 110 3 110 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 20 - A - - - ML 111 110 3 113 3 1 1 35 54 -9.220 -0.010 -7.538 1.197 -0.741 -0.648 -1.087 D 112 110 3 113 3 0 0 34 53 -5.620 -0.734 -1.403 IL 113 113 3 113 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 41 - A - - MR 114 113 3 116 3 1 1 34 53 -9.220 -0.010 -7.538 1.863 -3.527 -2.553 -3.260 D 115 113 3 116 3 0 0 33 51 -6.390 -1.568 -0.620 IR 116 116 3 116 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 40 - g - - MR 117 116 3 119 5 1 1 33 52 -7.915 -0.022 -7.730 -7.943 -8.834 0.370 -0.317 0.399 -0.770 D 118 116 3 119 5 0 0 32 51 -5.352 -0.707 -2.978 -4.409 -2.404 IR 119 119 3 119 5 1 1 34 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 21 39 C G - - MP 120 119 3 124 6 2 2 32 51 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -3.475 -3.560 -1.785 -0.162 -3.001 -4.312 3.316 -3.573 -3.592 -0.100 -1.558 -1.830 0.571 -3.748 0.091 -2.622 ML 121 119 3 124 6 1 1 31 49 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 122 119 3 124 6 1 1 31 49 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 123 119 3 124 6 0 0 28 47 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 32 51 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 32 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 22 38 C G - - MP 126 125 6 130 6 2 2 30 49 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -6.548 -6.624 -5.862 -2.804 -4.285 -6.011 3.884 -5.320 -6.066 -2.736 -6.018 -4.698 -1.072 -6.483 -2.132 -4.870 ML 127 125 6 130 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 128 125 6 130 6 1 1 29 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 129 125 6 130 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 30 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 131 131 6 131 5 1 1 30 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 23 37 A U - - MP 132 131 6 136 6 2 2 28 47 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -5.517 -4.259 -5.205 3.849 -6.644 -7.948 -2.252 -5.141 -5.282 -0.813 -5.899 -1.557 -2.624 -6.736 -4.170 -4.109 ML 133 131 6 136 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 134 131 6 136 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 135 131 6 136 6 0 0 25 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 6 1 1 28 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 137 137 6 137 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 32 ] 24 36 C G - - MP 138 137 6 142 6 2 2 26 45 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -3.642 -3.602 -3.676 0.062 -2.909 -1.140 3.078 -3.514 -3.669 0.824 -4.155 -1.626 1.309 -3.867 -0.611 -2.597 ML 139 137 6 142 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 140 137 6 142 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 141 137 6 142 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 142 142 5 142 6 1 1 26 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 143 143 6 143 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 33 ] 25 35 A U - - MP 144 143 6 148 6 2 2 24 43 -9.552 -9.492 -0.015 -8.268 -8.548 -8.943 -5.517 -4.259 -5.205 3.849 -6.644 -7.948 -2.252 -5.141 -5.282 -0.813 -5.899 -1.557 -2.624 -6.736 -4.170 -4.109 ML 145 143 6 148 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 146 143 6 148 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 147 143 6 148 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 148 148 5 148 6 1 1 24 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 149 149 6 149 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 26 34 U G - - MP 150 149 6 154 4 2 2 22 41 -7.909 -8.116 -0.027 -6.530 -5.636 -5.617 -5.050 -1.867 -3.503 -5.289 0.791 -4.365 -5.110 -1.898 -5.280 -3.614 -0.206 -5.591 3.633 -3.932 ML 151 149 6 154 4 1 1 24 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 152 149 6 154 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 153 149 6 154 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 154 154 5 154 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 155 155 6 155 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 35 ] 27 - C - - - ML 156 155 6 158 3 1 1 19 38 -8.874 -0.011 -7.528 -2.060 1.778 -3.534 -2.035 D 157 155 6 158 3 0 0 19 38 -6.174 -1.687 -0.566 IL 158 158 3 158 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 28 - A - - - ML 159 158 3 161 3 1 1 18 37 -8.874 -0.011 -7.528 1.148 -0.275 -1.117 -1.011 D 160 158 3 161 3 0 0 18 36 -6.174 -1.687 -0.566 IL 161 161 3 161 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 29 - A - - - ML 162 161 3 164 3 1 1 17 35 -8.874 -0.011 -7.528 1.312 -2.476 0.122 -2.008 D 163 161 3 164 3 0 0 17 35 -6.174 -1.687 -0.566 IL 164 164 3 164 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 30 - C - - - ML 165 164 3 167 3 1 1 16 34 -8.874 -0.011 -7.528 -0.574 1.050 -0.594 -0.747 D 166 164 3 167 3 0 0 16 34 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 39 ] 31 - U - - - ML 168 167 3 170 3 1 1 14 33 -8.874 -0.011 -7.528 -1.612 -1.793 -1.127 1.549 D 169 167 3 170 3 0 0 15 33 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 40 ] 32 - C - - - ML 171 170 3 173 3 1 1 12 31 -8.874 -0.011 -7.528 -1.358 1.524 -1.697 -1.230 D 172 170 3 173 3 0 0 13 32 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 41 ] 33 - C - - - ML 174 173 3 176 2 1 1 1 1 * 0.000 -1.922 1.560 -2.072 -0.864 D 175 173 3 176 2 0 0 0 0 * 0.000 IL 176 176 3 176 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 42 ] - - - - - - E 177 176 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME HCV_SL8001 ACC RF04306 DESC Hepatitis C virus stem-loop SL8001 RNA LENG 58 MAXL 131 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 5 02:22:25 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/HCV_SL8001/CM NSEQ 57 EFFN 7.886902 CKSUM 1308032242 STATS LOCAL MSV -7.5878 0.71922 STATS LOCAL VITERBI -8.3397 0.71922 STATS LOCAL FORWARD -4.2595 0.71922 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.31370 1.33502 1.37665 1.53432 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 0.00000 * 1 3.13519 0.35224 3.81244 1.46403 1 C - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 2 1.03027 2.64286 2.82074 0.66871 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 3 1.39659 1.84897 1.65697 0.90524 3 u - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 4 1.93905 2.04465 1.04639 0.97941 4 u - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 5 2.21066 0.38827 2.44719 2.07461 5 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 6 3.20246 0.41829 2.42331 1.54863 6 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 7 0.36600 1.88924 2.10559 3.39508 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 8 1.77973 2.31253 0.42472 2.54650 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 9 1.60936 1.14571 1.46813 1.37979 9 c - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 10 0.06316 4.85143 3.14985 4.55381 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 11 0.46560 3.56016 1.17801 3.32664 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 12 2.26176 4.32313 0.14161 4.22593 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 13 4.10729 5.13852 0.03273 4.61691 13 G - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 14 4.89529 0.04419 4.82773 3.58481 14 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 15 2.70835 0.19127 3.59945 2.52441 15 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 16 0.83519 2.17336 1.01551 2.40576 16 a - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 17 3.41566 2.63134 3.92962 0.13295 17 U - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 18 1.36153 1.92682 1.91879 0.79554 18 u - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 19 0.52664 1.93532 2.28484 1.81252 19 A - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 20 0.48844 1.92226 1.87415 2.44581 20 A - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 21 2.67124 0.38441 2.45383 1.80777 21 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 22 4.88039 0.04448 4.81838 3.58174 22 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 23 0.05815 4.66976 3.32669 4.49112 23 A - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 24 2.86939 0.44323 2.12621 1.70364 24 C - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 25 0.05849 4.65993 3.32410 4.47959 25 A - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 26 4.06895 2.45094 3.97226 0.13027 26 U - - < 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 27 3.00884 0.10792 4.25289 3.25119 27 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 28 0.52160 1.54668 2.28343 2.39095 28 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 29 0.42610 3.58605 1.26142 3.32451 29 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 30 1.92671 0.55699 1.80541 2.14529 30 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 31 2.91182 2.97333 2.19630 0.24427 31 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 32 2.57594 0.24847 2.66753 2.59700 32 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 33 3.10201 0.23869 2.94715 2.16373 33 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 34 3.06188 4.15967 0.08838 3.80890 34 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 35 4.68743 3.74466 4.47270 0.04528 35 U - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 36 1.87389 1.95952 0.45567 2.63770 36 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 37 4.71348 3.75004 4.48654 0.04474 37 U - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 38 3.86088 4.98333 0.03758 4.71298 38 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 39 2.46025 3.04276 0.21346 2.82858 39 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 40 1.12506 1.57898 1.04140 2.15223 40 g - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 41 0.06690 4.24685 3.38478 4.10342 41 A - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 42 1.20098 3.75858 0.43682 3.51670 42 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 43 3.87352 5.00724 0.03690 4.73848 43 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 44 0.03193 4.76268 4.38361 4.56555 44 A - - - 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 45 4.36835 0.08005 4.17819 3.01742 45 C - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 46 3.54847 0.89326 3.35039 0.64085 46 U - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 47 4.73523 3.66626 4.64959 0.04491 47 U - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 48 1.55438 1.69924 0.99459 1.44400 48 g - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 49 2.81432 0.47951 2.51229 1.42758 49 C - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 50 3.60410 2.79030 2.96556 0.15099 50 U - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 51 1.52819 3.14996 0.37294 2.96594 51 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 52 2.20531 2.42877 0.35649 2.28763 52 G - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 53 0.49121 2.17982 1.85752 2.12867 53 A - - > 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 54 0.61980 2.54021 1.45812 1.89430 54 A - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 55 4.10729 5.13852 0.03273 4.61691 55 G - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 56 0.03193 4.76268 4.38361 4.56555 56 A - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 57 4.50155 0.04028 4.92039 3.85876 57 C - - : 1.38629 1.38629 1.38629 1.38629 0.02116 4.55925 4.55925 1.46634 0.26236 1.09861 0.40547 58 0.50590 2.16527 2.75436 1.52019 58 A - - : 1.38629 1.38629 1.38629 1.38629 0.01064 4.54872 * 1.46634 0.26236 0.00000 * //