INFERNAL1/a [1.1.4 | Dec 2020] NAME Pestivirus-3UTR-SLIII-scrofae ACC RF04325 DESC Pestivirus 3' UTR SLIII P. scrofae Atypical porcine pestivirus STATES 202 NODES 51 CLEN 66 W 83 ALPH RNA RF no CONS yes MAP yes DATE Wed Apr 30 17:07:19 2025 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/15.1_nancy/Pestivirus/pestivirus_3utr_K/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 4 EFFN 1.511719 CKSUM 2640445115 NULL 0.000 0.000 0.000 0.000 GA 85.00 TC 89.60 NC 41.00 EFP7GF -10.4633 0.71916 ECMLC 0.62847 -6.43064 2.97322 1600000 442458 0.002712 ECMGC 0.38942 -18.11598 -3.63887 1600000 112319 0.003561 ECMLI 0.60953 -4.81636 4.20686 1600000 293598 0.004087 ECMGI 0.43270 -12.23493 -0.29807 1600000 70017 0.005713 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 83 103 -6.766 -6.973 -0.060 -5.387 IL 1 1 2 1 4 1 25 87 108 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 25 86 107 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - A - - - ML 3 2 3 5 3 1 24 83 103 -7.796 -0.023 -6.450 1.635 -2.035 -1.701 -1.546 D 4 2 3 5 3 0 20 82 102 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 24 85 106 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - A - - - ML 6 5 3 8 3 1 23 82 102 -8.198 -0.021 -6.516 1.635 -2.035 -1.701 -1.546 D 7 5 3 8 3 0 19 81 101 -5.620 -0.734 -1.403 IL 8 8 3 8 3 1 23 83 103 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 68 - C - - MR 9 8 3 11 3 1 23 81 101 -8.198 -0.021 -6.516 -1.341 1.496 -2.148 -0.838 D 10 8 3 11 3 0 17 80 100 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 22 82 102 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 67 - C - - MR 12 11 3 14 3 1 22 80 100 -8.198 -0.021 -6.516 -1.341 1.496 -2.148 -0.838 D 13 11 3 14 3 0 17 79 99 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 21 81 101 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 66 - A - - MR 15 14 3 17 3 1 21 79 99 -8.198 -0.021 -6.516 1.070 -1.294 -0.168 -0.731 D 16 14 3 17 3 0 16 78 98 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 20 80 100 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 65 - A - - MR 18 17 3 20 3 1 20 78 98 -8.198 -0.021 -6.516 1.635 -2.035 -1.701 -1.546 D 19 17 3 20 3 0 15 77 97 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 19 79 99 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 64 - C - - MR 21 20 3 23 5 1 20 77 97 -6.948 -0.043 -6.763 -6.975 -7.867 -1.341 1.496 -2.148 -0.838 D 22 20 3 23 5 0 14 76 96 -5.352 -0.707 -2.978 -4.409 -2.404 IR 23 23 3 23 5 1 18 78 98 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 3 63 A U - - MP 24 23 3 28 6 2 19 76 96 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -3.527 -2.630 -3.562 3.127 -3.771 -4.813 0.512 -3.620 -3.467 1.366 -4.002 -0.152 0.093 -4.044 -1.430 -2.414 ML 25 23 3 28 6 1 15 75 95 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 26 23 3 28 6 1 14 75 95 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 27 23 3 28 6 0 11 72 93 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 28 28 5 28 6 1 17 76 96 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 29 29 6 29 5 1 17 76 96 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 4 62 G C - - MP 30 29 6 34 6 2 17 74 94 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 31 29 6 34 6 1 14 73 94 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 32 29 6 34 6 1 13 73 93 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 6 34 6 0 10 71 92 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 15 74 94 -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 15 74 94 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 5 61 G C - - MP 36 35 6 40 4 2 15 72 92 -6.766 -6.973 -0.060 -5.387 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 37 35 6 40 4 1 13 72 93 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 38 35 6 40 4 1 11 72 92 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 39 35 6 40 4 0 10 71 91 -4.568 -4.250 -2.265 -0.520 IL 40 40 5 40 4 1 14 74 94 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 41 41 6 41 3 1 14 73 93 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 6 - G - - - ML 42 41 6 44 3 1 14 70 90 -8.198 -0.021 -6.516 -1.221 -2.381 1.625 -1.766 D 43 41 6 44 3 0 10 69 89 -5.620 -0.734 -1.403 IL 44 44 3 44 3 1 13 71 91 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 60 - G - - MR 45 44 3 47 5 1 13 69 89 -6.948 -0.043 -6.763 -6.975 -7.867 -1.221 -2.381 1.625 -1.766 D 46 44 3 47 5 0 8 68 88 -5.352 -0.707 -2.978 -4.409 -2.404 IR 47 47 3 47 5 1 11 69 89 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 7 59 G C - - MP 48 47 3 52 6 2 12 68 88 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 49 47 3 52 6 1 9 67 87 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 3 52 6 1 7 67 87 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 51 47 3 52 6 0 4 65 85 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 10 68 88 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 10 67 87 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 8 58 C G - - MP 54 53 6 58 4 2 11 66 86 -6.766 -6.973 -0.060 -5.387 -4.215 -4.088 -3.959 -0.354 -2.756 -4.414 3.432 -3.532 -4.000 -0.060 -4.294 -2.033 0.789 -4.305 -0.456 -2.852 ML 55 53 6 58 4 1 8 66 86 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 56 53 6 58 4 1 5 66 86 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 57 53 6 58 4 0 4 65 85 -4.568 -4.250 -2.265 -0.520 IL 58 58 5 58 4 1 9 67 88 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 59 59 6 59 3 1 9 66 87 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 9 - A - - - ML 60 59 6 62 3 1 9 64 83 -8.198 -0.021 -6.516 1.635 -2.035 -1.701 -1.546 D 61 59 6 62 3 0 3 62 82 -5.620 -0.734 -1.403 IL 62 62 3 62 3 1 8 64 84 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 57 - G - - MR 63 62 3 65 3 1 9 63 82 -8.198 -0.021 -6.516 -1.221 -2.381 1.625 -1.766 D 64 62 3 65 3 0 2 61 81 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 7 63 83 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 56 - A - - MR 66 65 3 68 5 1 8 62 81 -6.948 -0.043 -6.763 -6.975 -7.867 1.635 -2.035 -1.701 -1.546 D 67 65 3 68 5 0 1 60 80 -5.352 -0.707 -2.978 -4.409 -2.404 IR 68 68 3 68 5 1 5 62 82 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 10 55 a u - - MP 69 68 3 73 6 2 9 61 80 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -2.813 0.203 -2.928 2.456 -3.177 -3.907 0.765 -3.185 -2.921 1.832 -3.442 0.040 0.508 -3.150 -1.023 -1.930 ML 70 68 3 73 6 1 3 59 79 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 3 73 6 1 3 59 79 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 3 73 6 0 0 57 76 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 4 60 80 -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 5 60 80 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 11 54 G C - - MP 75 74 6 79 6 2 8 59 78 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 76 74 6 79 6 1 3 57 77 -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 3 57 77 -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 55 74 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 4 58 78 -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 4 58 78 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 12 53 U A - - MP 81 80 6 85 6 2 7 57 76 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -3.854 -3.666 -3.728 0.013 -2.746 -4.322 1.574 -3.416 -3.737 0.324 -4.126 -1.575 3.139 -4.017 -0.430 -2.592 ML 82 80 6 85 6 1 3 55 75 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 6 1 3 55 75 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 84 80 6 85 6 0 0 53 73 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 4 56 76 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 86 86 6 86 5 1 4 56 76 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 13 52 g c - - MP 87 86 6 91 6 2 6 55 74 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -3.391 -2.317 -3.494 1.190 -4.007 -4.467 0.351 -3.690 -3.352 2.515 -3.831 2.120 0.055 -3.749 -1.587 -2.337 ML 88 86 6 91 6 1 2 54 74 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 89 86 6 91 6 1 2 53 73 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 6 91 6 0 0 52 72 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 3 54 74 -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 3 54 74 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 14 51 g u - - MP 93 92 6 97 4 2 4 53 72 -6.766 -6.973 -0.060 -5.387 -3.409 -2.264 -3.557 1.252 -4.102 -4.836 0.249 -3.611 -3.280 1.636 -3.791 2.825 -0.112 -4.082 -1.690 -2.305 ML 94 92 6 97 4 1 1 53 73 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 4 1 1 52 72 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 96 92 6 97 4 0 0 51 71 -4.568 -4.250 -2.265 -0.520 IL 97 97 5 97 4 1 3 54 74 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 98 98 6 98 3 1 2 53 73 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 15 - C - - - ML 99 98 6 101 3 1 3 50 70 -7.796 -0.023 -6.450 -1.341 1.496 -2.148 -0.838 D 100 98 6 101 3 0 0 49 68 -6.174 -1.687 -0.566 IL 101 101 3 101 3 1 2 52 72 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 16 - C - - - ML 102 101 3 104 3 1 3 49 69 -7.796 -0.023 -6.450 -1.341 1.496 -2.148 -0.838 D 103 101 3 104 3 0 0 48 67 -6.174 -1.687 -0.566 IL 104 104 3 104 3 1 1 51 71 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 17 - a - - - ML 105 104 3 107 3 1 2 48 67 -7.796 -0.023 -6.450 0.653 -1.258 0.463 -0.665 D 106 104 3 107 3 0 0 47 66 -6.174 -1.687 -0.566 IL 107 107 3 107 3 1 1 50 70 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 18 - U - - - ML 108 107 3 110 3 1 2 47 66 -7.796 -0.023 -6.450 -1.182 -1.233 -1.898 1.519 D 109 107 3 110 3 0 0 46 65 -6.174 -1.687 -0.566 IL 110 110 3 110 3 1 1 49 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 27 ] 19 - A - - - ML 111 110 3 113 3 1 2 46 65 -7.796 -0.023 -6.450 1.635 -2.035 -1.701 -1.546 D 112 110 3 113 3 0 0 44 64 -6.174 -1.687 -0.566 IL 113 113 3 113 3 1 1 48 68 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 28 ] 20 - c - - - ML 114 113 3 116 3 1 1 45 64 -7.796 -0.023 -6.450 -0.697 0.894 -1.484 0.224 D 115 113 3 116 3 0 0 43 63 -6.174 -1.687 -0.566 IL 116 116 3 116 3 1 1 47 67 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 29 ] 21 - A - - - ML 117 116 3 119 3 1 1 44 63 -8.198 -0.021 -6.516 1.635 -2.035 -1.701 -1.546 D 118 116 3 119 3 0 0 42 62 -5.620 -0.734 -1.403 IL 119 119 3 119 3 1 1 45 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 30 ] - 50 - U - - MR 120 119 3 122 3 1 1 43 62 -3.152 -0.190 -6.516 -0.641 -0.117 -1.379 1.037 D 121 119 3 122 3 0 0 40 59 -6.390 -1.568 -0.620 IR 122 122 3 122 3 1 1 44 63 -1.492 -0.712 -4.877 0.000 0.000 0.000 0.000 [ MATR 31 ] - 47 - C - - MR 123 122 3 125 3 1 1 41 60 -8.198 -0.021 -6.516 -1.341 1.496 -2.148 -0.838 D 124 122 3 125 3 0 0 39 58 -6.390 -1.568 -0.620 IR 125 125 3 125 3 1 1 41 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 32 ] - 46 - C - - MR 126 125 3 128 3 1 1 40 59 -8.198 -0.021 -6.516 -1.341 1.496 -2.148 -0.838 D 127 125 3 128 3 0 0 38 57 -6.390 -1.568 -0.620 IR 128 128 3 128 3 1 1 40 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 33 ] - 45 - C - - MR 129 128 3 131 5 1 1 39 58 -6.948 -0.043 -6.763 -6.975 -7.867 -1.341 1.496 -2.148 -0.838 D 130 128 3 131 5 0 0 37 57 -5.352 -0.707 -2.978 -4.409 -2.404 IR 131 131 3 131 5 1 1 39 58 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 22 44 G C - - MP 132 131 3 136 6 2 2 38 57 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 133 131 3 136 6 1 1 37 56 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 134 131 3 136 6 1 1 37 56 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 135 131 3 136 6 0 0 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 6 1 1 37 57 -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 37 56 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 23 43 G C - - MP 138 137 6 142 4 2 2 36 55 -6.766 -6.973 -0.060 -5.387 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 139 137 6 142 4 1 1 36 55 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 140 137 6 142 4 1 1 36 55 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 141 137 6 142 4 0 0 35 54 -4.568 -4.250 -2.265 -0.520 IL 142 142 5 142 4 1 1 38 57 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 143 143 6 143 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 24 - C - - - ML 144 143 6 146 3 1 1 33 52 -7.796 -0.023 -6.450 -1.341 1.496 -2.148 -0.838 D 145 143 6 146 3 0 0 32 51 -6.174 -1.687 -0.566 IL 146 146 3 146 3 1 1 35 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 25 - U - - - ML 147 146 3 149 5 1 1 32 51 -6.948 -0.043 -6.763 -6.975 -7.867 -0.641 -0.117 -1.379 1.037 D 148 146 3 149 5 0 0 31 49 -4.959 -0.803 -4.221 -2.596 -2.508 IL 149 149 3 149 5 1 1 32 51 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 38 ] 26 42 G C - - MP 150 149 3 154 6 2 2 31 50 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 151 149 3 154 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 152 149 3 154 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 153 149 3 154 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 154 154 5 154 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 155 155 6 155 5 1 1 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 39 ] 27 41 G C - - MP 156 155 6 160 4 2 2 29 48 -6.698 -7.943 -0.091 -4.397 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 157 155 6 160 4 1 1 28 47 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 158 155 6 160 4 1 1 28 47 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 159 155 6 160 4 0 0 26 45 -12.737 -14.007 -2.036 -0.404 IL 160 160 5 160 4 1 1 28 47 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 161 161 6 161 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 40 ] - 40 - a - - MR 162 161 6 164 3 1 1 27 46 -8.198 -0.021 -6.516 0.996 -0.970 -1.024 0.005 D 163 161 6 164 3 0 0 25 44 -6.390 -1.568 -0.620 IR 164 164 3 164 3 1 1 28 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 41 ] - 39 - U - - MR 165 164 3 167 3 1 1 26 45 -8.198 -0.021 -6.516 -0.641 -0.117 -1.379 1.037 D 166 164 3 167 3 0 0 24 43 -6.390 -1.568 -0.620 IR 167 167 3 167 3 1 1 27 45 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 42 ] - 38 - G - - MR 168 167 3 170 5 1 1 25 44 -6.948 -0.043 -6.763 -6.975 -7.867 -1.221 -2.381 1.625 -1.766 D 169 167 3 170 5 0 0 23 42 -5.352 -0.707 -2.978 -4.409 -2.404 IR 170 170 3 170 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 28 37 G C - - MP 171 170 3 175 6 2 2 24 43 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 172 170 3 175 6 1 1 23 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 173 170 3 175 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 174 170 3 175 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 175 175 5 175 6 1 1 24 42 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 176 176 6 176 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 44 ] 29 36 G C - - MP 177 176 6 181 6 2 2 22 41 -9.041 -8.980 -0.022 -7.756 -8.036 -8.431 -4.417 -2.940 -4.492 0.412 -4.774 -4.562 -0.218 -4.707 -4.107 3.549 -4.469 -0.630 -0.613 -4.253 -2.239 -3.374 ML 178 176 6 181 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 179 176 6 181 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 180 176 6 181 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 181 181 5 181 6 1 1 22 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 182 182 6 182 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 30 35 c g - - MP 183 182 6 187 4 2 2 20 38 -6.766 -6.973 -0.060 -5.387 -3.577 -3.525 -3.440 0.155 -2.380 -3.982 2.929 -3.099 -3.464 0.415 -3.838 -1.559 1.242 -3.707 1.115 -2.348 ML 184 182 6 187 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 185 182 6 187 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 186 182 6 187 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 187 187 5 187 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 188 188 6 188 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 31 - g - - - ML 189 188 6 191 3 1 1 16 35 -7.796 -0.023 -6.450 0.126 -1.460 0.995 -0.857 D 190 188 6 191 3 0 0 16 34 -6.174 -1.687 -0.566 IL 191 191 3 191 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 32 - A - - - ML 192 191 3 194 3 1 1 15 33 -7.796 -0.023 -6.450 1.635 -2.035 -1.701 -1.546 D 193 191 3 194 3 0 0 15 33 -6.174 -1.687 -0.566 IL 194 194 3 194 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 48 ] 33 - U - - - ML 195 194 3 197 3 1 1 13 32 -7.796 -0.023 -6.450 -1.182 -1.233 -1.898 1.519 D 196 194 3 197 3 0 0 13 32 -6.174 -1.687 -0.566 IL 197 197 3 197 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 49 ] 34 - C - - - ML 198 197 3 200 2 1 1 1 1 * 0.000 -1.341 1.496 -2.148 -0.838 D 199 197 3 200 2 0 0 0 0 * 0.000 IL 200 200 3 200 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 50 ] - - - - - - E 201 200 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Pestivirus-3UTR-SLIII-scrofae ACC RF04325 DESC Pestivirus 3' UTR SLIII P. scrofae Atypical porcine pestivirus LENG 66 MAXL 152 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Apr 30 17:07:19 2025 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED NSEQ 4 EFFN 2.042969 CKSUM 2640445115 STATS LOCAL MSV -8.1842 0.71916 STATS LOCAL VITERBI -9.0259 0.71916 STATS LOCAL FORWARD -3.5653 0.71916 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.51682 1.14597 1.26866 1.70668 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 0.00000 * 1 0.18237 3.08994 2.82882 2.77865 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 2 0.18237 3.08994 2.82882 2.77865 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 3 0.40938 2.59391 1.70538 2.53188 3 A - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 4 2.48957 3.08517 0.19496 3.02701 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 5 2.49009 3.08574 0.19482 3.02783 5 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 6 2.54496 3.40044 0.17775 2.97568 6 G - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 7 2.48849 3.08398 0.19523 3.02534 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 8 3.04596 0.28007 2.80157 1.99506 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 9 0.18237 3.08994 2.82882 2.77865 9 A - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 10 0.68056 2.26921 1.31323 2.10931 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 11 2.48985 3.08547 0.19488 3.02744 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 12 2.80842 1.78471 2.53956 0.36679 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 13 1.86569 2.61130 0.37529 2.46883 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 14 1.85436 2.74539 0.34679 2.62737 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 15 2.66535 0.24182 3.23842 2.24427 15 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 16 2.66535 0.24182 3.23842 2.24427 16 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 17 0.90408 2.38247 1.01048 1.97530 17 a - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 18 2.47107 2.45894 2.98234 0.24935 18 U - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 19 0.18237 3.08994 2.82882 2.77865 19 A - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 20 2.01793 0.67659 2.58261 1.26179 20 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 21 0.18237 3.08994 2.82882 2.77865 21 A - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 22 2.48687 3.08219 0.19564 3.02281 22 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 23 2.48908 3.08463 0.19508 3.02625 23 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 24 2.66535 0.24182 3.23842 2.24427 24 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 25 1.95906 1.46655 2.48106 0.60764 25 U - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 26 2.49074 3.08645 0.19466 3.02883 26 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 27 2.49069 3.08640 0.19467 3.02876 27 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 28 2.48277 3.07767 0.19669 3.01643 28 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 29 2.48668 3.08198 0.19569 3.02251 29 G - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 30 2.58275 0.63554 2.34412 1.20780 30 C - - < 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 31 1.32976 2.55346 0.61540 2.14367 31 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 32 0.18237 3.08994 2.82882 2.77865 32 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 33 2.47107 2.45894 2.98234 0.24935 33 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 34 2.66535 0.24182 3.23842 2.24427 34 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 35 1.86370 2.50777 0.40337 2.34982 35 G - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 36 3.24216 0.22896 2.92004 2.19256 36 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 37 3.24571 0.22859 2.92154 2.19324 37 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 38 2.54496 3.40044 0.17775 2.97568 38 G - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 39 1.95906 1.46655 2.48106 0.60764 39 U - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 40 0.64381 2.14134 2.19006 1.40524 40 A - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 41 3.22849 0.23040 2.91425 2.18993 41 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 42 3.22021 0.23129 2.91072 2.18832 42 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 43 3.24519 0.22864 2.92132 2.19315 43 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 44 3.24948 0.22820 2.92312 2.19396 44 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 45 2.66535 0.24182 3.23842 2.24427 45 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 46 2.66535 0.24182 3.23842 2.24427 46 C - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 47 2.66535 0.24182 3.23842 2.24427 47 C - - - 1.38629 1.38629 1.38629 1.38629 0.20225 1.81980 3.86089 0.78473 0.60926 1.09861 0.40547 48 1.95906 1.46655 2.48106 0.60764 50 U - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 49 2.84236 1.78326 2.54763 0.36333 51 U - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 50 2.69172 1.00546 2.41883 0.73954 52 u - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 51 0.41636 2.72204 1.62165 2.56077 53 A - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 52 3.24616 0.22854 2.92173 2.19333 54 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 53 2.33817 1.21060 2.07383 0.73444 55 u - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 54 0.18237 3.08994 2.82882 2.77865 56 A - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 55 2.54496 3.40044 0.17775 2.97568 57 G - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 56 2.27368 2.97223 0.24138 2.80781 58 G - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 57 3.25097 0.22804 2.92375 2.19425 59 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 58 2.54496 3.40044 0.17775 2.97568 60 G - - - 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 59 3.24245 0.22893 2.92016 2.19262 61 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 60 3.24581 0.22858 2.92158 2.19326 62 C - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 61 2.77005 1.98324 2.41117 0.34248 63 U - - > 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 62 2.66535 0.24182 3.23842 2.24427 64 C - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 63 0.18237 3.08994 2.82882 2.77865 65 A - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 64 0.58903 2.41313 1.49399 2.03159 66 A - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 65 2.66535 0.24182 3.23842 2.24427 67 C - - : 1.38629 1.38629 1.38629 1.38629 0.04301 3.86089 3.86089 1.46634 0.26236 1.09861 0.40547 66 2.66535 0.24182 3.23842 2.24427 68 C - - : 1.38629 1.38629 1.38629 1.38629 0.02174 3.83962 * 1.46634 0.26236 0.00000 * //