INFERNAL1/a [1.1.4 | Dec 2020] NAME UPD-PKib ACC RF01080 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 100 NODES 27 CLEN 32 W 46 ALPH RNA RF no CONS yes MAP yes DATE Wed Mar 5 14:03:45 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 4 EFFN 4.000000 CKSUM 1475053414 NULL 0.000 0.000 0.000 0.000 GA 39.00 TC 39.90 NC 34.50 EFP7GF -5.9372 0.73905 ECMLC 0.56422 -8.31907 2.86544 1600000 660411 0.001817 ECMGC 0.44546 -15.17949 0.19539 1600000 377164 0.001061 ECMLI 0.53859 -7.74439 3.48459 1600000 507814 0.002363 ECMGI 0.45744 -13.39708 1.19940 1600000 317586 0.001260 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 46 65 -7.615 -7.822 -0.033 -6.236 IL 1 1 2 1 4 1 1 51 70 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 50 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - G - - - ML 3 2 3 5 3 1 1 46 65 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 4 2 3 5 3 0 0 45 64 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 49 68 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - G - - - ML 6 5 3 8 3 1 1 45 64 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 7 5 3 8 3 0 0 44 63 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 48 67 -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 1 44 63 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 10 8 3 11 3 0 0 43 62 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 47 66 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 1 43 62 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 13 11 3 14 3 0 0 42 61 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 46 65 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - C - - - ML 15 14 3 17 3 1 1 42 61 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 16 14 3 17 3 0 0 41 60 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 44 64 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 1 41 60 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 19 17 3 20 3 0 0 40 59 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 43 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - U - - - ML 21 20 3 23 5 1 1 40 59 -7.656 -0.026 -7.471 -7.683 -8.575 -2.677 -2.478 -3.451 1.837 D 22 20 3 23 5 0 0 38 57 -4.959 -0.803 -4.221 -2.596 -2.508 IL 23 23 3 23 5 1 1 40 59 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 8 32 G C - - MP 24 23 3 28 6 2 2 39 58 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -4.468 -3.088 -4.469 0.293 -5.042 -4.642 -0.503 -4.924 -4.364 3.412 -4.685 -0.825 -0.815 0.698 -2.469 -3.449 ML 25 23 3 28 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 26 23 3 28 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 27 23 3 28 6 0 0 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 28 28 5 28 6 1 1 39 57 -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 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 31 U A - - MP 30 29 6 34 6 2 2 37 56 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -4.537 -4.508 -4.290 -0.659 -3.015 -4.757 2.281 -3.793 -4.301 -0.487 -4.631 -2.455 3.064 -4.618 -0.671 -3.130 ML 31 29 6 34 6 1 1 35 54 -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 1 35 54 -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 0 33 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 1 37 55 -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 1 36 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 10 30 u a - - MP 36 35 6 40 6 2 2 35 54 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.702 -3.395 -3.726 1.762 -3.082 -4.557 1.253 -3.581 -3.687 0.484 -4.177 -1.194 2.797 -3.992 -0.767 -2.611 ML 37 35 6 40 6 1 1 33 52 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 38 35 6 40 6 1 1 33 52 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 39 35 6 40 6 0 0 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 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 41 41 6 41 5 1 1 34 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 11 29 a u - - MP 42 41 6 46 6 2 2 33 52 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.707 -3.193 -3.746 2.813 -3.387 -4.668 0.878 -3.720 -3.709 0.733 -4.208 -0.908 1.867 -4.040 -1.095 -2.652 ML 43 41 6 46 6 1 1 31 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 31 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 6 46 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 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 47 47 6 47 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 12 28 g c - - MP 48 47 6 52 6 2 2 31 50 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -3.838 -3.095 -3.811 0.541 -3.514 -4.502 0.943 -3.869 -3.866 2.690 -4.288 -0.819 2.117 -3.896 -1.092 -2.707 ML 49 47 6 52 6 1 1 30 49 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 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 51 47 6 52 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 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 53 53 6 53 5 1 1 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 13 27 U A - - MP 54 53 6 58 6 2 2 29 48 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.885 -5.729 -5.521 -1.951 -4.171 -5.925 0.158 -4.961 -5.516 -1.872 -5.808 -3.591 3.777 -5.942 -1.807 -4.074 ML 55 53 6 58 6 1 1 28 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 56 53 6 58 6 1 1 28 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 57 53 6 58 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 29 48 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 59 59 6 59 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 14 26 U A - - MP 60 59 6 64 4 2 2 27 46 -7.615 -7.822 -0.033 -6.236 -5.885 -5.729 -5.521 -1.951 -4.171 -5.925 0.158 -4.961 -5.516 -1.872 -5.808 -3.591 3.777 -5.942 -1.807 -4.074 ML 61 59 6 64 4 1 1 28 47 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 4 1 1 27 46 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 63 59 6 64 4 0 0 26 45 -4.568 -4.250 -2.265 -0.520 IL 64 64 5 64 4 1 1 29 48 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 65 65 6 65 3 1 1 28 47 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 15 - C - - - ML 66 65 6 68 3 1 1 24 43 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 67 65 6 68 3 0 0 23 42 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 27 46 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 16 - A - - - ML 69 68 3 71 3 1 1 23 42 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 D 70 68 3 71 3 0 0 22 41 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 26 45 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 17 - C - - - ML 72 71 3 74 3 1 1 22 41 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 73 71 3 74 3 0 0 21 40 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 18 - C - - - ML 75 74 3 77 3 1 1 21 39 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 76 74 3 77 3 0 0 20 39 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 19 - U - - - ML 78 77 3 80 3 1 1 19 38 -8.593 -0.013 -7.247 -0.904 -1.322 -0.257 1.156 D 79 77 3 80 3 0 0 19 38 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 20 - A - - - ML 81 80 3 83 3 1 1 18 37 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 D 82 80 3 83 3 0 0 18 37 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 21 - A - - - ML 84 83 3 86 3 1 1 17 36 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 D 85 83 3 86 3 0 0 17 35 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 22 - A - - - ML 87 86 3 89 3 1 1 16 34 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 D 88 86 3 89 3 0 0 16 34 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 23 - U - - - ML 90 89 3 92 3 1 1 14 33 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 91 89 3 92 3 0 0 15 33 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 24 - C - - - ML 93 92 3 95 3 1 1 13 31 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 94 92 3 95 3 0 0 13 32 -6.174 -1.687 -0.566 IL 95 95 3 95 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 25 - G - - - ML 96 95 3 98 2 1 1 1 1 * 0.000 -2.823 -4.195 1.895 -3.558 D 97 95 3 98 2 0 0 0 0 * 0.000 IL 98 98 3 98 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 26 ] - - - - - - E 99 98 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME UPD-PKib ACC RF01080 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 32 MAXL 102 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Mar 5 14:03:45 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 4 EFFN 3.472656 CKSUM 1475053414 STATS LOCAL MSV -6.5585 0.73905 STATS LOCAL VITERBI -7.5438 0.73905 STATS LOCAL FORWARD -3.1901 0.73905 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.33860 1.45091 1.50924 1.26459 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 0.00000 * 1 3.17317 4.10726 0.08740 3.67436 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 2 3.17317 4.10726 0.08740 3.67436 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 3 3.06612 2.95499 3.59810 0.13474 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 4 3.17317 4.10726 0.08740 3.67436 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 5 3.41784 0.11529 3.97941 2.85757 5 C - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 6 3.06612 2.95499 3.59810 0.13474 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 7 3.06612 2.95499 3.59810 0.13474 7 U - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 8 2.27622 2.78912 0.38493 1.86204 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 9 2.85552 1.13551 2.62497 0.60007 9 U - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 10 1.50506 1.72234 1.98405 0.77254 10 u - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 11 0.85744 1.94754 1.80861 1.31213 11 a - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 12 2.15113 1.93710 0.83600 1.18390 12 g - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 13 3.55315 2.35860 3.36446 0.17170 13 U - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 14 3.55168 2.35846 3.36370 0.17180 14 U - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 15 3.41784 0.11529 3.97941 2.85757 15 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 16 0.09317 3.71609 3.39644 3.46925 16 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 17 3.41784 0.11529 3.97941 2.85757 17 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 18 3.41784 0.11529 3.97941 2.85757 18 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 19 1.93400 2.22762 1.56894 0.61733 19 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 20 0.09317 3.71609 3.39644 3.46925 20 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 21 0.09317 3.71609 3.39644 3.46925 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 22 0.09317 3.71609 3.39644 3.46925 22 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 23 3.06612 2.95499 3.59810 0.13474 23 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 24 3.41784 0.11529 3.97941 2.85757 24 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 25 3.17317 4.10726 0.08740 3.67436 25 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 26 0.19498 3.55538 2.19399 3.29400 26 A - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 27 0.19490 3.55614 2.19412 3.29483 27 A - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 28 1.28901 0.90808 1.76807 1.89382 28 c - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 29 1.42950 2.01340 1.77511 0.78182 29 u - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 30 0.85401 2.18301 1.55618 1.38369 30 a - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 31 0.67161 2.79022 1.03745 2.61253 31 A - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 32 2.91042 0.30605 2.60391 2.00091 32 C - - > 1.38629 1.38629 1.38629 1.38629 0.01653 4.11087 * 1.46634 0.26236 0.00000 * //