INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV2_UPD-PKk ACC RF01111 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 67 NODES 20 CLEN 21 W 34 ALPH RNA RF no CONS yes MAP yes DATE Thu Jul 11 05:30:08 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01111/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 949982840 NULL 0.000 0.000 0.000 0.000 GA 35.00 TC 36.30 NC 33.50 EFP7GF -6.6262 0.74995 ECMLC 0.57715 -8.66318 2.77676 1600000 884419 0.001357 ECMGC 0.47265 -12.59830 2.48869 1600000 499961 0.000800 ECMLI 0.56733 -7.68732 3.47089 1600000 673678 0.001781 ECMGI 0.48784 -11.31473 3.04296 1600000 440497 0.000908 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 34 53 -7.487 -8.733 -0.052 -5.186 IL 1 1 2 1 4 1 1 36 55 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 21 - A - - MR 3 2 3 5 3 1 1 34 53 -8.950 -0.012 -7.267 1.889 -3.622 -3.140 -3.290 D 4 2 3 5 3 0 0 33 52 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 20 - G - - MR 6 5 3 8 3 1 1 33 52 -8.950 -0.012 -7.267 -2.823 -4.195 1.895 -3.558 D 7 5 3 8 3 0 0 32 51 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 19 - A - - MR 9 8 3 11 3 1 1 32 51 -8.950 -0.012 -7.267 1.889 -3.622 -3.140 -3.290 D 10 8 3 11 3 0 0 31 50 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 18 - A - - MR 12 11 3 14 3 1 1 31 50 -8.950 -0.012 -7.267 1.889 -3.622 -3.140 -3.290 D 13 11 3 14 3 0 0 30 49 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 17 - G - - MR 15 14 3 17 3 1 1 30 49 -8.950 -0.012 -7.267 -2.823 -4.195 1.895 -3.558 D 16 14 3 17 3 0 0 29 48 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 16 - A - - MR 18 17 3 20 3 1 1 29 48 -8.950 -0.012 -7.267 1.889 -3.622 -3.140 -3.290 D 19 17 3 20 3 0 0 28 47 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 15 - U - - MR 21 20 3 23 3 1 1 28 47 -8.950 -0.012 -7.267 -0.099 -1.325 -1.724 1.241 D 22 20 3 23 3 0 0 27 46 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 14 - A - - MR 24 23 3 26 5 1 1 27 46 -7.656 -0.026 -7.471 -7.683 -8.575 1.889 -3.622 -3.140 -3.290 D 25 23 3 26 5 0 0 26 45 -5.352 -0.707 -2.978 -4.409 -2.404 IR 26 26 3 26 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 1 13 C G - - MP 27 26 3 31 6 2 2 26 45 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.950 -5.973 -5.383 -2.142 -3.866 -5.609 3.825 -4.822 -5.519 -2.037 -5.588 -3.985 -0.541 -5.921 -1.647 -4.326 ML 28 26 3 31 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 29 26 3 31 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 30 26 3 31 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 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 32 32 6 32 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 2 12 G C - - MP 33 32 6 37 6 2 2 24 43 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.941 -3.685 -6.268 -0.655 -6.883 -5.136 -1.953 -6.515 -5.029 3.829 -5.299 -1.454 -2.316 -5.228 -4.074 -5.128 ML 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 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 38 38 6 38 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 3 11 U A - - MP 39 38 6 43 4 2 2 22 41 -7.615 -7.822 -0.033 -6.236 -4.429 -4.440 -4.216 -0.689 -3.012 -4.700 1.325 -3.776 -4.238 -0.541 -4.579 -2.474 3.075 -4.533 1.558 -3.097 ML 40 38 6 43 4 1 1 24 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 42 38 6 43 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 43 43 5 43 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 4 - G - - - ML 45 44 6 47 3 1 1 19 38 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 46 44 6 47 3 0 0 19 38 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 5 - G - - - ML 48 47 3 50 3 1 1 18 37 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 49 47 3 50 3 0 0 18 37 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 6 - U - - - ML 51 50 3 53 3 1 1 17 36 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 52 50 3 53 3 0 0 17 35 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 7 - C - - - ML 54 53 3 56 3 1 1 16 34 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 55 53 3 56 3 0 0 16 34 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 8 - U - - - ML 57 56 3 59 3 1 1 14 33 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 58 56 3 59 3 0 0 15 33 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 9 - U - - - ML 60 59 3 62 3 1 1 13 31 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 61 59 3 62 3 0 0 13 32 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 10 - C - - - ML 63 62 3 65 2 1 1 1 1 * 0.000 -3.231 1.864 -4.018 -2.379 D 64 62 3 65 2 0 0 0 0 * 0.000 IL 65 65 3 65 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 19 ] - - - - - - E 66 65 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV2_UPD-PKk ACC RF01111 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 21 MAXL 86 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Jul 11 05:30:08 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01111/CM NSEQ 4 EFFN 3.246094 CKSUM 949982840 STATS LOCAL MSV -6.3123 0.74995 STATS LOCAL VITERBI -6.6979 0.74995 STATS LOCAL FORWARD -2.8507 0.74995 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.28030 1.57239 1.21676 1.52185 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 0.00000 * 1 3.60778 0.15926 3.42875 2.43398 1 C - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 2 2.84223 3.62963 0.11994 3.56823 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 2.76996 1.64009 2.55612 0.40681 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 3.09151 4.01703 0.09554 3.58697 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 3.09151 4.01703 0.09554 3.58697 5 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 6 2.98369 2.88570 3.51354 0.14643 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 3.31784 0.12693 3.88493 2.77385 7 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 8 2.98369 2.88570 3.51354 0.14643 8 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 9 2.98369 2.88570 3.51354 0.14643 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 3.31784 0.12693 3.88493 2.77385 10 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 11 0.68440 2.72369 1.04679 2.53941 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 3.76406 0.14288 3.48017 2.53642 12 C - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 13 2.72283 3.60739 0.13540 3.38671 13 G - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 14 0.10190 3.63111 3.31869 3.37572 14 A - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 15 1.43535 2.19344 2.46389 0.57034 15 U - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 16 0.10190 3.63111 3.31869 3.37572 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 3.09151 4.01703 0.09554 3.58697 17 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 18 0.10190 3.63111 3.31869 3.37572 18 A - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 19 0.10190 3.63111 3.31869 3.37572 19 A - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 20 3.09151 4.01703 0.09554 3.58697 20 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 21 0.10190 3.63111 3.31869 3.37572 21 A - - : 1.38629 1.38629 1.38629 1.38629 0.01653 4.11087 * 1.46634 0.26236 0.00000 * //