INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV2_UPD-PKb ACC RF01104 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 91 NODES 28 CLEN 29 W 43 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 01:14:19 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/RF01104/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 3 EFFN 3.000000 CKSUM 63395763 NULL 0.000 0.000 0.000 0.000 GA 39.00 TC 43.50 NC 37.00 EFP7GF -4.9421 0.74482 ECMLC 0.60699 -7.77662 2.98240 1600000 822959 0.001458 ECMGC 0.43853 -14.22433 1.19031 1600000 344960 0.001160 ECMLI 0.60831 -6.36082 3.94279 1600000 632755 0.001896 ECMGI 0.44569 -12.57733 2.14596 1600000 283082 0.001413 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 43 62 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 48 67 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 47 66 -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 2 43 62 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 4 2 3 5 3 0 0 42 61 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 45 65 -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 42 61 -8.693 -0.015 -7.010 -2.322 -3.642 1.847 -3.026 D 7 5 3 8 3 0 0 41 59 -5.620 -0.734 -1.403 IL 8 8 3 8 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 29 - G - - MR 9 8 3 11 3 1 1 41 60 -8.693 -0.015 -7.010 -2.322 -3.642 1.847 -3.026 D 10 8 3 11 3 0 0 39 58 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 28 - G - - MR 12 11 3 14 3 1 1 40 59 -8.693 -0.015 -7.010 -2.322 -3.642 1.847 -3.026 D 13 11 3 14 3 0 0 38 57 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 27 - A - - MR 15 14 3 17 3 1 1 39 58 -8.693 -0.015 -7.010 1.129 -1.755 0.117 -1.210 D 16 14 3 17 3 0 0 37 56 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 26 - U - - MR 18 17 3 20 3 1 1 38 57 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 19 17 3 20 3 0 0 36 55 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 25 - G - - MR 21 20 3 23 3 1 1 37 56 -8.693 -0.015 -7.010 -2.322 -3.642 1.847 -3.026 D 22 20 3 23 3 0 0 35 54 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 24 - U - - MR 24 23 3 26 3 1 1 36 55 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 25 23 3 26 3 0 0 34 53 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 23 - C - - MR 27 26 3 29 3 1 1 35 54 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 28 26 3 29 3 0 0 33 52 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 22 - A - - MR 30 29 3 32 3 1 1 34 53 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 31 29 3 32 3 0 0 32 51 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 21 - A - - MR 33 32 3 35 3 1 1 33 52 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 34 32 3 35 3 0 0 31 50 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 20 - A - - MR 36 35 3 38 3 1 1 32 51 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 37 35 3 38 3 0 0 30 49 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 19 - U - - MR 39 38 3 41 3 1 1 31 50 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 40 38 3 41 3 0 0 29 48 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 18 - U - - MR 42 41 3 44 3 1 1 30 49 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 43 41 3 44 3 0 0 28 47 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 17 - U - - MR 45 44 3 47 5 1 1 29 48 -7.411 -0.031 -7.227 -7.439 -8.330 -2.168 -2.049 -2.929 1.767 D 46 44 3 47 5 0 0 27 46 -5.352 -0.707 -2.978 -4.409 -2.404 IR 47 47 3 47 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 3 16 C G - - MP 48 47 3 52 6 2 2 28 47 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 49 47 3 52 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 50 47 3 52 6 1 1 26 45 -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 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 28 46 -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 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 4 15 G C - - MP 54 53 6 58 6 2 2 26 45 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 55 53 6 58 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 56 53 6 58 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 57 53 6 58 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 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 59 59 6 59 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 5 14 U A - - MP 60 59 6 64 4 2 2 24 43 -7.331 -7.538 -0.041 -5.952 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 61 59 6 64 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 4 1 1 24 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 63 59 6 64 4 0 0 23 42 -4.568 -4.250 -2.265 -0.520 IL 64 64 5 64 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 65 65 6 65 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 6 - U - - - ML 66 65 6 68 3 1 1 21 40 -8.323 -0.016 -6.977 -1.063 0.146 -1.848 1.095 D 67 65 6 68 3 0 0 20 39 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 7 - C - - - ML 69 68 3 71 3 1 1 20 38 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 70 68 3 71 3 0 0 19 38 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 8 - c - - - ML 72 71 3 74 3 1 1 18 37 -8.323 -0.016 -6.977 -1.125 0.992 -1.971 0.376 D 73 71 3 74 3 0 0 18 37 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 9 - A - - - ML 75 74 3 77 3 1 1 17 36 -8.323 -0.016 -6.977 1.112 -1.750 0.146 -1.203 D 76 74 3 77 3 0 0 17 36 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 10 - C - - - ML 78 77 3 80 3 1 1 16 34 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 79 77 3 80 3 0 0 16 34 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 11 - A - - - ML 81 80 3 83 3 1 1 15 33 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 D 82 80 3 83 3 0 0 15 33 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 12 - G - - - ML 84 83 3 86 3 1 1 13 31 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 85 83 3 86 3 0 0 13 32 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 13 - U - - - ML 87 86 3 89 2 1 1 1 1 * 0.000 -2.168 -2.049 -2.929 1.767 D 88 86 3 89 2 0 0 0 0 * 0.000 IL 89 89 3 89 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 27 ] - - - - - - E 90 89 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV2_UPD-PKb ACC RF01104 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 29 MAXL 100 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 01:14:19 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/RF01104/CM NSEQ 3 EFFN 2.323242 CKSUM 63395763 STATS LOCAL MSV -7.3988 0.74482 STATS LOCAL VITERBI -7.5683 0.74482 STATS LOCAL FORWARD -2.9360 0.74482 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.45358 1.55427 1.24374 1.32192 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 2.69145 3.56810 0.14980 3.14362 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 2.69145 3.56810 0.14980 3.14362 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 3 3.18267 0.24300 2.95867 2.10074 3 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 2.57929 3.23066 0.17121 3.17009 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 2.95976 1.89558 2.70885 0.31290 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 1.98323 1.30860 2.51658 0.67052 6 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 2.83588 0.20350 3.41183 2.38072 7 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 2.01750 0.76672 2.58388 1.11781 8 c - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 0.66101 2.44589 1.31257 2.05654 9 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 10 2.83588 0.20350 3.41183 2.38072 10 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 0.15640 3.23068 2.95560 2.93365 11 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 2.69145 3.56810 0.14980 3.14362 12 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 2.60187 2.56721 3.11895 0.21702 13 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 14 0.35472 2.89447 1.73264 2.71076 14 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 3.38418 0.20155 3.07012 2.28063 15 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.38353 3.13452 0.20814 2.95339 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 2.60187 2.56721 3.11895 0.21702 17 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 2.60187 2.56721 3.11895 0.21702 18 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 2.60187 2.56721 3.11895 0.21702 19 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 0.15640 3.23068 2.95560 2.93365 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 0.15640 3.23068 2.95560 2.93365 21 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 0.15640 3.23068 2.95560 2.93365 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 23 2.83588 0.20350 3.41183 2.38072 23 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 2.60187 2.56721 3.11895 0.21702 24 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 2.69145 3.56810 0.14980 3.14362 25 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 2.60187 2.56721 3.11895 0.21702 26 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 27 0.65014 2.44849 1.33108 2.06034 27 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 28 2.69145 3.56810 0.14980 3.14362 28 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 29 2.69145 3.56810 0.14980 3.14362 29 G - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //