INFERNAL1/a [1.1.5 | Sep 2023] NAME TMV_UPD-PK3 ACC RF01072 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 97 NODES 29 CLEN 31 W 47 ALPH RNA RF no CONS yes MAP yes DATE Thu Jul 11 00:22:13 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/RF01072/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 25 EFFN 25.000000 CKSUM 4270387066 NULL 0.000 0.000 0.000 0.000 GA 34.00 TC 34.00 NC 33.90 EFP7GF -13.8687 0.72779 ECMLC 0.67251 -8.09271 1.43998 1600000 730055 0.001644 ECMGC 0.44801 -19.12374 -3.63862 1600000 412077 0.000971 ECMLI 0.67738 -7.18844 1.79194 1600000 526059 0.002281 ECMGI 0.44932 -18.21353 -3.14013 1600000 349487 0.001145 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 47 69 -9.675 -10.921 -0.095 -4.018 IL 1 1 2 1 4 1 2 49 71 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 3 49 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 33 - u - - MR 3 2 3 5 3 1 5 47 69 -11.014 -0.003 -9.332 -0.102 0.041 -0.392 0.353 D 4 2 3 5 3 0 0 46 68 -8.418 -0.256 -2.647 IR 5 5 3 5 3 1 1 48 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 32 - G - - MR 6 5 3 8 3 1 4 46 68 -11.096 -0.003 -9.414 -1.308 -1.385 1.478 -1.227 D 7 5 3 8 3 0 0 45 67 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 47 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 31 - g - - MR 9 8 3 11 3 1 4 45 67 -11.096 -0.003 -9.414 0.017 -0.873 0.884 -0.744 D 10 8 3 11 3 0 0 44 66 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 46 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 30 - G - - MR 12 11 3 14 3 1 3 44 66 -11.096 -0.003 -9.414 -0.690 -0.134 1.234 -3.092 D 13 11 3 14 3 0 0 43 65 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 45 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 29 - A - - MR 15 14 3 17 3 1 3 43 65 -11.096 -0.003 -9.414 1.988 -6.854 -6.202 -6.382 D 16 14 3 17 3 0 0 42 64 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 44 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 28 - A - - MR 18 17 3 20 3 1 2 42 64 -11.096 -0.003 -9.414 1.988 -6.854 -6.202 -6.382 D 19 17 3 20 3 0 0 41 63 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 43 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 27 - G - - MR 21 20 3 23 3 1 2 41 63 -11.096 -0.003 -9.414 -5.498 -7.208 1.985 -6.248 D 22 20 3 23 3 0 0 40 62 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 42 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 26 - C - - MR 24 23 3 26 3 1 1 40 62 -11.096 -0.003 -9.414 -1.355 1.822 -5.522 -4.278 D 25 23 3 26 3 0 0 39 61 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 41 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 25 - U - - MR 27 26 3 29 3 1 1 39 61 -11.096 -0.003 -9.414 -6.198 -5.636 -7.079 1.985 D 28 26 3 29 3 0 0 38 60 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 40 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 24 - A - - MR 30 29 3 32 3 1 1 38 60 -11.096 -0.003 -9.414 1.988 -6.854 -6.202 -6.382 D 31 29 3 32 3 0 0 37 59 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 39 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 23 - A - - MR 33 32 3 35 3 1 1 37 59 -11.096 -0.003 -9.414 1.988 -6.854 -6.202 -6.382 D 34 32 3 35 3 0 0 36 58 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 38 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 22 - A - - MR 36 35 3 38 3 1 1 36 58 -11.096 -0.003 -9.414 1.917 -5.539 -2.490 -5.361 D 37 35 3 38 3 0 0 35 57 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 37 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 21 - U - - MR 39 38 3 41 5 1 1 35 57 -9.751 -0.006 -9.566 -9.778 -10.670 -6.198 -5.636 -7.079 1.985 D 40 38 3 41 5 0 0 34 56 -5.352 -0.707 -2.978 -4.409 -2.404 IR 41 41 3 41 5 1 1 36 58 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 1 20 A U - - MP 42 41 3 46 6 2 2 34 56 -10.915 -10.854 -0.006 -9.631 -9.910 -10.305 -8.606 -7.418 -6.033 3.981 -10.091 -10.878 -6.107 -5.877 -8.422 -4.067 -8.990 -4.438 -6.272 -9.857 -7.871 -5.768 ML 43 41 3 46 6 1 1 33 55 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 3 46 6 1 1 33 55 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 3 46 6 0 0 30 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 34 56 -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 34 56 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 2 19 G C - - MP 48 47 6 52 6 2 2 32 54 -10.915 -10.854 -0.006 -9.631 -9.910 -10.305 -8.741 -5.484 -10.607 -2.914 -10.320 -6.679 -4.734 -10.230 -6.844 3.967 -7.048 -3.397 -5.099 -7.131 -7.145 -9.528 ML 49 47 6 52 6 1 1 31 53 -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 31 53 -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 28 51 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 32 54 -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 32 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 3 18 U A - - MP 54 53 6 58 6 2 2 30 52 -10.915 -10.854 -0.006 -9.631 -9.910 -10.305 -7.207 -6.379 -6.953 0.574 -5.993 -7.750 -1.686 -6.489 -6.809 -2.925 -7.181 -3.833 3.789 -7.736 -3.670 -5.722 ML 55 53 6 58 6 1 1 29 51 -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 29 51 -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 49 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 30 52 -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 30 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 4 17 G C - - MP 60 59 6 64 4 2 2 28 50 -5.128 -10.072 -0.140 -3.989 -8.741 -5.484 -10.607 -2.914 -10.320 -6.679 -4.734 -10.230 -6.844 3.967 -7.048 -3.397 -5.099 -7.131 -7.145 -9.528 ML 61 59 6 64 4 1 1 28 50 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 4 1 1 28 50 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 63 59 6 64 4 0 0 27 49 -4.568 -4.250 -2.265 -0.520 IL 64 64 5 64 4 1 1 31 53 -1.208 -3.864 -1.040 -6.350 0.000 0.000 0.000 0.000 IR 65 65 6 65 3 1 1 27 45 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 7 - U - - - ML 66 65 6 68 3 1 1 21 40 -10.700 -0.003 -9.354 -3.545 -1.192 -2.044 1.693 D 67 65 6 68 3 0 0 21 39 -8.468 -0.219 -2.859 IL 68 68 3 68 3 1 1 26 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 8 - U - - - ML 69 68 3 71 3 1 1 20 39 -10.789 -0.003 -9.443 -4.435 -1.972 -5.168 1.876 D 70 68 3 71 3 0 0 21 39 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 25 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 9 - U - - - ML 72 71 3 74 3 1 1 19 38 -10.789 -0.003 -9.443 -6.198 -5.636 -7.079 1.985 D 73 71 3 74 3 0 0 20 38 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 24 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 10 - U - - - ML 75 74 3 77 3 1 1 18 36 -10.789 -0.003 -9.443 -1.330 -1.881 -2.184 1.637 D 76 74 3 77 3 0 0 19 37 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 23 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 11 - U - - - ML 78 77 3 80 3 1 1 17 35 -10.789 -0.003 -9.443 -1.043 0.050 -1.061 1.000 D 79 77 3 80 3 0 0 18 36 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 12 - C - - - ML 81 80 3 83 3 1 1 15 34 -10.789 -0.003 -9.443 -1.213 1.513 -1.470 -1.504 D 82 80 3 83 3 0 0 17 35 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 13 - c - - - ML 84 83 3 86 3 1 1 14 33 -10.789 -0.003 -9.443 -0.750 0.861 -0.904 0.077 D 85 83 3 86 3 0 0 16 34 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 14 - C - - - ML 87 86 3 89 3 1 1 13 31 -10.789 -0.003 -9.443 -2.860 1.174 -0.107 -0.562 D 88 86 3 89 3 0 0 15 33 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 15 - U - - - ML 90 89 3 92 3 1 1 11 30 -10.789 -0.003 -9.443 -6.198 -5.636 -7.079 1.985 D 91 89 3 92 3 0 0 13 32 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 27 ] 16 - C - - - ML 93 92 3 95 2 1 1 1 1 * 0.000 -5.089 1.828 -5.786 -1.317 D 94 92 3 95 2 0 0 0 0 * 0.000 IL 95 95 3 95 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 28 ] - - - - - - E 96 95 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME TMV_UPD-PK3 ACC RF01072 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 31 MAXL 88 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Jul 11 00:22:13 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/RF01072/CM NSEQ 25 EFFN 24.179077 CKSUM 4270387066 STATS LOCAL MSV -6.7532 0.72779 STATS LOCAL VITERBI -6.9673 0.72779 STATS LOCAL FORWARD -3.7730 0.72779 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.31634 1.52115 1.68183 1.11660 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 0.00000 * 1 0.01312 5.99621 4.87155 5.84894 1 A - - < 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 2 4.51871 5.62643 0.01818 5.65089 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 3 2.34922 3.78806 4.23041 0.14229 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 4 4.50522 5.60195 0.01855 5.61591 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.09772 3.48755 2.77231 0.77788 0.61504 1.09861 0.40547 5 3.81128 2.21181 2.80242 0.21355 7 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00784 5.54516 5.54516 1.46634 0.26236 0.11120 2.25154 6 4.42628 2.75059 4.93439 0.08670 8 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 7 5.63047 5.24701 6.23788 0.01086 9 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 8 2.30394 2.68288 2.89516 0.25298 10 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 9 2.10037 1.35279 2.11954 0.69518 11 u - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 10 2.22299 0.33958 2.40508 2.41480 12 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 11 1.90052 0.79248 2.01221 1.33144 13 c - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 12 3.33221 0.57496 1.46391 1.77062 14 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 13 5.63047 5.24701 6.23788 0.01086 15 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 14 4.87373 0.11961 5.36081 2.29866 16 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 15 5.65484 0.02319 5.52650 4.17092 17 C - - > 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 16 0.14724 4.57647 3.62413 2.30309 18 A - - > 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 17 5.71480 0.02267 5.56160 4.18136 19 C - - > 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 18 6.34851 5.36283 5.93456 0.00912 20 U - - > 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 19 5.63047 5.24701 6.23788 0.01086 21 U - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 20 0.05816 5.18828 3.10981 5.06585 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 21 0.00889 6.10092 5.65161 5.77802 23 A - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 22 0.00889 6.10092 5.65161 5.77802 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 23 5.63047 5.24701 6.23788 0.01086 25 U - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 24 2.32885 0.12385 5.17997 4.30851 26 C - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 25 5.16813 6.35011 0.01089 5.68717 27 G - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 26 0.00889 6.10092 5.65161 5.77802 28 A - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 27 0.00889 6.10092 5.65161 5.77802 29 A - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 28 1.86117 1.48314 0.53235 3.49445 30 G - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 29 1.37405 1.99007 0.77642 1.89589 31 g - - : 1.38629 1.38629 1.38629 1.38629 0.00738 5.60580 5.60580 1.46634 0.26236 1.09861 0.40547 30 2.28603 2.34538 0.36330 2.23359 32 G - - : 1.38629 1.38629 1.38629 1.38629 0.06448 5.60580 2.83419 1.46634 0.26236 1.09861 0.40547 31 1.45420 1.35972 1.65852 1.14175 33 u - - : 1.38629 1.38629 1.38629 1.38629 0.00391 5.54524 * 1.46634 0.26236 0.00000 * //