INFERNAL1/a [1.1.5 | Sep 2023] NAME TMV_UPD-PK1 ACC RF01114 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 70 NODES 21 CLEN 22 W 36 ALPH RNA RF no CONS yes MAP yes DATE Thu Jul 4 17:47:40 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/RF01114/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 2 EFFN 2.000000 CKSUM 2375833036 NULL 0.000 0.000 0.000 0.000 GA 33.00 TC 33.40 NC 32.40 EFP7GF -3.0987 0.78080 ECMLC 0.61812 -5.32363 4.44302 1600000 502349 0.002389 ECMGC 0.56476 -5.89418 5.58249 1600000 261202 0.001531 ECMLI 0.66370 -3.20997 5.35289 1600000 352659 0.003403 ECMGI 0.58952 -4.82302 6.01574 1600000 238260 0.001679 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 36 55 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 41 60 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 40 59 -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 1 36 55 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 4 2 3 5 3 0 0 35 54 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 38 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - C - - - ML 6 5 3 8 3 1 1 35 54 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 7 5 3 8 3 0 0 34 52 -5.620 -0.734 -1.403 IL 8 8 3 8 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 22 - A - - MR 9 8 3 11 3 1 1 34 53 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 10 8 3 11 3 0 0 32 51 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 21 - C - - MR 12 11 3 14 3 1 1 33 52 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 13 11 3 14 3 0 0 31 50 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 20 - A - - MR 15 14 3 17 3 1 1 32 51 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 16 14 3 17 3 0 0 30 49 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 19 - C - - MR 18 17 3 20 3 1 1 31 50 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 19 17 3 20 3 0 0 29 48 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 18 - U - - MR 21 20 3 23 3 1 1 30 49 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 22 20 3 23 3 0 0 28 47 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 17 - A - - MR 24 23 3 26 3 1 1 29 48 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 27 46 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 16 - A - - MR 27 26 3 29 3 1 1 28 47 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 26 45 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 15 - U - - MR 30 29 3 32 3 1 1 27 46 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 25 44 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 28 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 14 - G - - MR 33 32 3 35 5 1 1 26 45 -7.117 -0.038 -6.932 -7.144 -8.036 -1.638 -2.867 1.736 -2.254 D 34 32 3 35 5 0 0 24 43 -5.352 -0.707 -2.978 -4.409 -2.404 IR 35 35 3 35 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 3 13 G C - - MP 36 35 3 40 6 2 2 25 44 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.798 -3.121 -4.902 0.163 -5.312 -4.716 -0.662 -5.149 -4.364 3.651 -4.697 -0.822 -1.046 -4.505 -2.702 -3.778 ML 37 35 3 40 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 38 35 3 40 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 39 35 3 40 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 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 41 41 6 41 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 4 12 G C - - MP 42 41 6 46 6 2 2 23 41 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.798 -3.121 -4.902 0.163 -5.312 -4.716 -0.662 -5.149 -4.364 3.651 -4.697 -0.822 -1.046 -4.505 -2.702 -3.778 ML 43 41 6 46 6 1 1 22 41 -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 22 41 -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 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 23 41 -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 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 5 11 A U - - MP 48 47 6 52 4 2 2 21 39 -6.977 -7.184 -0.052 -5.598 -3.842 -2.861 -3.857 3.364 -4.221 -5.288 0.082 -3.896 -3.747 1.023 -4.297 -0.328 -0.335 -4.467 -1.858 -2.688 ML 49 47 6 52 4 1 1 22 40 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 4 1 1 21 40 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 51 47 6 52 4 0 0 20 39 -4.568 -4.250 -2.265 -0.520 IL 52 52 5 52 4 1 1 23 42 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 53 53 6 53 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 6 - U - - - ML 54 53 6 56 3 1 1 18 36 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 55 53 6 56 3 0 0 17 36 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 7 - U - - - ML 57 56 3 59 3 1 1 16 35 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 58 56 3 59 3 0 0 16 34 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 8 - G - - - ML 60 59 3 62 3 1 1 15 33 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 61 59 3 62 3 0 0 15 33 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 9 - U - - - ML 63 62 3 65 3 1 1 13 31 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 64 62 3 65 3 0 0 13 32 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 10 - G - - - ML 66 65 3 68 2 1 1 1 1 * 0.000 -1.638 -2.867 1.736 -2.254 D 67 65 3 68 2 0 0 0 0 * 0.000 IL 68 68 3 68 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 20 ] - - - - - - E 69 68 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME TMV_UPD-PK1 ACC RF01114 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 22 MAXL 92 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Jul 4 17:47:40 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/RF01114/CM NSEQ 2 EFFN 1.480469 CKSUM 2375833036 STATS LOCAL MSV -6.7026 0.78080 STATS LOCAL VITERBI -7.6947 0.78080 STATS LOCAL FORWARD -2.6238 0.78080 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.30479 1.47587 1.42843 1.34513 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 0.25825 2.77873 2.54888 2.43827 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.29476 0.35769 2.85287 1.95022 2 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.29139 2.74785 0.26475 2.69697 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.29400 2.75022 0.26390 2.70050 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 0.58464 2.26394 1.47130 2.21523 5 A - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.18913 2.22772 2.68423 0.33977 6 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.18913 2.22772 2.68423 0.33977 7 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.21292 3.01323 0.26629 2.58672 8 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.18913 2.22772 2.68423 0.33977 9 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.21292 3.01323 0.26629 2.58672 10 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 2.44919 1.71537 2.08122 0.49600 11 U - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 2.92723 0.30652 2.58201 2.00374 12 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.92909 0.30625 2.58271 2.00410 13 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.21292 3.01323 0.26629 2.58672 14 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.18913 2.22772 2.68423 0.33977 15 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 0.25825 2.77873 2.54888 2.43827 16 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 0.25825 2.77873 2.54888 2.43827 17 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.18913 2.22772 2.68423 0.33977 18 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 2.29476 0.35769 2.85287 1.95022 19 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 0.25825 2.77873 2.54888 2.43827 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.29476 0.35769 2.85287 1.95022 21 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 0.25825 2.77873 2.54888 2.43827 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //