INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV1_UPD-PKb ACC RF01106 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 79 NODES 24 CLEN 25 W 39 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 12:55:54 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/RF01106/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 3944969595 NULL 0.000 0.000 0.000 0.000 GA 38.00 TC 39.50 NC 35.70 EFP7GF -2.6075 0.77506 ECMLC 0.48873 -9.31504 3.66634 1600000 683109 0.001757 ECMGC 0.45124 -9.11388 5.23950 1600000 259978 0.001539 ECMLI 0.51555 -6.51222 4.71667 1600000 392050 0.003061 ECMGI 0.48333 -7.12532 5.85043 1600000 211726 0.001889 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 39 58 -6.891 -8.136 -0.079 -4.590 IL 1 1 2 1 4 1 1 41 60 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 25 - C - - MR 3 2 3 5 3 1 1 39 58 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 4 2 3 5 3 0 0 37 56 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 24 - A - - MR 6 5 3 8 3 1 1 38 57 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 7 5 3 8 3 0 0 36 55 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 23 - U - - MR 9 8 3 11 3 1 1 37 56 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 10 8 3 11 3 0 0 35 54 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 22 - G - - MR 12 11 3 14 3 1 1 36 55 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 13 11 3 14 3 0 0 34 53 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 21 - U - - MR 15 14 3 17 3 1 1 35 54 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 16 14 3 17 3 0 0 33 52 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 20 - C - - MR 18 17 3 20 3 1 1 34 53 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 19 17 3 20 3 0 0 32 51 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 19 - A - - MR 21 20 3 23 3 1 1 33 52 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 22 20 3 23 3 0 0 31 50 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 18 - A - - MR 24 23 3 26 3 1 1 32 51 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 30 49 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 17 - A - - MR 27 26 3 29 3 1 1 31 50 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 29 48 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 16 - U - - MR 30 29 3 32 3 1 1 30 49 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 29 47 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 15 - U - - MR 33 32 3 35 5 1 1 29 48 -7.117 -0.038 -6.932 -7.144 -8.036 -1.535 -1.523 -2.271 1.632 D 34 32 3 35 5 0 0 28 47 -5.352 -0.707 -2.978 -4.409 -2.404 IR 35 35 3 35 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 1 14 C G - - MP 36 35 3 40 6 2 2 28 47 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 37 35 3 40 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 38 35 3 40 6 1 1 27 46 -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 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 28 47 -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 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 2 13 G C - - MP 42 41 6 46 6 2 2 26 45 -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 26 45 -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 25 44 -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 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 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 47 47 6 47 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 3 12 c g - - MP 48 47 6 52 4 2 2 24 43 -6.977 -7.184 -0.052 -5.598 -3.769 -3.764 -3.602 -0.084 -2.490 -4.116 2.729 -3.229 -3.632 0.123 -3.990 -1.832 1.089 -3.891 1.991 -2.516 ML 49 47 6 52 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 4 1 1 24 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 51 47 6 52 4 0 0 23 42 -4.568 -4.250 -2.265 -0.520 IL 52 52 5 52 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 53 53 6 53 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 4 - u - - - ML 54 53 6 56 3 1 1 21 40 -7.991 -0.020 -6.645 0.557 -0.859 -1.066 0.585 D 55 53 6 56 3 0 0 20 39 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 5 - G - - - ML 57 56 3 59 3 1 1 20 39 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 58 56 3 59 3 0 0 19 38 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 6 - U - - - ML 60 59 3 62 3 1 1 19 37 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 61 59 3 62 3 0 0 18 37 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 7 - A - - - ML 63 62 3 65 3 1 1 18 36 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 64 62 3 65 3 0 0 17 36 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 8 - C - - - ML 66 65 3 68 3 1 1 16 35 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 67 65 3 68 3 0 0 16 34 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 9 - A - - - ML 69 68 3 71 3 1 1 15 33 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 70 68 3 71 3 0 0 15 33 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 10 - G - - - ML 72 71 3 74 3 1 1 13 31 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 73 71 3 74 3 0 0 13 32 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 11 - U - - - ML 75 74 3 77 2 1 1 1 1 * 0.000 -1.535 -1.523 -2.271 1.632 D 76 74 3 77 2 0 0 0 0 * 0.000 IL 77 77 3 77 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 23 ] - - - - - - E 78 77 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV1_UPD-PKb ACC RF01106 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 25 MAXL 97 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 12:55:54 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/RF01106/CM NSEQ 2 EFFN 1.464844 CKSUM 3944969595 STATS LOCAL MSV -7.0116 0.77506 STATS LOCAL VITERBI -8.1227 0.77506 STATS LOCAL FORWARD -2.3569 0.77506 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.29728 1.50173 1.44408 1.31671 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.73200 0.38788 2.44506 1.77373 1 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.28823 2.74000 0.26639 2.69057 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.39025 0.88276 2.12969 0.97849 3 c - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 1.02264 1.91388 2.04942 1.01049 4 u - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.20300 3.00150 0.26963 2.57496 5 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.18095 2.22107 2.67548 0.34291 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 0.26097 2.76954 2.54060 2.42828 7 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.28405 0.36191 2.84157 1.94176 8 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 0.26097 2.76954 2.54060 2.42828 9 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.20300 3.00150 0.26963 2.57496 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 2.18095 2.22107 2.67548 0.34291 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 1.74169 2.29056 0.49716 2.16012 12 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.91750 0.30932 2.57172 1.99820 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 2.04930 2.61529 0.33433 2.49850 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 2.18095 2.22107 2.67548 0.34291 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 2.18095 2.22107 2.67548 0.34291 16 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 0.26097 2.76954 2.54060 2.42828 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 0.26097 2.76954 2.54060 2.42828 18 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 0.26097 2.76954 2.54060 2.42828 19 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.28405 0.36191 2.84157 1.94176 20 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.18095 2.22107 2.67548 0.34291 21 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 2.20300 3.00150 0.26963 2.57496 22 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.18095 2.22107 2.67548 0.34291 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 0.26097 2.76954 2.54060 2.42828 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.28405 0.36191 2.84157 1.94176 25 C - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //