INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV1_UPD-PKh ACC RF01082 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 79 NODES 21 CLEN 25 W 39 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 14:50:30 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/RF01082/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 2275878068 NULL 0.000 0.000 0.000 0.000 GA 32.00 TC 32.20 NC 31.40 EFP7GF -2.7515 0.78270 ECMLC 0.64560 -4.91068 4.49988 1600000 522047 0.002299 ECMGC 0.50957 -8.20781 4.85174 1600000 310594 0.001288 ECMLI 0.64708 -3.41455 5.34895 1600000 348281 0.003445 ECMGI 0.52828 -6.90553 5.41495 1600000 268384 0.001490 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 39 58 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 44 63 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 43 62 -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 1 39 59 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 4 2 3 5 3 0 0 38 57 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 42 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - U - - - ML 6 5 3 8 3 1 1 38 57 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 7 5 3 8 3 0 0 37 56 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - C - - - ML 9 8 3 11 3 1 1 37 56 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 10 8 3 11 3 0 0 36 55 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - U - - - ML 12 11 3 14 3 1 1 36 55 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 13 11 3 14 3 0 0 35 54 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - A - - - ML 15 14 3 17 3 1 1 35 54 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 16 14 3 17 3 0 0 34 53 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - A - - - ML 18 17 3 20 5 1 1 34 53 -7.117 -0.038 -6.932 -7.144 -8.036 1.730 -2.426 -2.052 -1.973 D 19 17 3 20 5 0 0 33 52 -4.959 -0.803 -4.221 -2.596 -2.508 IL 20 20 3 20 5 1 1 34 53 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 7 25 c g - - MP 21 20 3 25 6 2 2 33 52 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -3.683 -3.613 -3.564 0.132 -2.512 -4.142 2.671 -3.219 -3.574 0.382 -3.967 -1.587 2.332 -3.824 -0.184 -2.444 ML 22 20 3 25 6 1 1 31 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 3 25 6 1 1 31 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 3 25 6 0 0 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 33 52 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 8 24 u a - - MP 27 26 6 31 6 2 2 31 50 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -2.651 1.068 -2.765 0.908 -2.519 -3.574 1.448 -2.900 -2.787 1.312 -3.293 -0.498 1.996 -2.931 -0.396 -1.827 ML 28 26 6 31 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 29 26 6 31 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 30 26 6 31 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 31 50 -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 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 23 U A - - MP 33 32 6 37 6 2 2 29 48 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 34 32 6 37 6 1 1 28 46 -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 27 46 -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 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 29 48 -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 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 10 22 G C - - MP 39 38 6 43 6 2 2 27 46 -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 40 38 6 43 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 41 38 6 43 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 42 38 6 43 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 27 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 44 44 6 44 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 11 21 U A - - MP 45 44 6 49 6 2 2 25 44 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 46 44 6 49 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 47 44 6 49 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 48 44 6 49 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 25 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 50 50 6 50 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 12 20 C G - - MP 51 50 6 55 4 2 2 23 42 -6.977 -7.184 -0.052 -5.598 -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 52 50 6 55 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 54 50 6 55 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 55 55 5 55 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 56 56 6 56 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - G - - - ML 57 56 6 59 3 1 1 20 39 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 58 56 6 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 14 ] 14 - G - - - ML 60 59 3 62 3 1 1 19 37 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 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 15 ] 15 - G - - - ML 63 62 3 65 3 1 1 18 36 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 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 16 ] 16 - 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 17 ] 17 - u - - - ML 69 68 3 71 3 1 1 15 33 -7.991 -0.020 -6.645 0.557 -0.859 -1.066 0.585 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 18 ] 18 - 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 19 ] 19 - A - - - ML 75 74 3 77 2 1 1 1 1 * 0.000 1.730 -2.426 -2.052 -1.973 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 20 ] - - - - - - E 78 77 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV1_UPD-PKh ACC RF01082 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 14:50:30 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/RF01082/CM NSEQ 2 EFFN 1.613281 CKSUM 2275878068 STATS LOCAL MSV -7.0745 0.78270 STATS LOCAL VITERBI -8.0699 0.78270 STATS LOCAL FORWARD -2.3661 0.78270 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.39379 1.52749 1.17207 1.49139 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.29577 3.11081 0.24015 2.68468 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.25793 2.28376 2.75751 0.31460 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.38505 0.32432 2.94782 2.02160 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 2.25793 2.28376 2.75751 0.31460 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 0.23667 2.85568 2.61812 2.52207 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 0.23667 2.85568 2.61812 2.52207 6 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.35603 0.90111 2.07043 0.98630 7 c - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 1.37266 1.59715 1.44102 1.17958 8 u - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.58043 1.62424 2.27961 0.47021 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 2.34324 2.83592 0.24393 2.78427 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 2.57964 1.62425 2.27933 0.47034 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 2.81898 0.35482 2.54168 1.83073 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 2.29577 3.11081 0.24015 2.68468 13 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.29577 3.11081 0.24015 2.68468 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 2.29577 3.11081 0.24015 2.68468 15 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.38505 0.32432 2.94782 2.02160 16 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 1.01630 1.93286 2.07158 1.00144 17 u - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.29577 3.11081 0.24015 2.68468 18 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 0.23667 2.85568 2.61812 2.52207 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 2.10372 2.70734 0.30768 2.57531 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 0.53600 2.45539 1.46082 2.33265 21 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 3.00004 0.28545 2.66448 2.04868 22 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 0.53610 2.45511 1.46084 2.33224 23 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 1.33494 1.22935 1.41619 1.60094 24 c - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 1.13568 2.23140 0.79576 2.11875 25 g - - > 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //