INFERNAL1/a [1.1.5 | Sep 2023] NAME BMV3_UPD-PK3 ACC RF01113 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 73 NODES 22 CLEN 23 W 37 ALPH RNA RF no CONS yes MAP yes DATE Wed Jul 10 06:22:17 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/RF01113/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 3420387390 NULL 0.000 0.000 0.000 0.000 GA 36.00 TC 37.00 NC 34.40 EFP7GF -2.7540 0.78125 ECMLC 0.51101 -6.78094 5.23238 1600000 556261 0.002157 ECMGC 0.50106 -6.17150 6.93668 1600000 284759 0.001405 ECMLI 0.53492 -4.47632 6.17029 1600000 356879 0.003362 ECMGI 0.49857 -5.46421 7.34532 1600000 237490 0.001684 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 37 56 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 42 61 -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 60 -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 37 56 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 4 2 3 5 3 0 0 36 54 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 1 38 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 23 - U - - MR 6 5 3 8 3 1 1 36 55 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 7 5 3 8 3 0 0 34 53 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 22 - U - - MR 9 8 3 11 3 1 1 35 54 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 10 8 3 11 3 0 0 33 52 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 36 54 -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 34 53 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 13 11 3 14 3 0 0 32 51 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 20 - G - - MR 15 14 3 17 3 1 1 33 52 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 16 14 3 17 3 0 0 31 50 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 19 - A - - MR 18 17 3 20 3 1 1 32 51 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 19 17 3 20 3 0 0 30 49 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 18 - A - - MR 21 20 3 23 3 1 1 31 50 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 22 20 3 23 3 0 0 29 48 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 32 50 -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 30 49 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 28 47 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 31 49 -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 29 48 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 27 46 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 30 48 -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 28 47 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 26 45 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 14 - U - - MR 33 32 3 35 3 1 1 27 46 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 34 32 3 35 3 0 0 25 44 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 28 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 13 - u - - MR 36 35 3 38 5 1 1 26 45 -7.117 -0.038 -6.932 -7.144 -8.036 -0.382 -0.955 0.345 0.532 D 37 35 3 38 5 0 0 24 43 -5.352 -0.707 -2.978 -4.409 -2.404 IR 38 38 3 38 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 2 12 C G - - MP 39 38 3 43 6 2 2 25 44 -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 40 38 3 43 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 41 38 3 43 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 42 38 3 43 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 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 44 44 6 44 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 3 11 U A - - MP 45 44 6 49 6 2 2 23 41 -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 22 41 -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 22 41 -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 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 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 50 50 6 50 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 4 10 U A - - MP 51 50 6 55 4 2 2 21 39 -6.977 -7.184 -0.052 -5.598 -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 52 50 6 55 4 1 1 22 40 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 4 1 1 21 40 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 54 50 6 55 4 0 0 20 39 -4.568 -4.250 -2.265 -0.520 IL 55 55 5 55 4 1 1 23 42 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 56 56 6 56 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 5 - U - - - ML 57 56 6 59 3 1 1 18 36 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 58 56 6 59 3 0 0 17 36 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 6 - G - - - ML 60 59 3 62 3 1 1 16 35 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 61 59 3 62 3 0 0 16 34 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 7 - G - - - ML 63 62 3 65 3 1 1 15 33 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 64 62 3 65 3 0 0 15 33 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 19 37 -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 13 31 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 67 65 3 68 3 0 0 13 32 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 9 - U - - - ML 69 68 3 71 2 1 1 1 1 * 0.000 -1.535 -1.523 -2.271 1.632 D 70 68 3 71 2 0 0 0 0 * 0.000 IL 71 71 3 71 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 21 ] - - - - - - E 72 71 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME BMV3_UPD-PK3 ACC RF01113 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 23 MAXL 93 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Jul 10 06:22:17 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/RF01113/CM NSEQ 2 EFFN 1.574219 CKSUM 3420387390 STATS LOCAL MSV -6.7463 0.78125 STATS LOCAL VITERBI -7.8790 0.78125 STATS LOCAL FORWARD -1.8620 0.78125 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.23836 1.71359 1.51197 1.17296 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 0.24274 2.83327 2.59796 2.49763 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 2.79167 0.36392 2.51464 1.81498 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 2.55783 1.61049 2.25529 0.48144 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.55913 1.61047 2.25574 0.48120 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 2.23783 2.26735 2.73614 0.32172 5 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.27167 3.08250 0.24743 2.65625 6 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.27167 3.08250 0.24743 2.65625 7 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.35864 0.33368 2.92011 2.00070 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 2.23783 2.26735 2.73614 0.32172 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 0.54809 2.43254 1.44694 2.31420 10 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 0.54794 2.43296 1.44691 2.31480 11 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 2.09151 2.68582 0.31346 2.55849 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 1.59252 1.98575 1.18678 1.03815 13 u - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.23783 2.26735 2.73614 0.32172 14 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.23783 2.26735 2.73614 0.32172 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 0.24274 2.83327 2.59796 2.49763 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 0.24274 2.83327 2.59796 2.49763 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 0.24274 2.83327 2.59796 2.49763 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 0.24274 2.83327 2.59796 2.49763 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 2.27167 3.08250 0.24743 2.65625 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 2.35864 0.33368 2.92011 2.00070 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 2.23783 2.26735 2.73614 0.32172 22 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.23783 2.26735 2.73614 0.32172 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //