INFERNAL1/a [1.1.5 | Sep 2023] NAME SBRMV1_UPD-PKf ACC RF01107 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 85 NODES 25 CLEN 27 W 41 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 12 14:13:00 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/RF01107/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 1329811384 NULL 0.000 0.000 0.000 0.000 GA 39.00 TC 45.90 NC 33.50 EFP7GF -2.8378 0.76321 ECMLC 0.59402 -6.90086 3.48620 1600000 573915 0.002091 ECMGC 0.50405 -9.39956 3.87681 1600000 322379 0.001241 ECMLI 0.59948 -5.25916 4.53194 1600000 424928 0.002824 ECMGI 0.52133 -7.73463 4.69295 1600000 260486 0.001536 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 41 60 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 46 65 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 45 64 -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 41 60 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 4 2 3 5 3 0 0 40 59 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 27 - G - - MR 6 5 3 8 3 1 1 40 59 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 7 5 3 8 3 0 0 38 57 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 26 - C - - MR 9 8 3 11 3 1 1 39 58 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 10 8 3 11 3 0 0 37 56 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 25 - U - - MR 12 11 3 14 3 1 1 38 57 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 13 11 3 14 3 0 0 36 55 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 24 - A - - MR 15 14 3 17 3 1 1 37 56 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 16 14 3 17 3 0 0 35 54 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 23 - A - - MR 18 17 3 20 3 1 1 36 55 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 19 17 3 20 3 0 0 34 53 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 22 - A - - MR 21 20 3 23 3 1 1 35 54 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 22 20 3 23 3 0 0 33 52 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 21 - U - - MR 24 23 3 26 3 1 1 34 53 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 25 23 3 26 3 0 0 32 51 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 20 - A - - MR 27 26 3 29 3 1 1 33 52 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 31 50 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 19 - U - - MR 30 29 3 32 3 1 1 32 51 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 30 49 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 18 - U - - MR 33 32 3 35 3 1 1 31 50 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 34 32 3 35 3 0 0 29 48 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 17 - A - - MR 36 35 3 38 5 1 1 30 49 -7.117 -0.038 -6.932 -7.144 -8.036 1.730 -2.426 -2.052 -1.973 D 37 35 3 38 5 0 0 29 48 -5.352 -0.707 -2.978 -4.409 -2.404 IR 38 38 3 38 5 1 1 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 2 16 C G - - MP 39 38 3 43 6 2 2 29 48 -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 28 46 -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 27 46 -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 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 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 44 44 6 44 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 3 15 C G - - MP 45 44 6 49 6 2 2 27 46 -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 46 44 6 49 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 47 44 6 49 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 48 44 6 49 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 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 50 50 6 50 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 4 14 G C - - MP 51 50 6 55 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 52 50 6 55 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 53 50 6 55 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 54 50 6 55 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 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 56 56 6 56 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 5 13 C G - - MP 57 56 6 61 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 58 56 6 61 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 60 56 6 61 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 61 61 5 61 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 62 62 6 62 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 6 - U - - - ML 63 62 6 65 3 1 1 20 39 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 64 62 6 65 3 0 0 19 38 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 7 - G - - - ML 66 65 3 68 3 1 1 19 37 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 67 65 3 68 3 0 0 18 37 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 8 - G - - - ML 69 68 3 71 3 1 1 18 36 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 70 68 3 71 3 0 0 17 36 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 9 - G - - - ML 72 71 3 74 3 1 1 16 35 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 73 71 3 74 3 0 0 16 34 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 10 - A - - - ML 75 74 3 77 3 1 1 15 33 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 76 74 3 77 3 0 0 15 33 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 19 37 -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 13 31 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 79 77 3 80 3 0 0 13 32 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 12 - U - - - ML 81 80 3 83 2 1 1 1 1 * 0.000 -1.535 -1.523 -2.271 1.632 D 82 80 3 83 2 0 0 0 0 * 0.000 IL 83 83 3 83 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 24 ] - - - - - - E 84 83 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBRMV1_UPD-PKf ACC RF01107 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 27 MAXL 100 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 12 14:13:00 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/RF01107/CM NSEQ 2 EFFN 1.472656 CKSUM 1329811384 STATS LOCAL MSV -6.7940 0.76321 STATS LOCAL VITERBI -7.9465 0.76321 STATS LOCAL FORWARD -2.5426 0.76321 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.38224 1.62677 1.22000 1.35794 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.20796 3.00737 0.26795 2.58085 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 2.73643 0.38608 2.45013 1.77669 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 2.74124 0.38521 2.45199 1.77738 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 2.29214 2.74604 0.26480 2.69692 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 2.74357 0.38479 2.45288 1.77772 5 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.18504 2.22440 2.67986 0.34133 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 2.20796 3.00737 0.26795 2.58085 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 2.20796 3.00737 0.26795 2.58085 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 2.20796 3.00737 0.26795 2.58085 9 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 0.25961 2.77414 2.54474 2.43328 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 2.18504 2.22440 2.67986 0.34133 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 2.18504 2.22440 2.67986 0.34133 12 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.05086 2.61882 0.33344 2.50064 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 2.92076 0.30815 2.57627 2.00066 14 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.05177 2.61980 0.33302 2.50201 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 2.05232 2.62040 0.33277 2.50283 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 0.25961 2.77414 2.54474 2.43328 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 2.18504 2.22440 2.67986 0.34133 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 2.18504 2.22440 2.67986 0.34133 19 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 0.25961 2.77414 2.54474 2.43328 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 2.18504 2.22440 2.67986 0.34133 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 0.25961 2.77414 2.54474 2.43328 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 0.25961 2.77414 2.54474 2.43328 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 0.25961 2.77414 2.54474 2.43328 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 2.18504 2.22440 2.67986 0.34133 25 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 26 2.28940 0.35979 2.84722 1.94599 26 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 27 2.20796 3.00737 0.26795 2.58085 27 G - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //