INFERNAL1/a [1.1.5 | Sep 2023] NAME UPSK ACC RF00390 DESC UPSK RNA STATES 73 NODES 21 CLEN 23 W 37 ALPH RNA RF no CONS yes MAP yes DATE Wed Jul 10 12:02:05 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/RF00390/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 6 EFFN 6.000000 CKSUM 1333171827 NULL 0.000 0.000 0.000 0.000 GA 38.00 TC 38.60 NC 37.80 EFP7GF -7.9022 0.73793 ECMLC 0.60197 -8.00287 2.99349 1600000 899434 0.001334 ECMGC 0.47699 -13.29576 2.15553 1600000 635090 0.000630 ECMLI 0.55034 -8.27878 3.32068 1600000 710521 0.001689 ECMGI 0.51184 -11.32644 2.97753 1600000 604880 0.000661 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 37 55 -8.056 -8.263 -0.024 -6.677 IL 1 1 2 1 4 1 1 41 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 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - U - - - ML 3 2 3 5 3 1 1 37 55 -9.016 -0.010 -7.670 -3.412 -3.114 -4.199 1.902 D 4 2 3 5 3 0 0 36 55 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - a - - - ML 6 5 3 8 3 1 1 36 54 -9.016 -0.010 -7.670 0.906 -2.633 0.797 -2.136 D 7 5 3 8 3 0 0 35 54 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - A - - - ML 9 8 3 11 3 1 1 34 53 -9.016 -0.010 -7.670 1.935 -4.373 -3.846 -4.088 D 10 8 3 11 3 0 0 34 53 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 1 33 52 -9.016 -0.010 -7.670 -3.499 -4.936 1.936 -4.240 D 13 11 3 14 3 0 0 32 51 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 36 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - U - - - ML 15 14 3 17 3 1 1 32 51 -9.016 -0.010 -7.670 -3.412 -3.114 -4.199 1.902 D 16 14 3 17 3 0 0 31 50 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 1 31 50 -9.016 -0.010 -7.670 -3.412 -3.114 -4.199 1.902 D 19 17 3 20 3 0 0 30 49 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 34 53 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - C - - - ML 21 20 3 23 3 1 1 30 49 -9.016 -0.010 -7.670 -4.029 1.920 -4.711 -3.106 D 22 20 3 23 3 0 0 29 48 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - U - - - ML 24 23 3 26 5 1 1 29 48 -8.047 -0.020 -7.862 -8.075 -8.966 -3.412 -3.114 -4.199 1.902 D 25 23 3 26 5 0 0 28 47 -4.959 -0.803 -4.221 -2.596 -2.508 IL 26 26 3 26 5 1 1 29 48 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 23 C G - - MP 27 26 3 31 6 2 2 28 47 -9.635 -9.574 -0.015 -8.350 -8.630 -9.025 -6.834 -6.934 -6.087 -3.126 -4.489 -6.200 3.904 -5.571 -6.334 -3.072 -6.219 -5.044 -1.337 -6.755 -2.378 -5.137 ML 28 26 3 31 6 1 1 27 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 29 26 3 31 6 1 1 27 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 30 26 3 31 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 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 32 32 6 32 5 1 1 27 46 -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 33 32 6 37 6 2 2 26 45 -9.635 -9.574 -0.015 -8.350 -8.630 -9.025 -5.538 -3.637 -5.614 -0.425 -6.408 -5.122 -1.530 -6.109 -5.053 3.656 -5.307 -1.393 -1.845 0.358 -3.588 -4.561 ML 34 32 6 37 6 1 1 25 44 -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 25 44 -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 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 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 38 38 6 38 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 11 21 A U - - MP 39 38 6 43 6 2 2 24 43 -9.635 -9.574 -0.015 -8.350 -8.630 -9.025 -5.763 -4.492 -5.353 3.875 -6.979 -8.299 -2.588 -5.278 -5.522 -1.079 -6.143 -1.777 -2.943 -7.034 -4.498 -4.306 ML 40 38 6 43 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 41 38 6 43 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 42 38 6 43 6 0 0 22 41 -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 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 12 20 U A - - MP 45 44 6 49 4 2 2 22 41 -8.056 -8.263 -0.024 -6.677 -7.058 -6.921 -6.575 -3.159 -5.104 -6.888 -0.807 -5.937 -6.554 -3.163 -6.821 -4.808 3.894 -7.020 -2.691 -4.739 ML 46 44 6 49 4 1 1 24 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 48 44 6 49 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 49 49 5 49 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 50 50 6 50 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - C - - - ML 51 50 6 53 3 1 1 19 38 -9.016 -0.010 -7.670 -4.029 1.920 -4.711 -3.106 D 52 50 6 53 3 0 0 19 38 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 23 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 14 - U - - - ML 54 53 3 56 3 1 1 18 37 -9.016 -0.010 -7.670 -3.412 -3.114 -4.199 1.902 D 55 53 3 56 3 0 0 18 36 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 15 - C - - - ML 57 56 3 59 3 1 1 17 35 -9.016 -0.010 -7.670 -1.894 1.202 -2.833 0.367 D 58 56 3 59 3 0 0 17 35 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 16 - U - - - ML 60 59 3 62 3 1 1 15 34 -9.016 -0.010 -7.670 -3.412 -3.114 -4.199 1.902 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 17 ] 17 - A - - - ML 63 62 3 65 3 1 1 14 32 -9.016 -0.010 -7.670 1.935 -4.373 -3.846 -4.088 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 18 ] 18 - A - - - ML 66 65 3 68 3 1 1 12 31 -9.016 -0.010 -7.670 1.935 -4.373 -3.846 -4.088 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 19 ] 19 - A - - - ML 69 68 3 71 2 1 1 1 1 * 0.000 1.935 -4.373 -3.846 -4.088 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 20 ] - - - - - - E 72 71 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME UPSK ACC RF00390 DESC UPSK RNA LENG 23 MAXL 87 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Jul 10 12:02:05 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/RF00390/CM NSEQ 6 EFFN 5.194336 CKSUM 1333171827 STATS LOCAL MSV -5.6815 0.73793 STATS LOCAL VITERBI -6.6653 0.73793 STATS LOCAL FORWARD -2.9244 0.73793 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.26395 1.58130 1.83354 1.04438 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 0.00000 * 1 3.57115 3.38666 4.11327 0.08153 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 2 0.77647 3.05646 0.85453 2.69656 2 a - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 3 0.05450 4.23277 3.87704 4.02758 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 4 3.64896 4.62878 0.05270 4.16354 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 5 3.57115 3.38666 4.11327 0.08153 5 U - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 6 3.57115 3.38666 4.11327 0.08153 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 7 3.99170 0.06645 4.49372 3.36263 7 C - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 8 3.57115 3.38666 4.11327 0.08153 8 U - - : 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 9 4.30986 0.08083 4.18470 3.01616 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 10 2.71360 3.42774 0.22971 2.23984 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 11 0.10433 4.05109 2.78601 3.91185 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 12 4.26751 2.97238 4.14867 0.08445 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 13 3.99170 0.06645 4.49372 3.36263 13 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 14 3.57115 3.38666 4.11327 0.08153 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 15 2.57239 0.57941 3.20872 1.13008 15 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 16 3.57115 3.38666 4.11327 0.08153 16 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 17 0.05450 4.23277 3.87704 4.02758 17 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 18 0.05450 4.23277 3.87704 4.02758 18 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 19 0.05450 4.23277 3.87704 4.02758 19 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 20 0.09661 4.34449 2.80191 3.99433 20 A - - > 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 21 4.11650 3.18133 3.85202 0.08237 21 U - - > 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 22 3.54357 0.16989 3.25367 2.42245 22 C - - > 1.38629 1.38629 1.38629 1.38629 0.02469 4.40672 4.40672 1.46634 0.26236 1.09861 0.40547 23 3.29196 4.32734 0.06992 4.06594 23 G - - > 1.38629 1.38629 1.38629 1.38629 0.01242 4.39445 * 1.46634 0.26236 0.00000 * //