INFERNAL1/a [1.1.5 | Sep 2023] NAME toga_FSE ACC RF01837 DESC togavirus ribosomal frameshift element STATES 91 NODES 20 CLEN 29 W 43 ALPH RNA RF no CONS yes MAP yes DATE Mon Jul 8 10:42:46 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/RF01837/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 3 EFFN 3.000000 CKSUM 661255225 NULL 0.000 0.000 0.000 0.000 GA 40.00 TC 40.20 NC 37.50 EFP7GF -5.3078 0.74324 ECMLC 0.62255 -5.58648 4.14270 1600000 512480 0.002342 ECMGC 0.44536 -14.52935 1.04090 1600000 410758 0.000974 ECMLI 0.62528 -4.61666 4.80495 1600000 434192 0.002764 ECMGI 0.48653 -11.46145 2.11522 1600000 295663 0.001353 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 43 62 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 IL 1 1 2 1 6 1 1 45 64 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 2 2 3 2 5 1 1 44 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 29 G U - - MP 3 2 3 7 6 2 2 43 62 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.078 -2.747 -4.270 0.807 -5.343 -6.135 -0.882 -4.249 -3.844 0.733 -4.399 3.439 -1.218 -5.190 -2.817 -2.899 ML 4 2 3 7 6 1 1 42 61 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 5 2 3 7 6 1 1 41 60 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 6 2 3 7 6 0 0 39 58 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 7 7 5 7 6 1 1 43 62 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 8 8 6 8 5 1 1 42 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 28 A U - - MP 9 8 6 13 6 2 2 41 60 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.476 -3.353 -4.422 3.642 -5.136 -6.285 -0.788 -4.416 -4.312 0.335 -4.892 -0.734 -1.200 -5.339 -2.725 -3.234 ML 10 8 6 13 6 1 1 40 59 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 11 8 6 13 6 1 1 39 58 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 12 8 6 13 6 0 0 37 56 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 6 1 1 41 60 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 1 40 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 27 G C - - MP 15 14 6 19 6 2 2 39 58 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 16 14 6 19 6 1 1 38 57 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 17 14 6 19 6 1 1 37 56 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 18 14 6 19 6 0 0 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 39 58 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 26 G C - - MP 21 20 6 25 6 2 2 37 56 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 22 20 6 25 6 1 1 36 55 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 6 1 1 36 54 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 6 25 6 0 0 33 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 37 56 -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 36 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 5 25 G U - - MP 27 26 6 31 6 2 2 35 54 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.078 -2.747 -4.270 0.807 -5.343 -6.135 -0.882 -4.249 -3.844 0.733 -4.399 3.439 -1.218 -5.190 -2.817 -2.899 ML 28 26 6 31 6 1 1 34 53 -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 34 53 -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 32 51 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 35 54 -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 34 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 6 24 U A - - MP 33 32 6 37 6 2 2 33 52 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 34 32 6 37 6 1 1 33 52 -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 32 51 -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 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 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 38 38 6 38 5 1 1 33 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 7 23 G C - - MP 39 38 6 43 4 2 2 31 50 -7.331 -7.538 -0.041 -5.952 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 40 38 6 43 4 1 1 32 51 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 1 31 50 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 42 38 6 43 4 0 0 30 49 -4.568 -4.250 -2.265 -0.520 IL 43 43 5 43 4 1 1 33 52 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 1 32 51 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - G - - - ML 45 44 6 47 3 1 1 28 47 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 46 44 6 47 3 0 0 27 46 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 31 50 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 9 - U - - - ML 48 47 3 50 3 1 1 27 46 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 49 47 3 50 3 0 0 26 45 -5.620 -0.734 -1.403 IL 50 50 3 50 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 22 - U - - MR 51 50 3 53 3 1 1 26 45 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 52 50 3 53 3 0 0 25 43 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 1 27 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 21 - G - - MR 54 53 3 56 5 1 1 25 44 -7.411 -0.031 -7.227 -7.439 -8.330 -2.322 -3.642 1.847 -3.026 D 55 53 3 56 5 0 0 24 43 -5.352 -0.707 -2.978 -4.409 -2.404 IR 56 56 3 56 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 10 20 C G - - MP 57 56 3 61 6 2 2 24 43 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 58 56 3 61 6 1 1 23 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 59 56 3 61 6 1 1 23 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 60 56 3 61 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 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 62 62 6 62 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 11 19 a u - - MP 63 62 6 67 6 2 2 22 41 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -3.795 -2.699 -3.919 2.953 -4.813 -5.524 -0.522 -4.077 -3.713 1.128 -4.292 1.944 -0.728 -4.513 -2.403 -2.693 ML 64 62 6 67 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 6 67 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 22 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 68 68 6 68 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 12 18 G C - - MP 69 68 6 73 6 2 2 20 39 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 70 68 6 73 6 1 1 20 39 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 6 73 6 1 1 20 38 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 6 73 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 20 39 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 74 74 6 74 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 13 17 C G - - MP 75 74 6 79 4 2 2 18 37 -7.331 -7.538 -0.041 -5.952 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 76 74 6 79 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 77 74 6 79 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 78 74 6 79 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 79 79 5 79 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 80 80 6 80 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 14 - U - - - ML 81 80 6 83 3 1 1 15 33 -8.323 -0.016 -6.977 -1.065 0.137 -1.849 1.101 D 82 80 6 83 3 0 0 15 33 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 15 - C - - - ML 84 83 3 86 3 1 1 13 31 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 85 83 3 86 3 0 0 13 32 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 16 - U - - - ML 87 86 3 89 2 1 1 1 1 * 0.000 -2.168 -2.049 -2.929 1.767 D 88 86 3 89 2 0 0 0 0 * 0.000 IL 89 89 3 89 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 19 ] - - - - - - E 90 89 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME toga_FSE ACC RF01837 DESC togavirus ribosomal frameshift element LENG 29 MAXL 100 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jul 8 10:42:46 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/RF01837/CM NSEQ 3 EFFN 2.592773 CKSUM 661255225 STATS LOCAL MSV -7.3007 0.74324 STATS LOCAL VITERBI -7.5738 0.74324 STATS LOCAL FORWARD -2.9141 0.74324 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 2.00386 1.36023 1.09789 1.29095 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 1.98168 3.03607 0.27545 2.90206 1 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 0.29441 2.92681 1.93818 2.85599 2 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 3 2.66887 3.36863 0.15113 3.31047 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 2.66584 3.36485 0.15175 3.30524 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 1.97489 3.02102 0.27907 2.88266 5 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 3.10702 2.00468 2.87070 0.26931 6 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 2.66148 3.35941 0.15265 3.29773 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 2.82070 3.71452 0.12920 3.28948 8 G - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 2.72118 2.66635 3.24285 0.19159 9 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 10 3.31625 0.21279 3.10584 2.20182 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 0.74637 2.75994 0.95044 2.57638 11 a - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 2.66186 3.35989 0.15257 3.29839 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 3.31748 0.21267 3.10645 2.20204 13 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 14 2.04120 1.30444 2.57867 0.64831 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 2.98941 0.17473 3.56547 2.50451 15 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.72118 2.66635 3.24285 0.19159 16 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 2.48158 3.27505 0.18324 3.07892 17 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 3.50194 0.18079 3.19961 2.35949 18 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 2.79630 1.76600 2.55973 0.37016 19 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 2.48650 3.28206 0.18198 3.08720 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 2.82070 3.71452 0.12920 3.28948 21 G - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 2.72118 2.66635 3.24285 0.19159 22 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 23 3.49565 0.18129 3.19677 2.35830 23 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 0.30544 3.05755 1.84152 2.85382 24 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 3.09329 2.00659 2.81750 0.27385 25 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 3.51006 0.18014 3.20326 2.36101 26 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 27 3.51944 0.17941 3.20746 2.36275 27 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 28 3.09261 2.24747 2.73793 0.24303 28 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 29 3.12629 2.00885 2.83175 0.27041 29 U - - > 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //