INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV1_UPD-PKe ACC RF01081 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 82 NODES 23 CLEN 26 W 40 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 21:10:09 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/RF01081/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 2622241997 NULL 0.000 0.000 0.000 0.000 GA 38.00 TC 39.00 NC 35.00 EFP7GF -3.9937 0.75549 ECMLC 0.58329 -7.72857 3.17884 1600000 695406 0.001726 ECMGC 0.51125 -9.25810 3.80086 1600000 317393 0.001260 ECMLI 0.55367 -6.81126 3.95933 1600000 466680 0.002571 ECMGI 0.53167 -7.80742 4.43687 1600000 268703 0.001489 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 40 59 -7.220 -8.465 -0.063 -4.919 IL 1 1 2 1 4 1 1 41 60 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 26 - A - - MR 3 2 3 5 3 1 1 40 59 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 4 2 3 5 3 0 0 38 57 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 25 - A - - MR 6 5 3 8 3 1 1 39 58 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 7 5 3 8 3 0 0 37 56 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 24 - C - - MR 9 8 3 11 3 1 1 38 57 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 10 8 3 11 3 0 0 36 55 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 23 - A - - MR 12 11 3 14 3 1 1 37 56 -8.693 -0.015 -7.010 1.087 -1.745 0.190 -1.195 D 13 11 3 14 3 0 0 35 54 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 22 - U - - MR 15 14 3 17 3 1 1 36 55 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 16 14 3 17 3 0 0 34 53 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 21 - G - - MR 18 17 3 20 3 1 1 35 54 -8.693 -0.015 -7.010 -2.322 -3.642 1.847 -3.026 D 19 17 3 20 3 0 0 33 52 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 20 - A - - MR 21 20 3 23 3 1 1 34 53 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 22 20 3 23 3 0 0 32 51 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 19 - G - - MR 24 23 3 26 5 1 1 33 52 -7.411 -0.031 -7.227 -7.439 -8.330 -2.322 -3.642 1.847 -3.026 D 25 23 3 26 5 0 0 31 50 -5.352 -0.707 -2.978 -4.409 -2.404 IR 26 26 3 26 5 1 1 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 1 18 a u - - MP 27 26 3 31 6 2 2 32 51 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -3.482 1.476 -3.613 2.886 -4.186 -4.920 -0.171 -3.817 -3.484 1.209 -4.046 -0.168 -0.389 -4.044 -1.963 -2.496 ML 28 26 3 31 6 1 1 30 49 -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 30 49 -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 28 47 -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 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 2 17 g u - - MP 33 32 6 37 6 2 2 30 49 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -3.869 -2.669 -4.028 2.349 -5.076 -5.688 -0.704 -4.141 -3.739 1.036 -4.303 2.773 -0.909 -4.697 -2.604 -2.749 ML 34 32 6 37 6 1 1 28 47 -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 28 47 -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 26 45 -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 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 3 16 C G - - MP 39 38 6 43 6 2 2 28 47 -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 40 38 6 43 6 1 1 27 46 -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 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 28 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 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 4 15 C G - - MP 45 44 6 49 6 2 2 26 45 -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 46 44 6 49 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 47 44 6 49 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 48 44 6 49 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 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 50 50 6 50 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 5 14 U G - - MP 51 50 6 55 4 2 2 24 43 -7.331 -7.538 -0.041 -5.952 -4.813 -4.762 -4.353 -1.035 -2.919 -4.667 1.378 -3.748 -4.402 -0.961 -4.623 -2.746 0.441 -4.827 3.364 -3.241 ML 52 50 6 55 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 4 1 1 24 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 54 50 6 55 4 0 0 23 42 -4.568 -4.250 -2.265 -0.520 IL 55 55 5 55 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 56 56 6 56 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 6 - A - - - ML 57 56 6 59 3 1 1 21 40 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 D 58 56 6 59 3 0 0 20 39 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 7 - U - - - ML 60 59 3 62 3 1 1 20 38 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 61 59 3 62 3 0 0 19 38 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 8 - U - - - ML 63 62 3 65 3 1 1 18 37 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 64 62 3 65 3 0 0 18 37 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 9 - U - - - ML 66 65 3 68 3 1 1 17 36 -8.323 -0.016 -6.977 0.154 -1.061 -1.389 1.019 D 67 65 3 68 3 0 0 17 36 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 10 - G - - - ML 69 68 3 71 3 1 1 16 34 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 70 68 3 71 3 0 0 16 34 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 11 - U - - - ML 72 71 3 74 3 1 1 15 33 -8.323 -0.016 -6.977 -1.054 0.188 -1.841 1.070 D 73 71 3 74 3 0 0 15 33 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 12 - a - - - ML 75 74 3 77 3 1 1 13 31 -8.323 -0.016 -6.977 0.946 -1.133 -1.272 0.267 D 76 74 3 77 3 0 0 13 32 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 13 - C - - - ML 78 77 3 80 2 1 1 1 1 * 0.000 -2.619 1.795 -3.443 -1.863 D 79 77 3 80 2 0 0 0 0 * 0.000 IL 80 80 3 80 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 22 ] - - - - - - E 81 80 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV1_UPD-PKe ACC RF01081 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 26 MAXL 96 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 21:10:09 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/RF01081/CM NSEQ 3 EFFN 2.545898 CKSUM 2622241997 STATS LOCAL MSV -7.1402 0.75549 STATS LOCAL VITERBI -7.6760 0.75549 STATS LOCAL FORWARD -2.7808 0.75549 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.34216 1.57567 1.30505 1.34442 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 0.54296 2.48947 1.43844 2.31543 1 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 1.11832 2.84651 0.60680 2.65877 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 3 3.29510 0.21749 3.08158 2.18470 3 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 3.29461 0.21754 3.08134 2.18462 4 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 3.02657 1.62424 2.82987 0.36322 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 0.13959 3.33587 3.05057 3.04975 6 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 2.70090 2.64947 3.22182 0.19567 7 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 2.70090 2.64947 3.22182 0.19567 8 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 1.27651 2.05826 2.28335 0.71055 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 2.79901 3.69005 0.13242 3.26517 10 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 2.02455 1.27344 2.56299 0.67137 11 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 0.75706 2.11440 2.20844 1.20271 12 a - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 2.96347 0.17926 3.53968 2.48351 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 2.17745 3.00915 0.25549 2.76778 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 2.46386 3.25001 0.18748 3.05609 15 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.46496 3.25155 0.18719 3.05792 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 2.87500 1.80006 2.64510 0.34630 17 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 2.54250 1.12693 2.29162 0.70077 18 u - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 2.79901 3.69005 0.13242 3.26517 19 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 0.13959 3.33587 3.05057 3.04975 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 2.79901 3.69005 0.13242 3.26517 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 2.70090 2.64947 3.22182 0.19567 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 0.66216 2.49304 1.27388 2.10490 23 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 2.96347 0.17926 3.53968 2.48351 24 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 0.13959 3.33587 3.05057 3.04975 25 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 0.13959 3.33587 3.05057 3.04975 26 A - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //