INFERNAL1/a [1.1.4 | Dec 2020] NAME HIV-1_SL4 ACC RF01382 DESC HIV-1 stem-loop 4 packaging signal STATES 64 NODES 17 CLEN 20 W 32 ALPH RNA RF no CONS yes MAP yes DATE Tue Apr 8 09:33:15 2014 COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi 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 16 EFFN 16.000000 CKSUM 2686221353 NULL 0.000 0.000 0.000 0.000 GA 31.00 TC 31.10 NC 30.90 EFP7GF -10.6678 0.73925 ECMLC 0.63688 -6.14248 3.73005 1600000 645441 0.001859 ECMGC 0.54001 -12.90768 0.78327 1600000 649967 0.000615 ECMLI 0.64216 -5.49278 4.03575 1600000 545209 0.002201 ECMGI 0.57587 -11.16513 1.49995 1600000 588218 0.000680 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 32 51 -9.269 -9.476 -0.010 -7.890 IL 1 1 2 1 4 1 1 38 57 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 37 55 -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 32 51 -10.200 -0.004 -8.854 -1.652 -3.329 -4.182 1.819 D 4 2 3 5 3 0 0 32 50 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 36 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - G - - - ML 6 5 3 8 3 1 1 31 49 -10.514 -0.004 -8.832 -1.850 -5.225 1.870 -4.636 D 7 5 3 8 3 0 0 30 48 -5.620 -0.734 -1.403 IL 8 8 3 8 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 20 - A - - MR 9 8 3 11 3 1 1 30 48 -10.514 -0.004 -8.832 1.095 -1.365 -0.005 -1.062 D 10 8 3 11 3 0 0 28 47 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 19 - U - - MR 12 11 3 14 3 1 1 29 47 -10.514 -0.004 -8.832 -1.678 -3.332 -4.186 1.821 D 13 11 3 14 3 0 0 27 46 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 18 - G - - MR 15 14 3 17 3 1 1 28 46 -10.514 -0.004 -8.832 -0.441 -4.366 1.655 -3.909 D 16 14 3 17 3 0 0 26 45 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 17 - A - - MR 18 17 3 20 5 1 1 27 45 -9.177 -0.009 -8.992 -9.204 -10.096 1.756 -3.609 -3.819 -1.093 D 19 17 3 20 5 0 0 26 44 -5.352 -0.707 -2.978 -4.409 -2.404 IR 20 20 3 20 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 3 16 G C - - MP 21 20 3 25 6 2 2 26 44 -10.444 -10.383 -0.008 -9.159 -9.439 -9.834 -8.174 -5.007 -9.767 -2.401 -9.697 -6.224 -4.197 -9.502 -6.363 3.953 -6.574 -2.906 -4.563 -6.659 -6.576 -8.642 ML 22 20 3 25 6 1 1 25 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 3 25 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 24 20 3 25 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 26 44 -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 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 4 15 G U - - MP 27 26 6 31 6 2 2 24 42 -10.444 -10.383 -0.008 -9.159 -9.439 -9.834 -6.110 -4.787 -6.285 -1.099 -7.934 -9.258 -3.466 -6.295 -5.859 -1.445 -6.514 3.890 -3.619 -7.557 -5.339 -4.892 ML 28 26 6 31 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 29 26 6 31 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 30 26 6 31 6 0 0 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 24 42 -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 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 5 14 U G - - MP 33 32 6 37 6 2 2 22 40 -10.444 -10.383 -0.008 -9.159 -9.439 -9.834 -7.031 -7.031 -6.419 -3.287 -4.851 -6.641 -0.562 -5.721 -6.484 -3.345 -6.643 -5.048 -1.573 -6.972 3.869 -5.304 ML 34 32 6 37 6 1 1 22 40 -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 21 40 -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 20 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 22 40 -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 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 6 13 G C - - MP 39 38 6 43 6 2 2 20 38 -10.444 -10.383 -0.008 -9.159 -9.439 -9.834 -8.174 -5.007 -9.767 -2.401 -9.697 -6.224 -4.197 -9.502 -6.363 3.953 -6.574 -2.906 -4.563 -6.659 -6.576 -8.642 ML 40 38 6 43 6 1 1 21 39 -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 21 39 -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 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 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 44 44 6 44 5 1 1 20 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 7 12 C G - - MP 45 44 6 49 4 2 2 18 36 -9.269 -9.476 -0.010 -7.890 -8.948 -9.158 -7.533 -5.469 -5.842 -7.358 3.978 -7.630 -8.448 -5.447 -7.398 -7.497 -3.451 -8.851 -4.429 -7.250 ML 46 44 6 49 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 48 44 6 49 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 49 49 5 49 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 50 50 6 50 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 8 - G - - - ML 51 50 6 53 3 1 1 15 33 -10.200 -0.004 -8.854 -4.924 -6.562 1.977 -5.662 D 52 50 6 53 3 0 0 16 34 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 9 - A - - - ML 54 53 3 56 3 1 1 13 32 -10.200 -0.004 -8.854 1.980 -6.121 -5.518 -5.738 D 55 53 3 56 3 0 0 15 33 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 10 - G - - - ML 57 56 3 59 3 1 1 11 30 -10.200 -0.004 -8.854 -4.924 -6.562 1.977 -5.662 D 58 56 3 59 3 0 0 13 32 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 11 - A - - - ML 60 59 3 62 2 1 1 1 1 * 0.000 1.855 -4.032 -4.171 -1.916 D 61 59 3 62 2 0 0 0 0 * 0.000 IL 62 62 3 62 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 16 ] - - - - - - E 63 62 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME HIV-1_SL4 ACC RF01382 DESC HIV-1 stem-loop 4 packaging signal LENG 20 MAXL 77 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Apr 8 09:33:15 2014 COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED NSEQ 16 EFFN 16.000000 CKSUM 2686221353 STATS LOCAL MSV -5.9755 0.73925 STATS LOCAL VITERBI -6.3073 0.73925 STATS LOCAL FORWARD -3.3051 0.73925 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.64764 1.81024 0.82520 1.58116 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 0.00000 * 1 2.53137 3.69410 4.28522 0.12578 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 2 2.66852 5.00787 0.09003 4.59998 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 3 4.20546 5.31467 0.02494 5.34031 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 4 3.37837 4.90301 0.05283 4.61250 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 5 4.68316 3.06069 4.59158 0.06854 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 6 4.18108 5.27031 0.02586 5.27700 6 G - - < 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 7 5.71412 0.01688 5.73920 4.58358 7 C - - < 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 8 4.79908 5.93454 0.01595 5.31122 8 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 9 0.01383 5.62875 5.21139 5.36367 9 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 10 4.79908 5.93454 0.01595 5.31122 10 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 11 0.10026 4.18089 4.27740 2.71459 11 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 12 4.78617 5.87807 0.01477 5.65012 12 G - - > 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 13 5.32461 0.03229 5.18845 3.84783 13 C - - > 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 14 3.67503 4.78337 0.04671 4.42989 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 15 4.80032 3.64490 4.67904 0.04462 15 U - - > 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 16 5.43371 0.03102 5.25096 3.86623 16 C - - > 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 17 0.16886 3.88752 4.03341 2.14422 17 A - - : 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 18 1.69188 4.41278 0.23944 4.09597 18 G - - : 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 19 2.54942 3.69595 4.28806 0.12407 19 U - - : 1.38629 1.38629 1.38629 1.38629 0.01105 5.20401 5.20401 1.46634 0.26236 1.09861 0.40547 20 0.62719 2.33269 1.38983 2.12228 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.00554 5.19850 * 1.46634 0.26236 0.00000 * //