INFERNAL1/a [1.1.5 | Sep 2023] NAME HIV-1_SL3 ACC RF01381 DESC HIV-1 stem-loop 3 Psi packaging signal STATES 73 NODES 20 CLEN 23 W 35 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 16 18:20:49 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/RF01381/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 19 EFFN 19.000000 CKSUM 1618780558 NULL 0.000 0.000 0.000 0.000 GA 33.00 TC 33.70 NC 32.90 EFP7GF -11.3742 0.73267 ECMLC 0.67682 -5.88676 4.00320 1600000 968816 0.001239 ECMGC 0.54159 -15.22652 -0.79023 1600000 994529 0.000402 ECMLI 0.76881 -3.85889 4.70804 1600000 870170 0.001379 ECMGI 0.57909 -13.25895 0.09453 1600000 912835 0.000438 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 35 54 -9.496 -9.703 -0.009 -8.117 IL 1 1 2 1 4 1 1 41 60 -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 35 54 -10.424 -0.004 -9.078 -5.595 -5.100 -6.444 1.978 D 4 2 3 5 3 0 0 35 54 -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 - G - - - ML 6 5 3 8 3 1 1 34 53 -10.424 -0.004 -9.078 -5.148 -6.817 1.980 -5.891 D 7 5 3 8 3 0 0 34 52 -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 33 51 -10.735 -0.004 -9.053 1.983 -6.410 -5.790 -5.993 D 10 8 3 11 3 0 0 32 50 -5.620 -0.734 -1.403 IL 11 11 3 11 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 24 - G - - MR 12 11 3 14 3 1 1 32 50 -10.735 -0.004 -9.053 -0.100 -4.519 1.568 -4.092 D 13 11 3 14 3 0 0 30 49 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 23 - A - - MR 15 14 3 17 3 1 1 31 49 -10.735 -0.004 -9.053 1.590 -4.759 -0.133 -4.623 D 16 14 3 17 3 0 0 29 48 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 22 - G - - MR 18 17 3 20 3 1 1 30 48 -10.735 -0.004 -9.053 0.328 -4.488 1.402 -4.109 D 19 17 3 20 3 0 0 28 47 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 21 - G - - MR 21 20 3 23 3 1 1 29 47 -10.735 -0.004 -9.053 -1.736 -5.440 1.865 -4.847 D 22 20 3 23 3 0 0 27 46 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 20 - A - - MR 24 23 3 26 3 1 1 28 46 -10.735 -0.004 -9.053 1.772 -4.707 -0.986 -4.582 D 25 23 3 26 3 0 0 26 45 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 19 - A - - MR 27 26 3 29 5 1 1 27 45 -9.395 -0.008 -9.210 -9.422 -10.314 1.779 -4.712 -1.034 -4.587 D 28 26 3 29 5 0 0 26 44 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 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 ] 4 18 C G - - MP 30 29 3 34 6 2 2 26 44 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -7.311 -7.541 -6.644 -3.773 -5.009 -6.803 3.812 0.299 -6.741 -3.753 -6.869 -5.856 -1.732 -7.163 -2.710 -5.544 ML 31 29 3 34 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 32 29 3 34 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 33 29 3 34 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 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 35 35 6 35 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 5 17 U A - - MP 36 35 6 40 6 2 2 24 42 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -10.120 -10.002 -9.604 -6.573 -8.019 -9.787 -3.980 -8.964 -9.163 -6.646 -9.825 -8.206 3.986 -9.495 -4.914 -5.473 ML 37 35 6 40 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 38 35 6 40 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 39 35 6 40 6 0 0 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 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 41 41 6 41 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 6 16 A U - - MP 42 41 6 46 6 2 2 22 40 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -8.050 -6.815 -6.008 3.974 -9.580 -10.544 -5.422 -5.863 -7.840 -3.467 -8.437 -3.933 -5.617 -9.359 -7.236 -5.615 ML 43 41 6 46 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 44 41 6 46 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 45 41 6 46 6 0 0 20 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 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 47 47 6 47 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 7 15 G C - - MP 48 47 6 52 6 2 2 20 38 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -8.129 -5.151 -9.327 -2.458 -9.805 -6.432 -4.329 -9.256 -6.503 3.883 -6.734 -0.184 -4.647 -6.824 -6.672 -8.141 ML 49 47 6 52 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 50 47 6 52 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 51 47 6 52 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 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 53 53 6 53 5 1 1 20 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 8 14 C G - - MP 54 53 6 58 4 2 2 18 36 -9.496 -9.703 -0.009 -8.117 -7.690 -7.959 -6.892 -4.199 -0.312 -6.969 3.873 -6.292 -7.125 -4.166 -7.038 -6.345 -2.104 -7.535 -3.080 -5.926 ML 55 53 6 58 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 56 53 6 58 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 57 53 6 58 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 58 58 5 58 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 59 59 6 59 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 9 - G - - - ML 60 59 6 62 3 1 1 15 33 -10.424 -0.004 -9.078 -1.326 -5.164 1.821 -4.617 D 61 59 6 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 16 ] 10 - G - - - ML 63 62 3 65 3 1 1 13 31 -4.688 -0.060 -9.078 -5.148 -6.817 1.980 -5.891 D 64 62 3 65 3 0 0 13 31 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 14 32 -2.013 -0.486 -4.713 0.000 0.000 0.000 0.000 [ MATL 17 ] 12 - A - - - ML 66 65 3 68 3 1 1 11 30 -10.424 -0.004 -9.078 1.983 -6.410 -5.790 -5.993 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 18 ] 13 - G - - - ML 69 68 3 71 2 1 1 1 1 * 0.000 -4.274 -5.487 1.885 -2.109 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 19 ] - - - - - - E 72 71 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME HIV-1_SL3 ACC RF01381 DESC HIV-1 stem-loop 3 Psi packaging signal LENG 23 MAXL 79 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 16 18:20:49 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/RF01381/CM NSEQ 19 EFFN 17.399658 CKSUM 1618780558 STATS LOCAL MSV -6.0822 0.73267 STATS LOCAL VITERBI -6.2778 0.73267 STATS LOCAL FORWARD -3.7487 0.73267 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.15499 2.02706 0.90409 1.90848 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 0.00000 * 1 5.13593 4.80508 5.71840 0.01751 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 2 4.87538 6.02181 0.01473 5.38890 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 3 0.01260 5.72746 5.30403 5.45075 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 4 4.92090 0.04987 4.82527 3.40120 4 C - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 5 6.20201 5.14510 6.27360 0.00979 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 6 0.02038 5.63392 4.39912 5.44744 6 A - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 7 4.15262 5.28651 0.02636 5.25263 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 8 5.15007 0.03712 5.09804 3.70793 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 9 2.30438 4.86109 0.12649 4.48672 9 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 10 4.87538 6.02181 0.01473 5.38890 10 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04802 3.16612 5.35659 0.21043 1.66197 1.09861 0.40547 11 0.01260 5.72746 5.30403 5.45075 12 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 12 4.24229 5.07245 0.08157 2.85269 13 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 13 2.76185 5.23016 0.07860 4.95341 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 14 5.31784 0.08161 5.19158 2.68969 15 C - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 15 5.75887 4.85060 5.51070 0.01514 16 U - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 16 0.01264 6.49733 4.86226 5.70882 17 A - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 17 3.72159 4.97814 0.12265 2.47287 18 G - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 18 0.15543 4.55751 2.10387 4.46716 19 A - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 19 0.16035 4.55381 2.07061 4.46356 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 20 2.58678 5.05043 0.09571 4.64582 21 G - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 21 1.16195 4.39810 0.41740 4.13096 22 G - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 22 0.28630 4.58033 1.48125 4.47765 23 A - - : 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 23 1.45811 4.42214 0.30224 4.12541 24 G - - : 1.38629 1.38629 1.38629 1.38629 0.00475 5.35186 * 1.46634 0.26236 0.00000 * //