INFERNAL1/a [1.1.5 | Sep 2023] NAME HIV-1_SD ACC RF01380 DESC Human immunodeficiency virus type 1 major splice donor STATES 61 NODES 14 CLEN 19 W 31 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 16 23:53:13 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/RF01380/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 22 EFFN 22.000000 CKSUM 2631156883 NULL 0.000 0.000 0.000 0.000 GA 30.00 TC 30.00 NC 29.80 EFP7GF -11.1847 0.73887 ECMLC 0.67084 -3.98355 5.15146 1600000 550289 0.002181 ECMGC 0.54370 -12.84207 0.80135 1600000 666265 0.000600 ECMLI 0.67105 -3.66922 5.40132 1600000 528027 0.002273 ECMGI 0.56496 -11.22673 1.44281 1600000 513616 0.000779 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 31 49 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 IL 1 1 2 1 6 1 1 32 51 -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 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 19 G C - - MP 3 2 3 7 6 2 2 31 49 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 -5.052 -0.874 -4.884 1.381 -5.996 -0.667 -1.083 -5.564 0.556 3.116 -5.524 -0.208 -1.347 -4.724 -3.088 -3.851 ML 4 2 3 7 6 1 1 29 48 -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 29 48 -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 27 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 7 7 5 7 6 1 1 30 49 -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 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 18 G C - - MP 9 8 6 13 6 2 2 29 47 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 -8.580 -5.343 -10.382 -2.765 -10.148 -6.543 -4.581 -10.030 -6.702 3.963 -6.908 -3.253 -4.946 -6.992 -6.986 -9.289 ML 10 8 6 13 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 11 8 6 13 6 1 1 27 46 -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 25 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 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 14 14 6 14 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 17 C G - - MP 15 14 6 19 6 2 2 27 45 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 -9.631 -9.854 -7.846 -6.225 -6.134 -7.573 3.986 -8.358 -9.178 -6.192 -7.610 -8.259 -4.180 -9.559 -5.156 -7.978 ML 16 14 6 19 6 1 1 26 44 -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 25 44 -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 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 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 20 20 6 20 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 16 G C - - MP 21 20 6 25 4 2 2 25 43 -9.505 -10.750 -0.013 -7.204 -8.580 -5.343 -10.382 -2.765 -10.148 -6.543 -4.581 -10.030 -6.702 3.963 -6.908 -3.253 -4.946 -6.992 -6.986 -9.289 ML 22 20 6 25 4 1 1 24 43 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 4 1 1 24 42 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 24 20 6 25 4 0 0 22 40 -12.737 -14.007 -2.036 -0.404 IL 25 25 5 25 4 1 1 24 43 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 26 26 6 26 3 1 1 25 43 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 15 - A - - MR 27 26 6 29 5 1 1 23 41 -9.584 -0.007 -9.399 -9.611 -10.503 1.986 -6.651 -6.013 -6.204 D 28 26 6 29 5 0 0 21 40 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 5 14 A U - - MP 30 29 3 34 6 2 2 22 40 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 -8.349 -7.137 -6.025 3.979 -9.862 -10.734 -5.788 -5.874 -8.152 -3.787 -8.736 -4.207 -5.966 -9.631 -7.578 -5.704 ML 31 29 3 34 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 32 29 3 34 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 33 29 3 34 6 0 0 20 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 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 35 35 6 35 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 13 C G - - MP 36 35 6 40 6 2 2 20 38 -10.774 -10.713 -0.007 -9.490 -9.770 -10.165 -7.584 -7.794 0.043 -4.032 -5.259 -7.038 3.844 -6.198 -7.017 -4.022 -7.097 -6.079 -2.018 -7.445 -2.994 -5.823 ML 37 35 6 40 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 38 35 6 40 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 39 35 6 40 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 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 41 41 6 41 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 7 12 U A - - MP 42 41 6 46 4 2 2 18 36 -9.692 -9.899 -0.008 -8.313 -7.517 -7.762 -6.844 -3.999 1.602 -6.998 -0.915 -6.114 -6.943 -3.979 -7.068 -6.104 3.595 -7.363 -2.906 -5.746 ML 43 41 6 46 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 45 41 6 46 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520 IL 46 46 5 46 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 47 47 6 47 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 8 - G - - - ML 48 47 6 50 3 1 1 14 33 -10.618 -0.003 -9.272 -5.336 -7.028 1.983 -6.083 D 49 47 6 50 3 0 0 16 34 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 9 - G - - - ML 51 50 3 53 3 1 1 13 31 -10.618 -0.003 -9.272 -5.336 -7.028 1.983 -6.083 D 52 50 3 53 3 0 0 15 33 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 10 - U - - - ML 54 53 3 56 3 1 1 11 30 -10.618 -0.003 -9.272 -5.913 -5.384 -6.778 1.982 D 55 53 3 56 3 0 0 13 32 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 11 - G - - - ML 57 56 3 59 2 1 1 1 1 * 0.000 -5.336 -7.028 1.983 -6.083 D 58 56 3 59 2 0 0 0 0 * 0.000 IL 59 59 3 59 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 13 ] - - - - - - E 60 59 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME HIV-1_SD ACC RF01380 DESC Human immunodeficiency virus type 1 major splice donor LENG 19 MAXL 74 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 16 23:53:13 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/RF01380/CM NSEQ 22 EFFN 22.000000 CKSUM 2631156883 STATS LOCAL MSV -5.6366 0.73887 STATS LOCAL VITERBI -6.2893 0.73887 STATS LOCAL FORWARD -3.6215 0.73887 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.71449 1.37713 0.90994 1.80123 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 0.00000 * 1 1.60394 2.64005 0.37310 3.24568 1 G - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 2 4.45337 5.56855 0.01934 5.59978 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 3 6.15793 0.01048 6.17962 5.07796 3 C - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 4 4.43378 5.53278 0.01992 5.54845 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 5 0.01525 5.85807 4.72205 5.68966 5 A - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 6 2.66481 0.10699 5.05585 3.66969 6 C - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 7 5.09858 1.49570 5.03112 0.27014 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 8 5.08490 6.25797 0.01186 5.60241 8 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 9 5.08490 6.25797 0.01186 5.60241 9 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 10 5.48496 5.11805 6.08427 0.01249 10 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 11 5.08490 6.25797 0.01186 5.60241 11 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 12 0.05791 5.17623 3.14670 4.87634 12 A - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 13 3.98313 5.21612 0.03191 4.91348 13 G - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 14 6.16846 5.21320 5.81592 0.01057 14 U - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 15 0.00980 5.99620 5.55449 5.68637 15 A - - - 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 16 5.59056 0.02492 5.45617 4.09783 16 C - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 17 5.23915 6.32004 0.00928 6.15239 17 G - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 18 5.66200 0.02427 5.49762 4.11007 18 C - - > 1.38629 1.38629 1.38629 1.38629 0.00830 5.48894 5.48894 1.46634 0.26236 1.09861 0.40547 19 2.12372 0.48253 3.20508 1.50220 19 C - - > 1.38629 1.38629 1.38629 1.38629 0.00416 5.48480 * 1.46634 0.26236 0.00000 * //