INFERNAL1/a [1.1.4 | Dec 2020] NAME TYMV_upPK ACC RF00390 DESC turnip yellow mosaic virus upstream pseudo-knot (TYMV_upPK) STATES 73 NODES 21 CLEN 23 W 36 ALPH RNA RF no CONS yes MAP yes DATE Tue Mar 4 16:05:31 2025 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /homes/nancyontiveros/3D_families/3D_release15.1/RF00390/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 7 EFFN 7.000000 CKSUM 2138076842 NULL 0.000 0.000 0.000 0.000 GA 38.00 TC 38.10 NC 37.40 EFP7GF -8.7766 0.73581 ECMLC 0.53549 -9.75882 2.64454 1600000 919853 0.001305 ECMGC 0.45573 -14.72676 1.55900 1600000 668896 0.000598 ECMLI 0.59987 -7.42038 3.28495 1600000 738159 0.001626 ECMGI 0.48016 -13.01012 2.38689 1600000 649853 0.000616 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 36 55 -8.235 -8.442 -0.022 -6.856 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 36 55 -9.189 -0.009 -7.843 -3.688 -3.360 -4.479 1.918 D 4 2 3 5 3 0 0 36 55 -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 - A - - - ML 6 5 3 8 3 1 1 35 54 -9.189 -0.009 -7.843 1.093 -2.906 0.633 -2.449 D 7 5 3 8 3 0 0 34 53 -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 34 53 -9.189 -0.009 -7.843 1.946 -4.655 -4.116 -4.373 D 10 8 3 11 3 0 0 33 52 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 1 33 52 -9.189 -0.009 -7.843 -3.742 -5.207 1.946 -4.480 D 13 11 3 14 3 0 0 32 51 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 36 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - U - - - ML 15 14 3 17 3 1 1 32 51 -9.189 -0.009 -7.843 -3.688 -3.360 -4.479 1.918 D 16 14 3 17 3 0 0 31 50 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 1 31 50 -9.189 -0.009 -7.843 -3.688 -3.360 -4.479 1.918 D 19 17 3 20 3 0 0 30 49 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 34 53 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - C - - - ML 21 20 3 23 3 1 1 30 49 -9.189 -0.009 -7.843 -4.298 1.933 -4.936 -3.370 D 22 20 3 23 3 0 0 29 48 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - U - - - ML 24 23 3 26 5 1 1 29 48 -8.209 -0.018 -8.024 -8.237 -9.128 -3.688 -3.360 -4.479 1.918 D 25 23 3 26 5 0 0 28 46 -4.959 -0.803 -4.221 -2.596 -2.508 IL 26 26 3 26 5 1 1 29 48 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 23 C G - - MP 27 26 3 31 6 2 2 28 47 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -7.169 -7.295 -6.347 -3.505 -4.728 -6.418 3.924 -5.874 -6.655 -3.464 -6.446 -5.448 -1.657 -7.077 -2.679 -5.457 ML 28 26 3 31 6 1 1 27 45 -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 27 45 -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 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 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 32 32 6 32 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 ] 10 22 G C - - MP 33 32 6 37 6 2 2 26 45 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -5.949 -3.860 -6.102 -0.739 -6.901 -5.295 -1.937 -6.579 -5.279 3.710 -5.520 -1.637 -2.257 0.305 -4.028 -5.044 ML 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 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 38 38 6 38 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 ] 11 21 A U - - MP 39 38 6 43 6 2 2 24 43 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -6.054 -4.774 -5.505 3.900 -7.358 -8.681 -2.973 -5.421 -5.809 -1.389 -6.434 -2.046 -3.307 -7.368 -4.874 -4.528 ML 40 38 6 43 6 1 1 24 43 -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 24 43 -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 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 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 44 44 6 44 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 12 20 U A - - MP 45 44 6 49 4 2 2 22 41 -8.235 -8.442 -0.022 -6.856 -7.496 -7.368 -6.982 -3.626 -5.484 -7.271 -1.203 -6.329 -6.946 -3.654 -7.220 -5.277 3.921 -7.414 -3.036 -4.933 ML 46 44 6 49 4 1 1 24 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 48 44 6 49 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 49 49 5 49 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 50 50 6 50 3 1 1 24 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - C - - - ML 51 50 6 53 3 1 1 19 38 -9.189 -0.009 -7.843 -4.298 1.933 -4.936 -3.370 D 52 50 6 53 3 0 0 19 37 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 23 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 14 - U - - - ML 54 53 3 56 3 1 1 18 36 -9.189 -0.009 -7.843 -3.688 -3.360 -4.479 1.918 D 55 53 3 56 3 0 0 18 36 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 15 - C - - - ML 57 56 3 59 3 1 1 17 35 -9.189 -0.009 -7.843 -2.000 1.032 -2.939 0.656 D 58 56 3 59 3 0 0 17 35 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 16 - U - - - ML 60 59 3 62 3 1 1 15 34 -9.189 -0.009 -7.843 -3.688 -3.360 -4.479 1.918 D 61 59 3 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 17 ] 17 - A - - - ML 63 62 3 65 3 1 1 14 32 -9.189 -0.009 -7.843 1.946 -4.655 -4.116 -4.373 D 64 62 3 65 3 0 0 15 33 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 18 - A - - - ML 66 65 3 68 3 1 1 12 31 -9.189 -0.009 -7.843 1.946 -4.655 -4.116 -4.373 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 19 ] 19 - A - - - ML 69 68 3 71 2 1 1 1 1 * 0.000 1.946 -4.655 -4.116 -4.373 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 20 ] - - - - - - E 72 71 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME TYMV_upPK ACC RF00390 DESC turnip yellow mosaic virus upstream pseudo-knot (TYMV_upPK) LENG 23 MAXL 86 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Mar 4 16:05:31 2025 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED NSEQ 7 EFFN 6.053223 CKSUM 2138076842 STATS LOCAL MSV -5.7232 0.73581 STATS LOCAL VITERBI -6.5750 0.73581 STATS LOCAL FORWARD -3.0058 0.73581 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.25575 1.59572 1.84943 1.03550 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 0.00000 * 1 3.76251 3.55468 4.30778 0.06751 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 2 0.64666 3.22496 0.96551 2.88848 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 3 0.04465 4.42849 4.06287 4.23126 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 4 3.82145 4.81876 0.04403 4.33485 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 5 3.76251 3.55468 4.30778 0.06751 5 U - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 6 3.76251 3.55468 4.30778 0.06751 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 7 4.18975 0.05481 4.66127 3.54969 7 C - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 8 3.76251 3.55468 4.30778 0.06751 8 U - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 9 4.53838 0.06448 4.43157 3.22249 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 10 2.90893 3.67821 0.19405 2.33739 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 11 0.08380 4.28840 2.98332 4.13302 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 12 4.53703 3.22944 4.44749 0.06400 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 13 4.18975 0.05481 4.66127 3.54969 13 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 14 3.76251 3.55468 4.30778 0.06751 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 15 2.63756 0.69497 3.27367 0.93774 15 c - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 16 3.76251 3.55468 4.30778 0.06751 16 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 17 0.04465 4.42849 4.06287 4.23126 17 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 18 0.04465 4.42849 4.06287 4.23126 18 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 19 0.04465 4.42849 4.06287 4.23126 19 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 20 0.07357 4.64341 3.05474 4.25678 20 A - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 21 4.33576 3.39018 4.09010 0.06564 21 U - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 22 3.78905 0.13461 3.50999 2.61148 22 C - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 23 3.49554 4.56827 0.05580 4.30019 23 G - - > 1.38629 1.38629 1.38629 1.38629 0.12680 2.12790 * 1.12384 0.39309 0.00000 * //