INFERNAL1/a [1.1 | October 2013] NAME GNRA DESC GNRA tetraloop STATES 64 NODES 13 CLEN 20 W 75 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:35:44 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/GNRA/CM /share/data/people/ppg15/motifs/GNRA/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/GNRA/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 112 EFFN 112.000000 CKSUM 303233272 NULL 0.000 0.000 0.000 0.000 GA 7.00 EFP7GF 0.5649 0.88698 ECMLC 0.54200 -4.82265 5.72127 1600000 363996 0.003297 ECMGC 0.53368 -7.15984 7.21207 1600000 857279 0.000467 ECMLI 0.57920 -3.01183 6.43150 1600000 284845 0.004213 ECMGI 0.53844 -6.40007 7.50395 1600000 713541 0.000561 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 75 128 -12.800 -12.739 -0.705 -11.516 -11.795 -1.374 IL 1 1 2 1 6 1 1 77 129 -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 76 129 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 14 63 c g - - MP 3 2 3 7 6 2 2 75 128 -12.097 -12.037 -0.003 -10.813 -11.093 -11.488 -6.390 -6.098 -0.645 -1.980 -5.321 -7.229 2.292 -5.962 -6.274 1.941 -6.784 0.657 1.702 -6.572 0.490 -5.012 ML 4 2 3 7 6 1 1 73 126 -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 72 125 -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 71 123 -15.465 -14.163 -2.383 -4.628 -10.660 -0.382 IL 7 7 5 7 6 1 1 75 127 -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 74 127 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 15 62 g c - - MP 9 8 6 13 6 2 2 73 126 -2.947 -4.990 -0.256 -10.978 -11.258 -11.653 -6.542 -6.001 -6.511 0.214 -5.626 -7.304 2.002 -6.201 -6.466 2.656 -6.941 -1.756 1.324 -6.625 0.674 -5.163 ML 10 8 6 13 6 1 1 71 123 -8.125 -8.472 -0.256 -2.880 -8.321 -5.851 -1.670 1.604 -2.491 -1.098 MR 11 8 6 13 6 1 1 69 121 -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 69 122 -3.254 -13.785 -1.846 -10.264 -10.282 -0.700 IL 13 13 5 13 6 1 1 74 127 -1.266 -0.839 -5.548 -9.285 -10.061 -9.722 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 1 72 125 -1.232 -0.813 -10.275 -8.443 -9.549 0.000 0.000 0.000 0.000 [ MATP 3 ] 18 59 c g - - MP 15 14 6 19 6 2 2 70 123 -1.938 -12.451 -0.439 -11.228 -11.507 -11.902 -6.783 -6.496 -6.791 1.002 -3.520 -7.633 2.179 -6.342 -6.660 1.884 -7.174 -2.473 1.447 -6.969 1.427 -5.394 ML 16 14 6 19 6 1 1 63 115 -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 62 114 -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 60 111 -14.393 -4.653 -2.215 -9.571 -9.588 -0.430 IL 19 19 5 19 6 1 1 72 124 -0.586 -1.865 -4.109 -10.885 -11.661 -11.321 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 1 67 118 -0.640 -1.490 -11.330 -9.497 -10.603 0.000 0.000 0.000 0.000 [ MATP 4 ] 23 54 g c - - MP 21 20 6 25 6 2 2 62 113 -3.628 -3.510 -0.268 -11.308 -11.588 -11.983 -6.675 -5.685 -3.753 0.407 -6.473 -7.263 1.484 -6.741 -6.773 2.616 -7.144 0.610 0.799 -6.547 1.200 -5.409 ML 22 20 6 25 6 1 1 58 109 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 6 1 1 58 109 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 6 25 6 0 0 55 106 -13.973 -12.671 -2.302 -9.150 -9.167 -0.334 IL 25 25 5 25 6 1 1 63 114 -1.052 -1.629 -2.403 -8.725 -9.502 -9.162 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 61 112 -1.419 -0.690 -9.952 -8.119 -9.225 0.000 0.000 0.000 0.000 [ MATP 5 ] 26 50 c g - - MP 27 26 6 31 6 2 2 59 110 -2.441 -4.633 -0.368 -11.353 -11.633 -12.028 -6.944 -6.643 -6.946 1.167 -5.837 -7.787 2.677 -6.484 -6.812 0.998 -7.325 0.794 0.769 -7.125 0.867 -5.537 ML 28 26 6 31 6 1 1 51 102 -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 50 101 -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 36 87 -13.651 -12.349 -0.939 -8.828 -8.846 -1.078 IL 31 31 5 31 6 1 1 62 113 -0.551 -1.789 -5.250 -10.593 -11.369 -11.030 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 1 54 104 -0.533 -1.704 -11.568 -9.736 -10.842 0.000 0.000 0.000 0.000 [ MATP 6 ] 31 43 c g - - MP 33 32 6 37 6 2 2 25 44 -3.823 -12.667 -0.107 -11.443 -11.723 -12.118 -1.348 -6.090 -6.359 1.031 -5.713 -7.187 2.398 -6.247 -2.761 2.038 -6.861 -0.434 1.522 -6.498 -1.671 -5.220 ML 34 32 6 37 6 1 1 23 42 -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 22 41 -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 18 37 -12.597 -11.295 -0.701 -7.775 -7.792 -1.414 IL 37 37 5 37 6 1 1 26 45 -1.397 -0.942 -3.426 -8.410 -9.186 -8.846 0.000 0.000 0.000 0.000 IR 38 38 6 38 5 1 1 19 37 -4.912 -0.076 -8.423 -6.591 -7.697 0.000 0.000 0.000 0.000 [ MATP 7 ] 34 41 c g - - MP 39 38 6 43 6 2 2 18 36 -12.776 -12.715 -0.002 -11.492 -11.772 -12.167 -6.933 -6.669 0.324 0.878 -5.926 -7.795 2.543 -6.556 -6.840 1.517 -7.357 -1.002 1.494 -7.127 -0.299 -5.598 ML 40 38 6 43 6 1 1 19 38 -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 19 38 -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 16 35 -11.247 -9.945 -0.321 -6.424 -6.442 -2.517 IL 43 43 5 43 6 1 1 19 37 -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 18 37 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 35 40 c g - - MP 45 44 6 49 6 2 2 16 34 -12.800 -12.739 -0.002 -11.516 -11.795 -12.190 -7.874 -7.559 -7.760 0.233 -6.569 -8.435 2.946 -7.266 -7.684 2.329 -8.115 -5.184 -0.891 -7.985 0.557 -6.411 ML 46 44 6 49 6 1 1 19 37 -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 18 37 -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 17 36 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 18 36 -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 17 36 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 36 39 G A - - MP 51 50 6 55 4 2 2 14 32 -11.960 -12.167 -0.002 -10.581 -9.005 -7.838 -9.011 -4.146 -8.993 -10.661 -4.661 -8.800 3.847 -4.467 0.478 -5.173 -5.400 -10.058 -6.620 -7.686 ML 52 50 6 55 4 1 1 18 37 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 4 1 1 18 36 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 54 50 6 55 4 0 0 17 35 -4.568 -4.250 -2.265 -0.520 IL 55 55 5 55 4 1 1 20 38 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 56 56 6 56 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 37 - a - - - ML 57 56 6 59 3 1 1 10 28 -12.872 -0.001 -11.526 0.845 -0.146 -1.252 -0.184 D 58 56 6 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 11 ] 38 - A - - - ML 60 59 3 62 2 1 1 1 1 * 0.000 1.322 -7.233 0.519 -4.079 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 12 ] - - - - - - E 63 62 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME GNRA DESC GNRA tetraloop LENG 20 MAXL 77 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:35:44 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/GNRA/CM /share/data/people/ppg15/motifs/GNRA/SEED NSEQ 112 EFFN 112.000000 CKSUM 303233272 STATS LOCAL MSV -7.9483 0.88698 STATS LOCAL VITERBI -9.2145 0.88698 STATS LOCAL FORWARD -1.4775 0.88698 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.47838 1.38744 1.16446 1.55976 1.38629 1.38629 1.38629 1.38629 2.51395 0.08883 5.50969 1.68616 0.20485 0.00000 * 1 2.85383 1.17475 1.07925 1.22542 14 g - - < 1.38629 1.38629 1.38629 1.38629 0.00294 6.52518 6.52518 1.46634 0.26236 1.09861 0.40547 2 2.59172 1.32960 0.90315 1.36557 15 g - - < 1.38629 1.38629 1.38629 1.38629 0.14771 1.99469 6.67125 0.55966 0.84724 1.09861 0.40547 3 2.05729 1.24063 1.41510 1.07852 18 u - - < 1.38629 1.38629 1.38629 1.38629 0.32483 1.28638 6.83089 1.11646 0.39666 1.09861 0.40547 4 2.40688 1.73394 0.73657 1.36822 23 g - - < 1.38629 1.38629 1.38629 1.38629 0.09097 2.45416 6.88962 0.70145 0.68492 1.09861 0.40547 5 1.94866 0.91359 1.45212 1.50337 26 c - - < 1.38629 1.38629 1.38629 1.38629 0.21713 1.63892 6.92276 1.17359 0.36998 1.09861 0.40547 6 1.86833 1.10393 1.16356 1.60106 31 c - - < 1.38629 1.38629 1.38629 1.38629 0.07867 2.59387 6.98813 0.51407 0.91145 1.09861 0.40547 7 1.63717 1.00577 1.55578 1.47542 34 c - - < 1.38629 1.38629 1.38629 1.38629 0.00178 7.02326 7.02326 1.46634 0.26236 1.09861 0.40547 8 2.59316 0.72913 1.15200 2.06447 35 c - - < 1.38629 1.38629 1.38629 1.38629 0.00175 7.04054 7.04054 1.46634 0.26236 1.09861 0.40547 9 5.39544 5.78841 0.01054 5.84823 36 G - - < 1.38629 1.38629 1.38629 1.38629 0.00175 7.04054 7.04054 1.46634 0.26236 1.09861 0.40547 10 0.80081 1.48729 2.25422 1.51370 37 a - - _ 1.38629 1.38629 1.38629 1.38629 0.00175 7.04054 7.04054 1.46634 0.26236 1.09861 0.40547 11 0.46964 6.39975 1.02633 4.21378 38 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00175 7.04054 7.04054 1.46634 0.26236 1.09861 0.40547 12 0.10566 5.64272 2.40198 5.08514 39 A - - > 1.38629 1.38629 1.38629 1.38629 0.00175 7.04054 7.04054 1.46634 0.26236 1.09861 0.40547 13 3.33542 1.15706 0.55643 2.56733 40 G - - > 1.38629 1.38629 1.38629 1.38629 0.00178 7.02326 7.02326 1.46634 0.26236 1.09861 0.40547 14 1.72266 1.71346 0.70777 1.90767 41 g - - > 1.38629 1.38629 1.38629 1.38629 0.07109 2.69263 6.98813 0.02704 3.62393 1.09861 0.40547 15 1.53791 1.35320 1.04988 1.73286 43 g - - > 1.38629 1.38629 1.38629 1.38629 0.25639 1.49089 6.92276 1.20871 0.35465 1.09861 0.40547 16 2.21350 2.06842 0.66642 1.38328 50 G - - > 1.38629 1.38629 1.38629 1.38629 0.16349 1.89842 6.88962 0.49460 0.94114 1.09861 0.40547 17 2.19600 0.95468 1.12932 1.71168 54 c - - > 1.38629 1.38629 1.38629 1.38629 0.27612 1.42626 6.84032 1.08465 0.41252 1.09861 0.40547 18 1.72948 1.46057 0.79511 1.97337 59 g - - > 1.38629 1.38629 1.38629 1.38629 0.23863 1.55562 6.69503 0.69841 0.68791 1.09861 0.40547 19 1.83735 0.92676 1.04647 2.36707 62 c - - > 1.38629 1.38629 1.38629 1.38629 0.00294 6.52518 6.52518 1.46634 0.26236 1.09861 0.40547 20 1.57762 1.41887 0.83431 2.14241 63 g - - > 1.38629 1.38629 1.38629 1.38629 3.34884 0.03576 * 2.54087 0.08208 0.00000 * //