INFERNAL1/a [1.1 | October 2013] NAME CUYG DESC CUYG tetraloop STATES 82 NODES 16 CLEN 26 W 78 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:17:05 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/CUYG/CM /share/data/people/ppg15/motifs/CUYG/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/CUYG/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 8 EFFN 8.000000 CKSUM 1868336240 NULL 0.000 0.000 0.000 0.000 GA 19.00 EFP7GF -1.5955 0.82721 ECMLC 0.60729 -3.88367 5.50331 1600000 358850 0.003344 ECMGC 0.48101 -10.26649 5.28415 1600000 708948 0.000564 ECMLI 0.61910 -2.73346 6.19289 1600000 301463 0.003981 ECMGI 0.48656 -9.00630 5.72253 1600000 518102 0.000772 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 78 144 -9.837 -9.776 -0.292 -8.553 -8.832 -2.505 IL 1 1 2 1 6 1 1 79 146 -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 79 146 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 12 45 c g - - MP 3 2 3 7 6 2 2 78 145 -9.560 -9.499 -0.015 -8.276 -8.556 -8.951 -3.786 -3.671 -3.809 1.571 -2.955 -4.572 2.611 -3.570 -3.771 0.354 -4.262 -1.556 1.931 -4.002 -0.588 -2.645 ML 4 2 3 7 6 1 1 75 142 -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 75 141 -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 74 140 -11.609 -10.308 -0.944 -6.787 -6.804 -1.117 IL 7 7 5 7 6 1 1 77 144 -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 77 143 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 13 44 g c - - MP 9 8 6 13 6 2 2 76 143 -9.735 -9.674 -0.014 -8.450 -8.730 -9.125 -4.059 -3.254 -4.020 1.309 -3.814 -4.762 2.298 -4.123 -4.129 2.519 -4.550 -0.938 0.338 -4.076 -1.317 -2.887 ML 10 8 6 13 6 1 1 72 139 -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 72 138 -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 62 129 -10.594 -9.292 -5.089 -5.771 -5.789 -0.102 IL 13 13 5 13 6 1 1 75 142 -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 75 141 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 14 43 g c - - MP 15 14 6 19 6 2 2 74 141 -2.202 -9.674 -0.514 -8.450 -3.710 -9.125 -4.214 -3.071 -4.126 0.551 -4.495 -4.762 1.812 -4.493 -4.324 2.972 -4.674 0.475 -0.172 -4.073 -1.862 -3.037 ML 16 14 6 19 6 1 1 63 129 -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 61 128 -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 51 118 -10.594 -9.292 -5.089 -5.771 -5.789 -0.102 IL 19 19 5 19 6 1 1 78 144 -0.401 -6.926 -2.870 -8.581 -3.428 -9.017 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 1 34 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 23 42 c g - - MP 21 20 6 25 6 2 2 32 51 -9.455 -9.394 -0.017 -8.171 -8.451 -8.846 -3.601 -3.533 -3.624 1.698 -2.834 -4.357 2.666 -3.442 -3.614 0.375 -4.094 -1.523 0.988 -3.819 0.900 -2.529 ML 22 20 6 25 6 1 1 31 49 -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 31 49 -9.039 -7.768 -1.333 -7.746 -2.880 -1.133 -0.489 -1.015 0.161 0.744 D 24 20 6 25 6 0 0 28 47 -10.594 -9.292 -5.089 -5.771 -5.789 -0.102 IL 25 25 5 25 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 26 26 6 26 5 1 1 32 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 24 41 c g - - MP 27 26 6 31 6 2 2 30 49 -9.579 -9.518 -0.015 -8.295 -8.575 -8.970 -3.983 -3.656 -4.000 -0.035 -3.149 -4.656 2.521 -3.741 -3.929 0.251 -4.357 1.998 1.475 -4.194 -0.787 -2.832 ML 28 26 6 31 6 1 1 29 47 -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 29 47 -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 28 46 -11.532 -10.230 -1.019 -6.709 -6.727 -1.040 IL 31 31 5 31 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 32 32 6 32 5 1 1 30 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 25 40 g c - - MP 33 32 6 37 6 2 2 28 47 -9.735 -9.674 -0.014 -8.450 -8.730 -9.125 -3.531 -2.901 -3.550 1.353 -3.590 -4.303 1.560 0.468 -3.706 2.585 -4.149 -0.731 0.341 -3.591 -1.257 -2.556 ML 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 26 45 -10.594 -9.292 -0.542 -5.771 -5.789 -1.864 IL 37 37 5 37 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 38 38 6 38 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 26 39 g c - - MP 39 38 6 43 6 2 2 26 45 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -3.740 -3.302 -3.774 1.573 -3.343 -4.555 2.011 -3.790 -3.830 2.109 -4.309 -1.121 1.532 -3.862 -0.949 -2.669 ML 40 38 6 43 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 41 38 6 43 6 1 1 25 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 26 45 -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 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 27 38 g c - - MP 45 44 6 49 6 2 2 24 43 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.219 -2.935 -4.084 1.251 -5.009 -4.732 0.860 -4.669 -4.418 2.930 -4.718 1.396 -0.486 -3.993 -2.211 -3.032 ML 46 44 6 49 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 47 44 6 49 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 48 44 6 49 6 0 0 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 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 50 50 6 50 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 28 37 C G - - MP 51 50 6 55 6 2 2 22 41 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.592 -4.431 -4.521 1.600 -3.431 -5.202 3.037 -4.115 -4.465 -0.271 -4.908 -2.204 1.429 -4.760 -1.017 -3.274 ML 52 50 6 55 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 53 50 6 55 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 54 50 6 55 6 0 0 19 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 1 22 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 56 56 6 56 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 29 36 C G - - MP 57 56 6 61 6 2 2 20 39 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.834 -4.672 -4.705 0.979 -3.510 -5.328 3.252 -4.229 -4.650 -0.469 -5.063 -2.420 1.408 -4.971 -1.091 -3.438 ML 58 56 6 61 6 1 1 20 38 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 6 1 1 20 38 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 60 56 6 61 6 0 0 18 36 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 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 62 62 6 62 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 30 35 c g - - MP 63 62 6 67 6 2 2 18 37 -9.837 -9.776 -0.013 -8.553 -8.832 -9.227 -4.409 -3.929 -4.390 0.864 -3.597 -5.197 2.987 -4.135 -4.339 1.800 -4.813 -1.581 0.496 -4.591 -1.133 -3.134 ML 64 62 6 67 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 65 62 6 67 6 1 1 19 37 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 6 67 6 0 0 17 36 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 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 68 68 6 68 5 1 1 18 37 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 31 34 C G - - MP 69 68 6 73 4 2 2 16 35 -8.394 -8.601 -0.019 -7.015 -7.457 -7.604 -6.566 -3.829 -4.931 -6.600 3.938 -6.143 -6.935 -3.797 -6.634 -5.792 -1.938 -7.358 -2.946 -5.738 ML 70 68 6 73 4 1 1 18 37 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 71 68 6 73 4 1 1 18 36 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 72 68 6 73 4 0 0 17 35 -4.568 -4.250 -2.265 -0.520 IL 73 73 5 73 4 1 1 20 38 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 74 74 6 74 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 32 - U - - - ML 75 74 6 77 3 1 1 12 31 -9.343 -0.008 -7.997 -3.927 -3.576 -4.722 1.931 D 76 74 6 77 3 0 0 13 32 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 33 - U - - - ML 78 77 3 80 2 1 1 1 1 * 0.000 -2.319 0.161 -3.154 1.361 D 79 77 3 80 2 0 0 0 0 * 0.000 IL 80 80 3 80 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 15 ] - - - - - - E 81 80 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME CUYG DESC CUYG tetraloop LENG 26 MAXL 95 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:17:05 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/CUYG/CM /share/data/people/ppg15/motifs/CUYG/SEED NSEQ 8 EFFN 7.386719 CKSUM 1868336240 STATS LOCAL MSV -8.0530 0.82721 STATS LOCAL VITERBI -8.8773 0.82721 STATS LOCAL FORWARD -2.0457 0.82721 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.80891 1.23877 1.18226 1.42777 1.38629 1.38629 1.38629 1.38629 0.88689 0.74749 2.16708 2.07512 0.13415 0.00000 * 1 1.61902 0.93419 2.16582 1.22300 12 c - - < 1.38629 1.38629 1.38629 1.38629 0.02692 4.32143 4.32143 1.46634 0.26236 0.18910 1.75855 2 1.76920 1.16158 0.93347 2.09271 13 g - - < 1.38629 1.38629 1.38629 1.38629 0.02209 4.51685 4.51685 1.46634 0.26236 1.09861 0.40547 3 2.19019 1.49275 0.55758 2.39957 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.64196 1.05695 2.06967 1.48007 0.25828 1.09861 0.40547 4 1.52989 0.90330 2.12549 1.35157 23 c - - < 1.38629 1.38629 1.38629 1.38629 0.22879 4.39434 1.64944 1.46634 0.26236 0.15963 1.91366 5 2.49033 1.00680 1.12364 1.48441 24 c - - < 1.38629 1.38629 1.38629 1.38629 0.02632 4.34360 4.34360 1.46634 0.26236 0.12090 2.17265 6 1.70817 1.28812 0.88430 2.04014 25 g - - < 1.38629 1.38629 1.38629 1.38629 0.02209 4.51685 4.51685 1.46634 0.26236 1.09861 0.40547 7 1.60023 1.33265 1.18648 1.47369 26 g - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 8 1.78826 2.10867 0.45175 2.59242 27 G - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 9 1.62580 0.66691 2.56538 1.54618 28 C - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 10 2.02268 0.52358 2.69867 1.57017 29 C - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 11 2.06158 0.70624 1.40919 2.00313 30 c - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 12 4.69486 0.05100 4.65991 3.47007 31 C - - < 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 13 4.00927 3.77551 4.55873 0.05292 32 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 14 2.90642 1.27998 3.48256 0.45168 33 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 15 3.72385 4.79810 0.04422 4.52197 34 G - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 16 2.23316 1.48934 0.65785 1.90162 35 G - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 17 1.71314 2.87426 0.48334 1.92056 36 G - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 18 1.69296 2.74071 0.61834 1.54805 37 G - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 19 2.83619 0.72221 2.00116 1.13789 38 c - - > 1.38629 1.38629 1.38629 1.38629 0.01980 4.62497 4.62497 1.46634 0.26236 1.09861 0.40547 20 1.61856 1.26941 1.23395 1.47108 39 g - - > 1.38629 1.38629 1.38629 1.38629 0.02209 4.51685 4.51685 1.46634 0.26236 1.09861 0.40547 21 2.25561 0.96391 1.50198 1.23408 40 c - - > 1.38629 1.38629 1.38629 1.38629 0.19958 4.51685 1.77195 1.46634 0.26236 1.09861 0.40547 22 1.63468 2.34293 0.93456 1.15144 41 g - - > 1.38629 1.38629 1.38629 1.38629 0.02632 4.34360 4.34360 1.46634 0.26236 0.12090 2.17265 23 1.87006 2.26528 0.74337 1.32210 42 g - - > 1.38629 1.38629 1.38629 1.38629 0.02209 4.51685 4.51685 1.46634 0.26236 1.09861 0.40547 24 2.64681 0.70200 1.42219 1.64848 43 c - - > 1.38629 1.38629 1.38629 1.38629 0.02209 4.51685 4.51685 1.46634 0.26236 1.09861 0.40547 25 2.33297 1.00472 1.09221 1.60260 44 c - - > 1.38629 1.38629 1.38629 1.38629 0.13517 4.42968 2.16708 1.46634 0.26236 1.09861 0.40547 26 1.36648 2.34196 0.84976 1.50805 45 g - - > 1.38629 1.38629 1.38629 1.38629 0.76527 0.62588 * 1.64441 0.21459 0.00000 * //