INFERNAL1/a [1.1 | October 2013] NAME ANYA DESC ANYA tetraloop STATES 61 NODES 14 CLEN 19 W 32 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:12:57 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/ANYA/CM /share/data/people/ppg15/motifs/ANYA/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/ANYA/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 15 EFFN 15.000000 CKSUM 1219685093 NULL 0.000 0.000 0.000 0.000 GA 20.00 EFP7GF -4.0885 0.78088 ECMLC 0.72979 -2.54986 5.40788 1600000 399324 0.003005 ECMGC 0.50595 -9.45630 4.83693 1600000 552971 0.000723 ECMLI 0.76632 -1.27740 6.16520 1600000 359867 0.003335 ECMGI 0.53196 -8.16843 5.17397 1600000 483606 0.000827 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 32 51 -10.380 -10.320 -0.044 -9.096 -9.376 -5.314 IL 1 1 2 1 6 1 1 34 52 -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 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 3 23 g c - - MP 3 2 3 7 6 2 2 32 51 -10.345 -10.285 -0.009 -9.061 -9.341 -9.736 -5.395 -4.026 -5.376 2.657 -6.797 -6.469 -1.948 -5.779 -5.386 2.761 -5.837 1.067 -2.146 -5.606 -3.924 -4.190 ML 4 2 3 7 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 5 2 3 7 6 1 1 30 49 -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 46 -10.036 -8.734 -4.531 -5.213 -5.231 -0.152 IL 7 7 5 7 6 1 1 32 50 -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 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 4 22 c g - - MP 9 8 6 13 6 2 2 30 49 -10.345 -10.285 -0.009 -9.061 -9.341 -9.736 -4.985 -4.008 -4.908 1.674 -4.762 -5.683 2.536 -4.994 -5.008 2.433 -5.413 -1.607 -0.541 -4.996 -2.196 -3.726 ML 10 8 6 13 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 11 8 6 13 6 1 1 28 47 -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 44 -10.036 -8.734 -4.531 -5.213 -5.231 -0.152 IL 13 13 5 13 6 1 1 30 48 -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 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 5 21 A U - - MP 15 14 6 19 6 2 2 28 47 -10.345 -10.285 -0.009 -9.061 -9.341 -9.736 -6.457 -5.859 -6.141 3.077 -4.971 -6.746 2.716 -5.613 -6.060 -2.237 -6.386 -3.411 -1.523 -6.775 -2.640 -4.932 ML 16 14 6 19 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 17 14 6 19 6 1 1 26 45 -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 -10.036 -8.734 -4.531 -5.213 -5.231 -0.152 IL 19 19 5 19 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 20 20 6 20 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 6 20 U A - - MP 21 20 6 25 6 2 2 26 45 -10.345 -10.285 -0.009 -9.061 -9.341 -9.736 -6.223 -5.175 -6.156 -1.466 -5.730 -7.450 -1.380 -5.854 -5.902 -1.743 -6.392 1.630 3.535 -7.064 -3.368 -4.857 ML 22 20 6 25 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 23 20 6 25 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 24 20 6 25 6 0 0 22 40 -10.036 -8.734 -4.531 -5.213 -5.231 -0.152 IL 25 25 5 25 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 26 26 6 26 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 7 19 G C - - MP 27 26 6 31 4 2 2 24 43 -2.426 -9.344 -0.308 -7.758 -5.330 -4.524 -5.155 -0.745 -4.473 -5.722 1.792 -5.012 -5.265 3.010 -5.604 -2.194 1.625 -5.243 -1.981 -3.968 ML 28 26 6 31 4 1 1 23 41 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 29 26 6 31 4 1 1 22 41 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 30 26 6 31 4 0 0 21 39 -5.508 -5.189 -3.205 -0.248 IL 31 31 5 31 4 1 1 23 42 -3.911 -0.273 -3.343 -7.080 0.000 0.000 0.000 0.000 IR 32 32 6 32 3 1 1 22 41 -2.933 -0.236 -5.633 0.000 0.000 0.000 0.000 [ MATL 6 ] 9 - A - - - ML 33 32 6 35 5 1 1 21 40 -9.051 -0.010 -8.867 -9.079 -9.970 1.749 -2.184 -1.680 -3.227 D 34 32 6 35 5 0 0 20 39 -5.754 -0.408 -5.015 -3.390 -3.303 IL 35 35 3 35 5 1 1 22 40 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 10 17 G C - - MP 36 35 3 40 6 2 2 20 39 -10.380 -10.320 -0.009 -9.096 -9.376 -9.771 -6.369 -5.270 -6.111 -1.750 -5.195 -6.302 2.550 -5.798 -5.982 3.179 -6.248 -2.971 -1.573 -6.217 -2.800 -4.959 ML 37 35 3 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 3 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 3 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 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 11 16 G C - - MP 42 41 6 46 4 2 2 18 36 -9.184 -9.391 -0.011 -7.805 -7.005 -4.806 -7.179 -1.787 -7.030 -6.104 0.758 -7.243 -6.093 3.760 -6.324 -2.611 -2.950 -6.220 -4.432 -6.082 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 38 -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 ] 12 - A - - - ML 48 47 6 50 3 1 1 15 33 -10.117 -0.005 -8.771 1.885 -2.461 -4.104 -3.894 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 ] 13 - U - - - ML 51 50 3 53 3 1 1 13 32 -10.117 -0.005 -8.771 -5.106 -4.656 -5.934 1.969 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 ] 14 - u - - - ML 54 53 3 56 3 1 1 12 30 -10.117 -0.005 -8.771 -1.522 0.581 -2.061 0.938 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 ] 15 - A - - - ML 57 56 3 59 2 1 1 1 1 * 0.000 1.979 -6.010 -5.414 -5.640 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 [i1.1 | October 2013] NAME ANYA DESC ANYA tetraloop LENG 19 MAXL 75 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:12:57 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/ANYA/CM /share/data/people/ppg15/motifs/ANYA/SEED NSEQ 15 EFFN 14.578857 CKSUM 1219685093 STATS LOCAL MSV -6.5258 0.78088 STATS LOCAL VITERBI -7.0848 0.78088 STATS LOCAL FORWARD -2.6268 0.78088 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.31128 1.38802 1.36845 1.48520 1.38629 1.38629 1.38629 1.38629 0.38412 1.16172 5.11589 0.49402 0.94205 0.00000 * 1 0.91792 3.92974 0.58566 3.71875 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 2 1.57291 1.00641 1.01928 2.71543 4 c - - < 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 3 0.63944 0.88358 3.79435 3.30739 5 A - - < 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 4 3.56641 3.56126 1.54106 0.31583 6 U - - < 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 5 3.07001 1.50398 0.66023 1.53896 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.21016 1.69529 5.11589 0.06415 2.77843 1.09861 0.40547 6 0.17556 2.89481 2.54738 3.59659 9 A - - - 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 7 3.73363 1.00034 0.55592 3.35818 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 8 3.75884 2.23012 0.15681 4.24719 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 9 0.08094 3.08907 4.20315 4.05934 12 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 10 4.88567 4.57776 5.45816 0.02234 13 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 11 2.42748 0.98600 2.80486 0.73781 14 u - - _ 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 12 0.01535 5.51790 5.10690 5.26531 15 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 13 4.43298 0.16718 2.20621 3.44333 16 C - - > 1.38629 1.38629 1.38629 1.38629 0.01170 5.14749 5.14749 1.46634 0.26236 1.09861 0.40547 14 3.61712 0.56914 0.98117 3.43406 17 C - - > 1.38629 1.38629 1.38629 1.38629 0.21016 1.69529 5.11589 0.06415 2.77843 1.09861 0.40547 15 1.61412 0.68271 1.44566 2.81176 19 C - - > 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 16 0.32330 3.78691 3.38996 1.51474 20 A - - > 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 17 3.59233 4.08390 0.86393 0.62713 21 U - - > 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 18 2.96080 1.06820 0.97357 1.48341 22 g - - > 1.38629 1.38629 1.38629 1.38629 0.01207 5.11589 5.11589 1.46634 0.26236 1.09861 0.40547 19 3.97350 0.84446 3.72552 0.63998 23 U - - > 1.38629 1.38629 1.38629 1.38629 0.37810 1.15570 * 0.80609 0.59168 0.00000 * //