INFERNAL1/a [1.1 | October 2013] NAME VTS1_binding DESC VTS1 binding site STATES 73 NODES 15 CLEN 23 W 40 ALPH RNA RF no CONS yes MAP yes DATE Mon Jun 2 11:13:10 2014 COM [1] cmbuild -F CM SEED COM [2] cmcalibrate 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 10 EFFN 10.000000 CKSUM 3507832301 NULL 0.000 0.000 0.000 0.000 GA 12.00 EFP7GF -0.3776 0.88945 ECMLC 0.63372 -3.09774 5.53065 1600000 284381 0.004220 ECMGC 0.55681 -6.03769 6.89697 1600000 536906 0.000745 ECMLI 0.68814 -1.29463 6.44381 1600000 246512 0.004868 ECMGI 0.58619 -4.75599 7.19497 1600000 441087 0.000907 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 40 60 -10.014 -9.953 -0.449 -8.730 -9.010 -1.937 IL 1 1 2 1 6 1 1 42 62 -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 41 62 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 6 34 c g - - MP 3 2 3 7 6 2 2 40 60 -9.580 -2.870 -0.227 -8.296 -8.576 -8.971 -3.319 -3.151 -3.404 1.658 -2.859 -4.225 2.051 -3.366 -3.407 1.396 -3.927 -1.102 1.955 -3.543 -0.544 -2.328 ML 4 2 3 7 6 1 1 38 58 -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 38 58 -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 36 57 -12.257 -10.956 -2.129 -7.435 -7.452 -0.398 IL 7 7 5 7 6 1 1 39 60 -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 39 59 -3.492 -0.213 -7.003 -5.171 -6.277 0.000 0.000 0.000 0.000 [ MATP 2 ] 7 32 u a - - MP 9 8 6 13 6 2 2 38 58 -9.700 -9.639 -0.014 -8.415 -8.695 -9.090 -3.516 -3.363 -3.595 1.567 -2.966 -4.420 1.915 -3.499 -3.578 1.221 -4.100 -1.284 2.308 -3.746 -0.627 -2.484 ML 10 8 6 13 6 1 1 36 56 -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 36 56 -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 34 54 -11.900 -10.598 -2.521 -7.078 -7.095 -0.304 IL 13 13 5 13 6 1 1 37 58 -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 37 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 8 31 u a - - MP 15 14 6 19 6 2 2 36 56 -3.078 -9.704 -0.195 -8.480 -8.760 -9.155 -3.571 -3.420 -3.651 1.840 -3.028 -4.475 1.853 -3.559 -3.635 1.089 -4.156 -1.347 2.257 -3.804 -0.694 -2.545 ML 16 14 6 19 6 1 1 34 54 -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 34 54 -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 32 53 -11.644 -10.343 -1.762 -6.822 -6.839 -0.543 IL 19 19 5 19 6 1 1 35 55 -4.072 -4.335 -0.227 -5.990 -6.766 -6.427 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 1 35 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 10 30 g c - - MP 21 20 6 25 6 2 2 33 54 -2.203 -9.792 -0.367 -8.569 -8.849 -9.244 -4.087 -2.962 -3.997 1.358 -4.649 -4.692 -0.031 -4.494 -4.278 2.768 -4.625 0.933 1.501 -3.950 -2.015 -2.956 ML 22 20 6 25 6 1 1 31 52 -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 52 -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 31 51 -11.169 -9.868 -0.341 -6.347 -6.364 -2.440 IL 25 25 5 25 6 1 1 32 53 -4.768 -5.030 -0.136 -6.686 -7.462 -7.122 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 32 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 12 29 a u - - MP 27 26 6 31 6 2 2 31 51 -10.014 -3.304 -0.165 -8.730 -9.010 -9.405 -4.155 -4.109 -4.189 2.476 -3.389 -4.939 1.602 -3.999 -4.169 -0.222 -4.660 -2.096 2.109 -4.382 0.458 -3.082 ML 28 26 6 31 6 1 1 28 49 -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 49 -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 26 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 31 51 -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 32 52 -1.308 -0.825 -7.615 -5.782 -6.888 0.000 0.000 0.000 0.000 [ MATP 6 ] 13 26 u a - - MP 33 32 6 37 6 2 2 25 44 -10.014 -9.953 -0.011 -8.730 -9.010 -9.405 -3.639 -3.454 -3.724 0.195 -3.205 -4.542 1.543 -3.703 -3.735 1.858 -4.254 0.532 2.059 -3.853 0.904 -2.652 ML 34 32 6 37 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 35 32 6 37 6 1 1 24 42 -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 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 25 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 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 14 25 g c - - MP 39 38 6 43 6 2 2 23 42 -10.014 -9.953 -0.011 -8.730 -9.010 -9.405 -4.132 -3.395 -4.102 0.317 -3.856 -4.835 1.426 -4.206 -4.227 2.529 -4.653 0.322 2.004 -4.133 -1.362 -2.974 ML 40 38 6 43 6 1 1 22 41 -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 22 40 -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 20 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 23 42 -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 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 15 24 c g - - MP 45 44 6 49 6 2 2 21 40 -10.014 -9.953 -0.011 -8.730 -9.010 -9.405 -3.672 -3.432 -3.747 1.668 -3.257 -4.557 1.991 -3.742 -3.770 1.942 -4.281 -1.356 1.398 -3.866 0.216 -2.673 ML 46 44 6 49 6 1 1 20 39 -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 20 39 -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 18 36 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 21 40 -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 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 16 23 u a - - MP 51 50 6 55 4 2 2 19 38 -8.499 -2.791 -0.326 -4.182 -4.212 -3.958 -4.251 -0.095 -3.453 -5.079 1.711 -4.020 -4.194 0.918 -4.702 1.483 2.586 -4.433 -1.034 -3.035 ML 52 50 6 55 4 1 1 19 37 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 4 1 1 18 37 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 54 50 6 55 4 0 0 17 35 -12.737 -14.007 -2.036 -0.404 IL 55 55 5 55 4 1 1 19 37 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 56 56 6 56 3 1 1 18 37 -3.172 -0.208 -5.410 0.000 0.000 0.000 0.000 [ MATR 10 ] - 21 - a - - MR 57 56 6 59 5 1 1 17 36 -8.550 -0.014 -8.365 -8.577 -9.469 0.550 -0.331 -0.926 0.281 D 58 56 6 59 5 0 0 17 35 -6.001 -0.409 -3.627 -5.058 -3.053 IR 59 59 3 59 5 1 1 18 37 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 17 20 C G - - MP 60 59 3 64 4 2 2 16 35 -8.667 -8.874 -0.016 -7.288 -7.937 -8.111 -6.912 -4.363 -5.257 -6.882 3.956 -6.606 -7.411 -4.340 -6.922 -6.355 -2.415 -7.831 -3.407 -6.215 ML 61 59 3 64 4 1 1 18 37 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 62 59 3 64 4 1 1 18 36 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 63 59 3 64 4 0 0 17 35 -4.568 -4.250 -2.265 -0.520 IL 64 64 5 64 4 1 1 20 38 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 65 65 6 65 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 18 - a - - - ML 66 65 6 68 3 1 1 12 30 -9.610 -0.007 -8.264 0.608 -0.913 -0.681 0.401 D 67 65 6 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 13 ] 19 - G - - - ML 69 68 3 71 2 1 1 1 1 * 0.000 -4.276 -5.814 1.963 -5.009 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 14 ] - - - - - - E 72 71 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME VTS1_binding DESC VTS1 binding site LENG 23 MAXL 83 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jun 2 11:13:10 2014 COM [1] cmbuild -F CM SEED NSEQ 10 EFFN 9.204102 CKSUM 3507832301 STATS LOCAL MSV -8.4032 0.88945 STATS LOCAL VITERBI -9.4110 0.88945 STATS LOCAL FORWARD -1.4288 0.88945 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.52376 1.46890 1.20166 1.38136 1.38629 1.38629 1.38629 1.38629 1.23354 0.66627 1.63415 0.74685 0.64218 0.00000 * 1 1.53833 1.28601 1.57323 1.19893 6 u - - < 1.38629 1.38629 1.38629 1.38629 0.02629 4.34469 4.34469 1.46634 0.26236 0.52815 0.89085 2 1.60207 1.37360 1.69140 1.01870 7 u - - < 1.38629 1.38629 1.38629 1.38629 0.02296 4.47872 4.47872 1.46634 0.26236 0.23961 1.54616 3 1.43814 1.41426 1.76645 1.05387 8 u - - < 1.38629 1.38629 1.38629 1.38629 0.22522 1.65507 4.54869 0.10729 2.28537 1.09861 0.40547 4 1.72241 2.59281 0.61176 1.58885 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.41798 1.10266 4.64201 0.05709 2.89161 1.09861 0.40547 5 1.05301 1.57673 2.49600 1.01597 12 u - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 6 2.36305 1.61064 1.13628 0.95426 13 u - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 7 2.32881 1.71346 0.82474 1.25879 14 g - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 8 1.54454 1.34100 1.30014 1.37629 15 g - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 9 2.57618 1.51665 1.21966 0.89365 16 u - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 10 4.86808 0.03949 4.89650 3.74826 17 C - - < 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 11 0.97038 2.00319 1.85195 1.11101 18 a - - _ 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 12 4.26692 5.32034 0.02773 4.77514 19 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 13 4.05163 5.16980 0.03100 4.90044 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.05854 4.80402 3.02292 1.46634 0.26236 1.09861 0.40547 14 1.01019 1.61490 2.01633 1.19139 21 a - - - 1.38629 1.38629 1.38629 1.38629 0.17770 1.86910 4.76272 0.10729 2.28537 0.29036 1.37831 15 0.96819 2.03075 1.40411 1.41301 23 a - - > 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 16 1.69429 1.37834 1.11790 1.43840 24 g - - > 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 17 1.35056 1.00088 1.60009 1.76333 25 c - - > 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 18 1.29098 1.43480 1.18239 1.71318 26 g - - > 1.38629 1.38629 1.38629 1.38629 0.17256 1.89513 4.80402 0.73143 0.65627 1.09861 0.40547 19 1.26857 2.66982 1.25585 1.00876 29 u - - > 1.38629 1.38629 1.38629 1.38629 0.01946 4.64201 4.64201 1.46634 0.26236 1.09861 0.40547 20 1.68333 0.83165 2.40675 1.24199 30 c - - > 1.38629 1.38629 1.38629 1.38629 0.02139 4.54869 4.54869 1.46634 0.26236 1.09861 0.40547 21 1.16361 1.89663 1.28953 1.33876 31 a - - > 1.38629 1.38629 1.38629 1.38629 0.09293 4.54869 2.54899 1.46634 0.26236 1.09861 0.40547 22 1.12995 1.81669 1.24875 1.48050 32 a - - > 1.38629 1.38629 1.38629 1.38629 0.42291 1.56982 1.98936 0.10571 2.29941 2.23930 0.11265 23 1.34346 1.69733 1.16447 1.41141 34 g - - > 1.38629 1.38629 1.38629 1.38629 1.01648 0.44921 * 0.56304 0.84275 0.00000 * //