INFERNAL1/a [1.1 | October 2013] NAME CsrA_binding DESC CsrA/RsmA binding motif STATES 43 NODES 11 CLEN 13 W 60 ALPH RNA RF no CONS yes MAP yes DATE Mon Jun 30 15:17:24 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/CsrA_binding/CM /share/data/people/ppg15/motifs/CsrA_binding/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/CsrA_binding/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 1247 EFFN 1247.000000 CKSUM 3796081296 NULL 0.000 0.000 0.000 0.000 GA 11.00 EFP7GF 0.0646 0.85349 ECMLC 0.65442 -2.50496 6.35593 1600000 395876 0.003031 ECMGC 0.66637 -1.72704 8.03209 1600000 266897 0.001499 ECMLI 0.70256 -1.18189 6.81582 1600000 330704 0.003629 ECMGI 0.67263 -1.42855 8.20544 1600000 260815 0.001534 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 60 108 -16.194 -16.133 -0.208 -14.910 -6.625 -3.011 IL 1 1 2 1 6 1 2 62 110 -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 2 61 109 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 3 33 g c - - MP 3 2 3 7 6 2 4 60 108 -15.986 -15.926 -0.000 -14.702 -14.982 -15.377 -10.248 -9.755 -3.029 1.303 -9.267 -11.027 2.070 -9.864 -10.153 2.270 -10.636 -1.109 1.692 -10.352 -0.548 -8.851 ML 4 2 3 7 6 1 1 58 106 -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 50 98 -11.064 -9.793 -5.701 -9.771 -0.038 -7.984 -5.197 1.964 -5.701 -4.294 D 6 2 3 7 6 0 0 58 106 -17.211 -15.910 -0.009 -12.389 -12.406 -7.478 IL 7 7 5 7 6 1 1 59 108 -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 59 107 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 4 32 g c - - MP 9 8 6 13 6 2 2 58 106 -3.012 -16.118 -0.192 -14.895 -15.175 -10.247 -10.156 -5.882 -5.768 1.126 -11.032 -10.577 2.111 -10.642 -10.405 2.756 -4.634 -0.275 0.872 -9.836 -8.129 -8.937 ML 10 8 6 13 6 1 1 54 101 -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 46 93 -11.064 -9.793 -5.701 -9.771 -0.038 -7.984 -4.774 -4.353 -5.590 1.961 D 12 8 6 13 6 0 0 51 98 -9.901 -8.600 -1.018 -5.079 -5.096 -1.172 IL 13 13 5 13 6 1 3 61 110 -0.587 -1.587 -9.703 -13.440 -14.216 -13.876 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 3 55 101 -1.005 -0.997 -13.561 -11.728 -12.834 0.000 0.000 0.000 0.000 [ MATP 3 ] 8 29 C G - - MP 15 14 6 19 6 2 3 52 98 -2.285 -16.118 -0.843 -2.895 -3.279 -15.569 -4.953 -10.183 -10.482 0.556 -9.347 -11.325 3.113 -10.000 -10.340 0.393 -10.853 -4.727 2.011 -10.665 -1.125 -9.059 ML 16 14 6 19 6 1 1 52 99 -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 43 90 -11.064 -9.793 -5.701 -9.771 -0.038 -7.984 -5.197 1.964 -5.701 -4.294 D 18 14 6 19 6 0 0 50 97 -0.628 -9.247 -5.044 -5.726 -5.743 -1.819 IL 19 19 5 19 6 1 2 51 98 -2.028 -0.409 -9.257 -12.994 -13.770 -13.430 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 2 50 96 -2.011 -0.412 -13.704 -11.872 -12.977 0.000 0.000 0.000 0.000 [ MATP 4 ] 11 26 C G - - MP 21 20 6 25 4 2 3 48 95 -3.096 -15.218 -0.180 -13.632 -12.547 -12.682 -6.820 0.549 -4.788 -12.215 3.694 -7.613 -12.052 -8.682 -3.346 -6.132 -1.573 -12.450 0.131 -10.840 ML 22 20 6 25 4 1 1 52 99 -0.311 -11.432 -2.682 -4.719 -7.992 -9.765 1.997 -8.753 MR 23 20 6 25 4 1 1 42 88 -12.479 -3.314 -1.973 -0.633 -0.336 -0.777 -2.168 1.264 D 24 20 6 25 4 0 0 44 91 -4.568 -4.250 -2.265 -0.520 IL 25 25 5 25 4 1 2 52 98 -0.652 -1.462 -10.831 -14.569 0.000 0.000 0.000 0.000 IR 26 26 6 26 3 1 1 46 92 -0.575 -1.606 -13.064 0.000 0.000 0.000 0.000 [ MATL 5 ] 16 - A - - - ML 27 26 6 29 3 1 1 12 30 -1.831 -0.476 -14.865 1.882 -3.293 -3.263 -3.204 D 28 26 6 29 3 0 0 12 30 -0.006 -9.576 -8.455 IL 29 29 3 29 3 1 1 11 30 -9.456 -0.002 -12.156 0.000 0.000 0.000 0.000 [ MATL 6 ] 18 - G - - - ML 30 29 3 32 3 1 1 10 29 -16.328 -0.000 -14.982 -3.655 -4.208 1.951 -11.441 D 31 29 3 32 3 0 0 16 34 -6.174 -1.687 -0.566 IL 32 32 3 32 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 19 - G - - - ML 33 32 3 35 3 1 1 9 27 -16.328 -0.000 -14.982 -10.869 -12.601 1.974 -3.843 D 34 32 3 35 3 0 0 14 33 -6.174 -1.687 -0.566 IL 35 35 3 35 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 20 - A - - - ML 36 35 3 38 3 1 1 7 26 -16.328 -0.078 -4.250 1.954 -4.594 -4.529 -4.644 D 37 35 3 38 3 0 0 13 32 -6.174 -1.687 -0.566 IL 38 38 3 38 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 21 - U - - - ML 39 38 3 41 2 1 1 1 1 * 0.000 -0.574 0.003 -2.916 1.133 D 40 38 3 41 2 0 0 0 0 * 0.000 IL 41 41 3 41 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 10 ] - - - - - - E 42 41 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME CsrA_binding DESC CsrA/RsmA binding motif LENG 13 MAXL 56 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jun 30 15:17:24 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/CsrA_binding/CM /share/data/people/ppg15/motifs/CsrA_binding/SEED NSEQ 1247 EFFN 32.285267 CKSUM 3796081296 STATS LOCAL MSV -6.9761 0.85349 STATS LOCAL VITERBI -7.6363 0.85349 STATS LOCAL FORWARD -1.8075 0.85349 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.38370 1.51269 1.04106 1.73753 1.38629 1.38629 1.38629 1.38629 0.23193 1.57591 8.61663 0.26266 1.46535 0.00000 * 1 1.80533 1.31389 1.17168 1.35883 3 g - - < 1.38629 1.38629 1.38629 1.38629 0.00018 9.32264 9.32264 1.46634 0.26236 1.09861 0.40547 2 1.86423 1.43590 0.73235 2.06906 4 g - - < 1.38629 1.38629 1.38629 1.38629 0.13311 2.08303 9.42229 1.09879 0.40538 1.09861 0.40547 3 2.24584 0.70505 2.20969 1.23669 8 c - - < 1.38629 1.38629 1.38629 1.38629 0.37015 1.58022 2.26876 0.28300 1.40047 1.09861 0.40547 4 2.39151 0.45772 1.87373 2.10182 11 C - - < 1.38629 1.38629 1.38629 1.38629 0.25009 1.50878 9.31355 1.01307 0.45114 0.00156 6.46230 5 0.11573 3.31790 3.36945 3.25319 16 A - - _ 1.38629 1.38629 1.38629 1.38629 0.30034 1.34957 9.43284 0.00062 7.39062 1.09861 0.40547 6 3.67786 4.21452 0.04709 5.12640 18 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00016 9.43284 9.43284 1.46634 0.26236 1.09861 0.40547 7 5.28348 6.37120 0.02424 4.06500 19 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00016 9.43284 9.43284 1.46634 0.26236 1.09861 0.40547 8 0.05533 4.02983 4.02892 4.00310 20 A - - _ 1.38629 1.38629 1.38629 1.38629 0.05412 9.43284 2.94505 1.46634 0.26236 1.09861 0.40547 9 1.69333 1.39835 2.87569 0.66804 21 U - - _ 1.38629 1.38629 1.38629 1.38629 0.28236 1.51806 3.61706 0.92751 0.50342 0.00304 5.79768 10 2.43723 3.08471 0.32684 1.92649 26 G - - > 1.38629 1.38629 1.38629 1.38629 0.23475 1.56471 9.40714 0.28706 1.38817 0.00627 5.07495 11 1.36882 2.27756 0.64056 2.15362 29 G - - > 1.38629 1.38629 1.38629 1.38629 0.13167 2.09323 9.43249 0.69360 0.69269 1.09861 0.40547 12 2.14458 0.85324 1.39673 1.56327 32 c - - > 1.38629 1.38629 1.38629 1.38629 0.00018 9.33390 9.33390 1.46634 0.26236 1.09861 0.40547 13 1.56220 1.27388 1.14666 1.64565 33 g - - > 1.38629 1.38629 1.38629 1.38629 0.35973 1.19689 * 0.61281 0.78051 0.00000 * //