INFERNAL1/a [1.1 | October 2013] NAME HuR_binding DESC HuR binding site STATES 55 NODES 13 CLEN 17 W 40 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:36:34 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/HuR_binding/CM /share/data/people/ppg15/motifs/HuR_binding/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/HuR_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 9 EFFN 9.000000 CKSUM 3700701663 NULL 0.000 0.000 0.000 0.000 GA 12.00 EFP7GF 0.0524 0.99625 ECMLC 0.67108 -0.08402 8.33117 1600000 340223 0.003527 ECMGC 0.79933 1.99595 10.21233 1600000 284664 0.001405 ECMLI 0.71588 0.89053 8.61893 1600000 303353 0.003956 ECMGI 0.82209 2.39698 10.30434 1600000 266215 0.001503 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 40 68 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 IL 1 1 2 1 6 1 1 41 70 -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 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 20 u a - - MP 3 2 3 7 6 2 2 40 68 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -4.208 -3.521 -4.281 1.097 -4.248 -5.302 0.121 -4.384 -4.253 1.501 -4.775 1.682 2.561 -4.520 -1.882 -3.159 ML 4 2 3 7 6 1 1 38 66 -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 66 -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 35 63 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 7 7 5 7 6 1 1 39 68 -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 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 19 u a - - MP 9 8 6 13 6 2 2 38 66 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -3.768 -3.534 -3.844 0.117 -3.323 -4.676 1.020 -3.806 -3.842 1.249 -4.356 1.711 2.298 -4.002 0.631 -2.762 ML 10 8 6 13 6 1 1 36 64 -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 64 -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 33 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 6 1 1 37 66 -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 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 18 g c - - MP 15 14 6 19 6 2 2 36 64 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -3.617 -2.985 -3.637 1.735 -3.696 -4.382 1.167 -3.934 -3.803 2.174 -4.245 1.031 1.399 -3.662 -1.355 -2.646 ML 16 14 6 19 6 1 1 34 62 -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 62 -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 31 59 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 35 64 -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 35 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 17 a u - - MP 21 20 6 25 6 2 2 34 62 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -3.333 -3.217 -3.459 2.536 -3.157 -4.320 0.898 -3.569 -3.477 0.504 -4.016 0.235 1.699 -3.622 0.625 -2.498 ML 22 20 6 25 6 1 1 32 60 -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 32 60 -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 29 57 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 33 62 -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 33 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 5 16 a u - - MP 27 26 6 31 6 2 2 32 60 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -3.730 -3.400 -3.798 2.507 -3.481 -4.612 0.742 -3.884 -3.844 1.407 -4.342 -1.312 0.994 -3.939 1.500 -2.782 ML 28 26 6 31 6 1 1 30 58 -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 30 58 -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 27 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 31 60 -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 31 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 6 15 u a - - MP 33 32 6 37 4 2 2 30 58 -1.977 -8.744 -0.441 -7.158 -3.317 -3.204 -3.443 1.912 -3.138 -4.303 0.922 -3.553 -3.462 0.519 -4.001 1.485 1.918 -3.605 0.448 -2.482 ML 34 32 6 37 4 1 1 27 55 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 4 1 1 26 54 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 36 32 6 37 4 0 0 25 53 -4.568 -4.250 -2.265 -0.520 IL 37 37 5 37 4 1 1 30 58 -0.945 -5.425 -1.142 -7.910 0.000 0.000 0.000 0.000 IR 38 38 6 38 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 10 - U - - - ML 39 38 6 41 3 1 1 16 35 -9.483 -0.007 -8.137 -4.138 -3.769 -4.938 1.940 D 40 38 6 41 3 0 0 17 35 -6.174 -1.687 -0.566 IL 41 41 3 41 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 11 - U - - - ML 42 41 3 44 3 1 1 15 34 -9.483 -0.007 -8.137 -1.696 -2.159 0.350 1.133 D 43 41 3 44 3 0 0 15 34 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 1 19 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 12 - u - - - ML 45 44 3 47 3 1 1 14 32 -9.483 -0.103 -3.886 -0.290 -0.019 -0.412 0.529 D 46 44 3 47 3 0 0 14 33 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 18 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 13 - g - - - ML 48 47 3 50 3 1 1 12 30 -9.387 -0.288 -2.478 0.026 -0.692 0.353 0.118 D 49 47 3 50 3 0 0 12 31 -7.606 -3.119 -0.185 IL 50 50 3 50 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 14 - U - - - ML 51 50 3 53 2 1 1 1 1 * 0.000 -0.721 -2.027 -2.622 1.578 D 52 50 3 53 2 0 0 0 0 * 0.000 IL 53 53 3 53 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 12 ] - - - - - - E 54 53 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME HuR_binding DESC HuR binding site LENG 17 MAXL 76 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:36:34 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/HuR_binding/CM /share/data/people/ppg15/motifs/HuR_binding/SEED NSEQ 9 EFFN 9.000000 CKSUM 3700701663 STATS LOCAL MSV -9.1817 0.99625 STATS LOCAL VITERBI -10.2443 0.99625 STATS LOCAL FORWARD -1.1686 0.99625 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.52179 1.93062 1.45692 0.90716 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 0.00000 * 1 1.92306 2.57532 0.96074 0.92861 1 u - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 2 2.48783 1.96516 1.02152 0.87532 2 u - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 3 1.48507 1.88070 0.87568 1.58741 3 g - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 4 0.96576 2.02371 1.76074 1.15447 4 a - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 5 0.99417 2.14278 1.61709 1.15784 5 a - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 6 1.36850 2.00725 1.29533 1.08664 6 u - - < 1.38629 1.38629 1.38629 1.38629 0.29498 1.40030 4.71850 0.81469 0.58479 1.09861 0.40547 7 4.25462 3.99884 4.80894 0.04154 10 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 8 2.56175 2.88291 1.14395 0.60093 11 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 9 1.58701 1.39922 1.67194 1.01945 12 u - - _ 1.38629 1.38629 1.38629 1.38629 0.08342 4.71850 2.64362 1.46634 0.26236 1.09861 0.40547 10 1.36796 1.86591 1.14155 1.30455 13 g - - _ 1.38629 1.38629 1.38629 1.38629 0.20960 4.65431 1.71718 1.46634 0.26236 2.29893 0.10577 11 1.88580 2.79115 3.20352 0.29260 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02321 4.46792 4.46792 1.46634 0.26236 0.07459 2.63279 12 1.36415 2.25260 1.54468 0.85356 15 u - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 13 1.96525 1.72385 1.24301 0.93398 16 u - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 14 1.50390 2.26342 1.50334 0.79549 17 u - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 15 1.71579 1.21278 1.75248 1.05135 18 u - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 16 1.13138 1.83021 1.46555 1.25148 19 a - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 17 0.97133 1.67835 2.40018 1.06701 20 a - - > 1.38629 1.38629 1.38629 1.38629 0.00905 4.70953 * 1.46634 0.26236 0.00000 * //