INFERNAL1/a [1.1 | October 2013] NAME Roquin_binding DESC Roquin binding motif STATES 64 NODES 16 CLEN 20 W 33 ALPH RNA RF no CONS yes MAP yes DATE Mon Jun 30 17:31:15 2014 COM [1] cmbuild -F Roquin_binding/CM Roquin_binding/SEED COM [2] cmcalibrate Roquin_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 7 EFFN 7.000000 CKSUM 1656452584 NULL 0.000 0.000 0.000 0.000 GA 19.00 EFP7GF -2.7156 0.80460 ECMLC 0.55755 -4.44111 5.91921 1600000 387118 0.003100 ECMGC 0.47123 -6.89402 7.24868 1600000 313621 0.001275 ECMLI 0.58074 -2.72714 6.43975 1600000 246142 0.004875 ECMGI 0.47873 -6.32582 7.39726 1600000 285234 0.001402 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 33 52 -8.235 -8.442 -0.209 -2.955 IL 1 1 2 1 4 1 1 38 57 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - g - - - ML 3 2 3 5 3 1 1 33 52 -9.010 -0.010 -7.664 -1.156 -1.826 0.928 0.451 D 4 2 3 5 3 0 0 32 51 -7.990 -0.314 -2.382 IL 5 5 3 5 3 1 1 36 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - u - - - ML 6 5 3 8 3 1 1 32 51 -9.189 -0.009 -7.843 0.126 -0.538 -0.062 0.335 D 7 5 3 8 3 0 0 31 50 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - U - - - ML 9 8 3 11 3 1 1 31 49 -9.524 -0.008 -7.842 0.048 -1.817 -2.193 1.301 D 10 8 3 11 3 0 0 30 48 -5.620 -0.734 -1.403 IL 11 11 3 11 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 21 - a - - MR 12 11 3 14 3 1 1 30 48 -9.524 -0.008 -7.842 0.872 -1.448 -0.686 0.240 D 13 11 3 14 3 0 0 28 47 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 20 - u - - MR 15 14 3 17 5 1 1 29 47 -8.209 -0.018 -8.024 -8.237 -9.128 0.174 -0.652 -0.170 0.429 D 16 14 3 17 5 0 0 28 46 -5.352 -0.707 -2.978 -4.409 -2.404 IR 17 17 3 17 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 4 19 g c - - MP 18 17 3 22 6 2 2 28 46 -2.468 -9.679 -0.302 -8.455 -8.735 -9.130 -0.167 -2.432 -2.630 0.743 -2.607 -3.447 1.889 -2.947 -2.720 2.115 -3.255 -0.735 0.747 0.284 -0.666 -1.815 ML 19 17 3 22 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 20 17 3 22 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 21 17 3 22 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 22 22 5 22 6 1 1 27 45 -4.479 -4.741 -0.168 -6.397 -7.173 -6.833 0.000 0.000 0.000 0.000 IR 23 23 6 23 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 18 a u - - MP 24 23 6 28 6 2 2 26 44 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -4.011 -3.892 -4.024 2.373 -3.201 -4.769 2.196 -3.809 -4.002 0.093 -4.482 -1.807 1.860 -4.227 -0.859 -2.893 ML 25 23 6 28 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 26 23 6 28 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 27 23 6 28 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 28 28 5 28 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 29 29 6 29 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 7 17 u a - - MP 30 29 6 34 6 2 2 24 42 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -4.360 -4.227 -4.312 1.235 -3.300 -5.005 1.851 -3.966 -4.269 -0.157 -4.720 -2.060 2.959 -4.547 -0.915 -3.112 ML 31 29 6 34 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 32 29 6 34 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 6 34 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 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 35 35 6 35 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 8 16 U A - - MP 36 35 6 40 6 2 2 22 40 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -7.496 -7.368 -6.982 -3.626 -5.484 -7.271 -1.203 -6.329 -6.946 -3.654 -7.220 -5.277 3.921 -7.414 -3.036 -4.933 ML 37 35 6 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 6 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 6 40 6 0 0 19 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 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 41 41 6 41 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 9 15 U A - - MP 42 41 6 46 6 2 2 20 38 -9.739 -9.679 -0.014 -8.455 -8.735 -9.130 -5.595 -5.645 -5.148 -1.751 -3.657 -5.458 1.995 -4.508 -5.189 -1.625 -5.421 -3.649 3.401 -5.568 -1.323 -3.987 ML 43 41 6 46 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 44 41 6 46 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 45 41 6 46 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 20 38 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 1 19 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 10 14 C G - - MP 48 47 6 52 4 2 2 17 36 -8.235 -8.442 -0.022 -6.856 -7.169 -7.295 -6.347 -3.505 -4.728 -6.418 3.924 -5.874 -6.655 -3.464 -6.446 -5.448 -1.657 -7.077 -2.679 -5.457 ML 49 47 6 52 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 51 47 6 52 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 52 52 5 52 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 53 53 6 53 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 11 - U - - - ML 54 53 6 56 3 1 1 14 32 -9.189 -0.009 -7.843 -0.508 -2.033 -2.576 1.528 D 55 53 6 56 3 0 0 15 33 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 12 - G - - - ML 57 56 3 59 3 1 1 12 31 -9.189 -0.009 -7.843 0.192 -2.982 1.353 -2.501 D 58 56 3 59 3 0 0 13 32 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 13 - U - - - ML 60 59 3 62 2 1 1 1 1 * 0.000 -3.688 -3.360 -4.479 1.918 D 61 59 3 62 2 0 0 0 0 * 0.000 IL 62 62 3 62 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 15 ] - - - - - - E 63 62 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME Roquin_binding DESC Roquin binding motif LENG 20 MAXL 81 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jun 30 17:31:15 2014 COM [1] cmbuild -F Roquin_binding/CM Roquin_binding/SEED NSEQ 7 EFFN 6.265137 CKSUM 1656452584 STATS LOCAL MSV -6.8366 0.80460 STATS LOCAL VITERBI -7.9120 0.80460 STATS LOCAL FORWARD -2.2925 0.80460 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.36309 1.76746 1.47836 1.06319 1.38629 1.38629 1.38629 1.38629 0.14399 4.52179 2.09367 1.46634 0.26236 0.00000 * 1 2.10817 2.56837 0.77084 1.08100 1 g - - : 1.38629 1.38629 1.38629 1.38629 0.02480 4.40259 4.40259 1.46634 0.26236 0.16246 1.89744 2 1.29482 1.75189 1.43686 1.15539 2 u - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 3 1.35111 2.55858 2.81421 0.50471 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 4 1.68145 1.37393 1.14506 1.41642 4 g - - < 1.38629 1.38629 1.38629 1.38629 0.35774 1.23830 4.52179 0.07338 2.64860 1.09861 0.40547 5 1.12705 1.20703 2.28244 1.29137 6 a - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 6 1.84636 1.41398 2.45342 0.66744 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 7 4.57012 3.28481 4.49731 0.06075 8 U - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 8 3.54479 1.33447 3.36192 0.39577 9 U - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 9 4.51593 0.06325 4.44180 3.25485 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 10 1.72412 2.70089 3.06593 0.34543 11 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 11 1.25443 3.34677 0.46207 3.00406 12 G - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 12 3.80529 3.59264 4.35127 0.06472 13 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 13 3.52747 4.59580 0.05415 4.32494 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 14 0.43190 3.52287 1.25723 3.30307 15 A - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 15 0.06954 4.69934 3.11056 4.30494 16 A - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 16 0.73170 2.63317 1.30324 1.74062 17 a - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 17 1.41997 2.45781 1.11250 1.06734 18 u - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 18 1.68602 1.04752 1.24801 1.73239 19 c - - > 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 19 1.26325 1.82608 1.51014 1.09260 20 u - - : 1.38629 1.38629 1.38629 1.38629 0.02198 4.52179 4.52179 1.46634 0.26236 1.09861 0.40547 20 0.79476 2.33897 1.85140 1.22123 21 a - - : 1.38629 1.38629 1.38629 1.38629 0.01105 4.51086 * 1.46634 0.26236 0.00000 * //