INFERNAL1/a [1.1 | October 2013] NAME U-turn DESC U-turn STATES 67 NODES 15 CLEN 21 W 74 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 16:42:24 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/U-turn/CM /share/data/people/ppg15/motifs/U-turn/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/U-turn/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 19 EFFN 19.000000 CKSUM 2449239062 NULL 0.000 0.000 0.000 0.000 GA 10.00 EFP7GF -1.1720 0.83797 ECMLC 0.61055 -2.64060 6.31306 1600000 284004 0.004225 ECMGC 0.55752 -4.75542 7.69477 1600000 413638 0.000967 ECMLI 0.65192 -1.09687 7.04391 1600000 242125 0.004956 ECMGI 0.58048 -3.79133 7.91730 1600000 357927 0.001118 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 74 138 -10.618 -10.558 -0.277 -4.390 -9.614 -3.006 IL 1 1 2 1 6 1 1 75 139 -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 75 139 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 7 39 c g - - MP 3 2 3 7 6 2 3 74 138 -10.350 -10.289 -0.009 -9.066 -9.346 -9.741 -2.482 -2.651 -0.546 1.170 -1.170 -3.517 2.058 -2.965 -2.727 1.691 -3.294 -1.217 1.190 -2.808 -0.734 -0.053 ML 4 2 3 7 6 1 1 72 135 -7.709 -8.055 -2.769 -0.291 -7.905 -5.434 -0.942 -2.049 1.520 -1.433 MR 5 2 3 7 6 1 1 72 136 -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 69 133 -11.848 -10.546 -6.343 -7.026 -7.043 -0.042 IL 7 7 5 7 6 1 1 74 137 -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 73 137 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 8 38 g c - - MP 9 8 6 13 6 2 2 72 136 -10.350 -10.289 -0.009 -9.066 -9.346 -9.741 -3.984 -1.071 -3.960 1.966 -4.491 -4.656 1.395 -4.480 -4.232 2.480 -4.619 0.185 -0.518 -3.924 -2.116 -0.108 ML 10 8 6 13 6 1 1 70 134 -7.709 -8.055 -2.769 -0.291 -7.905 -5.434 -0.942 -2.049 1.520 -1.433 MR 11 8 6 13 6 1 1 70 134 -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 69 133 -11.848 -10.546 -1.701 -7.026 -7.043 -0.565 IL 13 13 5 13 6 1 1 72 135 -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 71 135 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 9 37 G C - - MP 15 14 6 19 6 2 2 70 134 -10.422 -10.362 -0.008 -9.138 -9.418 -9.813 1.017 -3.870 -5.070 -0.292 -5.821 -5.691 0.241 -5.535 0.599 3.227 -5.581 -1.488 -1.483 -5.026 -3.124 -3.994 ML 16 14 6 19 6 1 1 69 133 -7.709 -8.055 -0.353 -2.464 -7.905 -5.434 -1.044 1.365 -1.833 -0.604 MR 17 14 6 19 6 1 1 67 131 -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 68 132 -11.343 -10.041 -0.298 -6.521 -6.538 -2.613 IL 19 19 5 19 6 1 1 69 133 -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 69 133 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 10 36 g c - - MP 21 20 6 25 6 2 2 68 132 -3.255 -10.558 -0.167 -9.334 -9.614 -10.009 -4.144 -3.571 -0.157 0.372 -4.172 -4.928 0.821 -4.445 -4.326 2.221 -4.779 1.153 2.123 -4.212 -1.850 -3.185 ML 22 20 6 25 6 1 1 65 128 -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 64 128 -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 59 122 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 68 132 -1.148 -5.613 -0.962 -7.269 -8.045 -7.705 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 67 131 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 13 35 g c - - MP 27 26 6 31 6 2 2 66 130 -2.889 -4.417 -0.296 -9.334 -9.614 -10.009 -4.692 -3.534 -4.570 1.467 -5.179 -5.211 0.505 -5.082 -4.907 2.925 -5.220 -1.205 1.284 -4.478 -2.495 -0.288 ML 28 26 6 31 6 1 1 57 121 -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 57 121 -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 51 115 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 71 134 -0.676 -1.655 -4.378 -8.115 -8.891 -8.552 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 1 67 131 -0.416 -2.035 -9.871 -8.038 -9.144 0.000 0.000 0.000 0.000 [ MATP 6 ] 17 28 G C - - MP 33 32 6 37 6 2 2 24 42 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -6.497 -4.657 -6.602 0.948 -7.848 -6.427 -2.861 -7.021 -6.050 3.650 -6.378 0.108 -3.099 -6.182 -4.915 -5.452 ML 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 24 42 -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 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 18 27 C G - - MP 39 38 6 43 6 2 2 22 40 -10.618 -10.558 -0.007 -9.334 -9.614 -10.009 -6.100 -5.368 -5.971 -0.122 -5.105 -6.756 3.231 -5.615 -5.877 2.254 -6.297 -2.895 -1.198 -6.352 -2.658 -4.687 ML 40 38 6 43 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 41 38 6 43 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 42 38 6 43 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 22 40 -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 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 19 26 g a - - MP 45 44 6 49 4 2 2 20 38 -1.626 -9.703 -0.754 -3.616 -0.146 -2.774 -2.791 0.117 -2.039 -3.637 0.414 -3.124 1.796 -0.053 0.754 1.054 0.610 0.572 -1.010 -2.049 ML 46 44 6 49 4 1 1 20 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 48 44 6 49 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520 IL 49 49 5 49 4 1 1 19 37 -4.896 -5.580 -0.087 -8.065 0.000 0.000 0.000 0.000 IR 50 50 6 50 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 21 - U - - - ML 51 50 6 53 3 1 1 16 34 -10.309 -0.004 -8.963 -1.715 -1.759 -3.952 1.738 D 52 50 6 53 3 0 0 15 34 -8.471 -0.218 -2.863 IL 53 53 3 53 3 1 1 20 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 22 - G - - - ML 54 53 3 56 3 1 1 14 33 -10.424 -0.004 -9.078 0.627 -1.750 1.028 -3.067 D 55 53 3 56 3 0 0 15 34 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 19 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 23 - A - - - ML 57 56 3 59 3 1 1 13 32 -10.424 -0.660 -1.448 1.983 -6.410 -5.790 -5.993 D 58 56 3 59 3 0 0 14 33 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 24 - a - - - ML 60 59 3 62 3 1 1 12 30 -9.770 -0.006 -8.424 0.667 -0.110 -0.542 -0.325 D 61 59 3 62 3 0 0 10 29 -10.463 -0.052 -4.854 IL 62 62 3 62 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 25 - a - - - ML 63 62 3 65 2 1 1 1 1 * 0.000 0.748 -1.151 -0.048 -0.147 D 64 62 3 65 2 0 0 0 0 * 0.000 IL 65 65 3 65 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 14 ] - - - - - - E 66 65 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME U-turn DESC U-turn LENG 21 MAXL 88 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 16:42:24 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/U-turn/CM /share/data/people/ppg15/motifs/U-turn/SEED NSEQ 19 EFFN 19.000000 CKSUM 2449239062 STATS LOCAL MSV -7.8187 0.83797 STATS LOCAL VITERBI -9.1409 0.83797 STATS LOCAL FORWARD -1.7242 0.83797 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.43570 1.38892 1.19570 1.55963 1.38629 1.38629 1.38629 1.38629 1.44733 0.27915 4.78243 1.33173 0.30655 0.00000 * 1 1.60672 1.24366 1.30801 1.42391 7 c - - < 1.38629 1.38629 1.38629 1.38629 0.01120 5.19025 5.19025 1.46634 0.26236 1.09861 0.40547 2 1.29235 1.78951 0.82218 2.12981 8 g - - < 1.38629 1.38629 1.38629 1.38629 0.01120 5.19025 5.19025 1.46634 0.26236 1.09861 0.40547 3 1.70867 2.29912 0.38864 3.20481 9 G - - < 1.38629 1.38629 1.38629 1.38629 0.01054 5.25079 5.25079 1.46634 0.26236 1.09861 0.40547 4 1.91467 2.12438 0.83551 1.20581 10 g - - < 1.38629 1.38629 1.38629 1.38629 0.14923 2.01058 5.35659 0.71785 0.66904 1.09861 0.40547 5 1.69051 2.35619 0.68705 1.52448 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.19370 1.76387 5.35659 1.10601 0.40179 1.09861 0.40547 6 2.07036 4.44985 0.16455 4.27580 17 G - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 7 2.76919 0.53175 1.17840 3.17155 18 C - - < 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 8 1.94129 2.19685 0.67205 1.44958 19 G - - < 1.38629 1.38629 1.38629 1.38629 0.50847 1.14527 2.52014 0.02939 3.54162 1.09861 0.40547 9 2.57500 2.60580 4.12536 0.18171 21 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01026 5.27783 5.27783 1.46634 0.26236 0.11089 2.25418 10 0.95156 2.59903 0.67397 3.51211 22 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 11 0.01145 5.82962 5.39950 5.54049 23 A - - _ 1.38629 1.38629 1.38629 1.38629 0.45919 5.35659 1.01201 1.46634 0.26236 1.09861 0.40547 12 0.92410 1.46224 1.76164 1.61127 24 a - - _ 1.38629 1.38629 1.38629 1.38629 0.01482 4.91222 4.91222 1.46634 0.26236 0.02562 3.67705 13 0.86794 2.18387 1.41963 1.48822 25 a - - _ 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 14 0.95780 1.78677 1.47542 1.51376 26 a - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 15 3.40554 1.20333 0.51815 2.64511 27 G - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 16 4.42370 0.24391 4.27490 1.65788 28 C - - > 1.38629 1.38629 1.38629 1.38629 0.26573 1.47563 5.35659 1.55111 0.23827 1.09861 0.40547 17 1.83591 0.72831 2.25581 1.37429 35 c - - > 1.38629 1.38629 1.38629 1.38629 0.00948 5.35659 5.35659 1.46634 0.26236 1.09861 0.40547 18 1.26406 1.19898 1.68064 1.47082 36 c - - > 1.38629 1.38629 1.38629 1.38629 0.01126 5.18503 5.18503 1.46634 0.26236 1.09861 0.40547 19 1.40658 0.52654 2.46673 2.53180 37 C - - > 1.38629 1.38629 1.38629 1.38629 0.01202 5.12024 5.12024 1.46634 0.26236 1.09861 0.40547 20 2.90475 0.95644 1.68505 0.97938 38 c - - > 1.38629 1.38629 1.38629 1.38629 0.01202 5.12024 5.12024 1.46634 0.26236 1.09861 0.40547 21 1.65446 1.48665 1.05903 1.44442 39 g - - > 1.38629 1.38629 1.38629 1.38629 1.43892 0.27074 * 1.03400 0.43941 0.00000 * //