INFERNAL1/a [1.1 | October 2013] NAME UNCG DESC UNCG tetraloop STATES 58 NODES 13 CLEN 18 W 84 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 1 13:31:43 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/UNCG/CM /share/data/people/ppg15/motifs/UNCG/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/UNCG/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 31 EFFN 31.000000 CKSUM 1202672221 NULL 0.000 0.000 0.000 0.000 GA 8.00 EFP7GF -4.1331 0.81392 ECMLC 0.61315 -3.92439 5.18136 1600000 319095 0.003761 ECMGC 0.45102 -11.49745 5.33978 1600000 794379 0.000504 ECMLI 0.64448 -2.70359 5.69897 1600000 269791 0.004448 ECMGI 0.45634 -10.69949 5.52779 1600000 657790 0.000608 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 84 158 -11.161 -11.100 -0.357 -9.876 -10.156 -2.209 IL 1 1 2 1 6 1 1 86 160 -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 85 159 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 9 43 g c - - MP 3 2 3 7 6 2 2 84 158 -10.810 -10.750 -0.006 -9.526 -9.806 -10.201 -5.005 -3.838 -4.867 1.721 -5.293 -5.499 0.602 -5.297 -5.188 2.827 -5.497 -1.493 0.061 -4.783 1.216 -3.790 ML 4 2 3 7 6 1 1 82 156 -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 81 155 -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 78 152 -13.062 -11.761 -7.558 -8.240 -8.257 -0.018 IL 7 7 5 7 6 1 1 84 158 -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 83 157 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 10 42 a u - - MP 9 8 6 13 6 2 2 82 156 -2.200 -10.750 -0.361 -9.526 -9.806 -10.201 -4.788 -3.897 -4.732 2.275 -4.777 -5.438 1.235 -4.989 -4.933 2.153 -5.324 -0.104 1.490 -4.717 -2.241 -3.643 ML 10 8 6 13 6 1 1 80 154 -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 78 152 -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 78 152 -13.062 -11.761 -1.095 -8.240 -8.257 -0.930 IL 13 13 5 13 6 1 1 83 157 -2.123 -0.511 -4.094 -7.831 -8.607 -8.268 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 1 81 155 -1.391 -0.723 -8.940 -7.108 -8.214 0.000 0.000 0.000 0.000 [ MATP 3 ] 13 39 c g - - MP 15 14 6 19 6 2 2 80 154 -10.994 -10.933 -0.060 -4.709 -9.989 -10.384 -5.146 -4.591 -5.150 1.986 -4.555 -5.962 2.193 -5.029 -5.156 1.188 -5.634 1.528 0.796 -5.263 -2.063 -3.925 ML 16 14 6 19 6 1 1 79 153 -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 75 149 -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 75 149 -12.166 -10.864 -0.891 -7.343 -7.361 -1.160 IL 19 19 5 19 6 1 1 79 153 -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 78 152 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 14 38 g c - - MP 21 20 6 25 6 2 2 77 152 -1.663 -10.985 -0.554 -9.761 -10.041 -10.436 -5.407 -5.061 -5.401 -0.992 -4.386 -6.213 1.870 -5.011 -5.307 2.372 -5.804 -1.204 1.841 -5.564 1.236 -4.044 ML 22 20 6 25 6 1 1 79 153 -0.621 -8.092 -2.806 -2.501 -7.942 -5.471 -0.989 -2.106 1.540 -1.490 MR 23 20 6 25 6 1 1 64 138 -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 51 126 -11.078 -9.777 -1.370 -6.256 -6.273 -0.772 IL 25 25 5 25 6 1 1 80 154 -0.506 -1.983 -6.328 -10.065 -5.114 -10.501 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 75 149 -0.359 -2.202 -11.104 -9.272 -10.377 0.000 0.000 0.000 0.000 [ MATP 5 ] 22 31 c g - - MP 27 26 6 31 6 2 2 21 40 -11.078 -11.017 -0.005 -9.794 -10.074 -10.469 -0.191 -4.595 -5.158 -0.780 -4.602 -5.936 2.222 -5.074 -5.194 2.127 -5.658 1.465 1.152 -5.246 -2.114 -3.957 ML 28 26 6 31 6 1 1 21 40 -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 21 39 -8.356 -7.085 -0.438 -7.063 -2.197 -5.277 -1.094 1.390 -1.886 -0.643 D 30 26 6 31 6 0 0 19 38 -10.421 -9.120 -0.628 -5.599 -5.616 -1.692 IL 31 31 5 31 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 32 32 6 32 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 23 30 c g - - MP 33 32 6 37 6 2 2 19 38 -11.161 -11.100 -0.005 -9.876 -10.156 -10.551 -5.023 -4.882 -1.282 0.181 -1.105 -5.932 2.315 -4.840 -5.018 1.781 -5.547 -2.691 2.286 -5.257 -1.830 -3.866 ML 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 20 39 -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 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 24 29 C G - - MP 39 38 6 43 4 2 2 17 36 -10.158 -10.365 -0.006 -8.780 -7.988 -8.258 -7.309 -4.492 -5.663 -7.456 3.886 -6.577 -7.412 -4.465 -7.532 -6.639 -0.087 -7.826 -3.366 -6.214 ML 40 38 6 43 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 1 20 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 42 38 6 43 4 0 0 19 37 -4.568 -4.250 -2.265 -0.520 IL 43 43 5 43 4 1 1 22 40 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 25 - U - - - ML 45 44 6 47 3 1 1 14 32 -11.080 -0.002 -9.734 -6.691 -6.067 -7.604 1.989 D 46 44 6 47 3 0 0 16 34 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 26 - U - - - ML 48 47 3 50 3 1 1 13 31 -11.080 -0.002 -9.734 -1.541 -4.184 -5.061 1.837 D 49 47 3 50 3 0 0 15 33 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 27 - C - - - ML 51 50 3 53 3 1 1 11 29 -11.080 -0.002 -9.734 -6.462 1.985 -6.912 -5.553 D 52 50 3 53 3 0 0 13 32 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 28 - G - - - ML 54 53 3 56 2 1 1 1 1 * 0.000 -5.770 -7.502 1.987 -6.524 D 55 53 3 56 2 0 0 0 0 * 0.000 IL 56 56 3 56 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 12 ] - - - - - - E 57 56 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME UNCG DESC UNCG tetraloop LENG 18 MAXL 91 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 1 13:31:43 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/UNCG/CM /share/data/people/ppg15/motifs/UNCG/SEED NSEQ 31 EFFN 27.900757 CKSUM 1202672221 STATS LOCAL MSV -7.0133 0.81392 STATS LOCAL VITERBI -7.8783 0.81392 STATS LOCAL FORWARD -2.5150 0.81392 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.73312 1.31313 1.22071 1.34988 1.38629 1.38629 1.38629 1.38629 1.04900 0.44070 5.09564 1.60361 0.22461 0.00000 * 1 1.54189 2.28208 0.75909 1.53313 9 g - - < 1.38629 1.38629 1.38629 1.38629 0.00805 5.51917 5.51917 1.46634 0.26236 1.09861 0.40547 2 1.18110 1.86462 1.07655 1.62285 10 g - - < 1.38629 1.38629 1.38629 1.38629 0.31397 1.32634 5.51917 0.29048 1.37793 1.09861 0.40547 3 1.37978 1.23895 1.12550 2.00850 13 g - - < 1.38629 1.38629 1.38629 1.38629 0.00692 5.67044 5.67044 1.46634 0.26236 1.09861 0.40547 4 3.13635 1.46977 1.01300 1.01211 14 u - - < 1.38629 1.38629 1.38629 1.38629 0.44625 1.03058 5.75321 1.33633 0.30491 1.09861 0.40547 5 2.29316 1.22438 0.81681 1.81232 22 g - - < 1.38629 1.38629 1.38629 1.38629 0.00620 5.77870 5.77870 1.46634 0.26236 1.09861 0.40547 6 2.25957 1.07578 1.48255 1.11622 23 c - - < 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 7 5.13170 0.08413 5.13491 2.67514 24 C - - < 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 8 5.85556 5.44474 6.47685 0.00876 25 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 9 2.45498 4.18560 4.79091 0.11584 26 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 10 5.75733 0.01144 6.06956 5.13200 27 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 11 5.29369 6.48721 0.00957 5.81486 28 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 12 2.75120 5.19993 0.07994 4.89849 29 G - - > 1.38629 1.38629 1.38629 1.38629 0.00604 5.80514 5.80514 1.46634 0.26236 1.09861 0.40547 13 1.09362 1.52372 1.03716 2.37908 30 g - - > 1.38629 1.38629 1.38629 1.38629 0.00620 5.77870 5.77870 1.46634 0.26236 1.09861 0.40547 14 1.63326 1.23241 1.20611 1.54290 31 g - - > 1.38629 1.38629 1.38629 1.38629 0.51091 1.03058 3.14071 1.59163 0.22765 1.09861 0.40547 15 1.46666 1.13047 0.97516 2.66945 38 g - - > 1.38629 1.38629 1.38629 1.38629 0.00723 5.62593 5.62593 1.46634 0.26236 0.13689 2.05624 16 2.12914 1.88551 1.19333 0.85308 39 u - - > 1.38629 1.38629 1.38629 1.38629 0.31397 1.32634 5.51917 0.53917 0.87522 1.09861 0.40547 17 1.70219 1.24683 1.78685 1.01386 42 u - - > 1.38629 1.38629 1.38629 1.38629 0.00805 5.51917 5.51917 1.46634 0.26236 1.09861 0.40547 18 2.61435 0.79933 1.41869 1.44764 43 c - - > 1.38629 1.38629 1.38629 1.38629 1.22867 0.34627 * 1.82904 0.17503 0.00000 * //