INFERNAL1/a [1.1 | October 2013] NAME UMAC DESC UMAC tetraloop STATES 58 NODES 13 CLEN 18 W 59 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 16:41:03 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/UMAC/CM /share/data/people/ppg15/motifs/UMAC/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/UMAC/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 14 EFFN 14.000000 CKSUM 332001651 NULL 0.000 0.000 0.000 0.000 GA 12.00 EFP7GF -3.9799 0.78565 ECMLC 0.60422 -4.20483 5.53597 1600000 431766 0.002779 ECMGC 0.52025 -8.09693 6.22246 1600000 687727 0.000582 ECMLI 0.64857 -2.56141 6.15395 1600000 342010 0.003509 ECMGI 0.52144 -7.68083 6.30669 1600000 588379 0.000680 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 59 110 -10.314 -10.253 -0.516 -9.030 -9.310 -1.757 IL 1 1 2 1 6 1 1 60 112 -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 60 111 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 3 26 c g - - MP 3 2 3 7 6 2 2 59 110 -9.811 -9.750 -0.013 -8.526 -8.806 -9.201 -5.125 -4.705 -4.957 2.713 -3.919 -5.625 2.831 -4.547 -4.899 -0.824 -5.288 -2.368 -0.244 -5.376 -1.564 -3.759 ML 4 2 3 7 6 1 1 57 108 -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 56 107 -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 54 105 -12.694 -11.392 -7.190 -7.872 -7.889 -0.023 IL 7 7 5 7 6 1 1 58 110 -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 58 109 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 4 25 C G - - MP 9 8 6 13 6 2 2 57 108 -1.991 -9.750 -0.433 -8.526 -8.806 -9.201 -7.382 -7.523 -6.510 -3.744 -4.879 -6.553 3.935 -6.072 -6.861 -3.711 -6.586 -5.703 -1.864 -7.284 -2.876 -5.665 ML 10 8 6 13 6 1 1 53 104 -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 53 104 -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 54 105 -12.694 -11.392 -0.109 -7.872 -7.889 -3.964 IL 13 13 5 13 6 1 1 57 108 -1.111 -6.013 -0.971 -7.668 -8.445 -8.105 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 1 55 106 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 7 24 g u - - MP 15 14 6 19 6 2 2 54 106 -10.314 -2.494 -0.292 -9.030 -9.310 -9.705 -4.855 -3.700 -5.194 2.038 -5.232 -5.797 2.071 -5.073 -4.728 -0.675 -0.979 2.508 -1.350 -5.441 -2.892 -3.912 ML 16 14 6 19 6 1 1 46 97 -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 47 99 -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 43 94 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 53 105 -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 57 108 -0.520 -1.772 -9.341 -7.509 -8.615 0.000 0.000 0.000 0.000 [ MATP 4 ] 8 19 c g - - MP 21 20 6 25 6 2 2 24 43 -10.314 -10.253 -0.009 -9.030 -9.310 -9.705 -1.123 -2.498 -2.537 1.449 -2.517 -3.381 1.896 -0.637 -2.609 1.763 -3.173 -0.463 0.874 -2.670 -0.722 -0.255 ML 22 20 6 25 6 1 1 23 41 -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 23 41 -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 21 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 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 26 26 6 26 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 9 18 c g - - MP 27 26 6 31 6 2 2 22 41 -10.314 -10.253 -0.009 -9.030 -9.310 -9.705 0.919 -3.170 1.204 -0.127 -0.990 -3.992 2.027 -3.404 -3.221 -0.220 -3.773 1.605 0.254 -3.324 -1.076 -2.371 ML 28 26 6 31 6 1 1 22 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 40 -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 20 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 22 41 -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 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 10 17 G C - - MP 33 32 6 37 6 2 2 20 39 -10.314 -10.253 -0.009 -9.030 -9.310 -9.705 -5.181 -3.798 -5.078 -0.226 -5.754 -5.576 1.940 -5.520 -5.202 3.204 -5.517 0.289 -1.293 -4.962 -2.993 -3.977 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 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 11 16 C G - - MP 39 38 6 43 4 2 2 18 37 -9.095 -9.302 -0.012 -7.716 -6.787 -6.981 -6.176 -3.138 -4.564 -6.367 3.747 -5.462 -6.258 -3.062 -6.411 -5.197 0.415 -6.662 -0.304 -5.052 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 39 -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 38 -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 ] 12 - U - - - ML 45 44 6 47 3 1 1 15 33 -10.029 -0.005 -8.683 -4.968 -4.531 -5.791 1.966 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 ] 13 - A - - - ML 48 47 3 50 3 1 1 13 32 -10.029 -0.005 -8.683 1.199 0.524 -3.330 -2.575 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 ] 14 - A - - - ML 51 50 3 53 3 1 1 12 30 -10.029 -0.005 -8.683 1.977 -5.890 -5.301 -5.534 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 ] 15 - C - - - ML 54 53 3 56 2 1 1 1 1 * 0.000 -5.336 1.968 -5.826 -4.438 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 UMAC DESC UMAC tetraloop LENG 18 MAXL 80 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 16:41:03 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/UMAC/CM /share/data/people/ppg15/motifs/UMAC/SEED NSEQ 14 EFFN 13.962402 CKSUM 332001651 STATS LOCAL MSV -6.8217 0.78565 STATS LOCAL VITERBI -7.2454 0.78565 STATS LOCAL FORWARD -2.2569 0.78565 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.58323 1.18874 1.24924 1.59276 1.38629 1.38629 1.38629 1.38629 0.54354 0.89347 4.59769 0.71040 0.67618 0.00000 * 1 0.87849 0.79414 2.96041 2.51550 3 c - - < 1.38629 1.38629 1.38629 1.38629 0.02036 4.59769 4.59769 1.46634 0.26236 1.09861 0.40547 2 4.82781 0.04641 4.77067 3.54481 4 C - - < 1.38629 1.38629 1.38629 1.38629 0.50973 0.94350 4.59769 0.71129 0.67533 1.09861 0.40547 3 1.32524 1.32186 0.85058 3.20758 7 g - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 4 1.50542 1.24196 1.29424 1.53642 8 c - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 5 1.12088 1.22059 1.36741 2.08597 9 a - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 6 2.75785 1.41384 0.42717 3.19396 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 7 4.50272 0.17504 4.41292 1.98503 11 C - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 8 4.82625 4.52348 5.39663 0.02368 12 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 9 0.55562 1.02377 3.69103 3.16770 13 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 10 0.01613 5.46599 5.05778 5.21899 14 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 11 5.08253 0.02244 5.42206 4.45962 15 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 12 2.41843 4.54216 0.12062 4.27475 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 13 3.42969 0.54345 1.38397 1.99304 17 C - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 14 1.46238 2.62790 0.84235 1.32656 18 g - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 15 1.79545 1.43366 1.24665 1.17750 19 u - - > 1.38629 1.38629 1.38629 1.38629 0.28060 1.43341 5.08760 1.38760 0.28725 1.09861 0.40547 16 3.41620 3.04207 1.19128 0.48517 24 U - - > 1.38629 1.38629 1.38629 1.38629 0.02036 4.59769 4.59769 1.46634 0.26236 1.09861 0.40547 17 3.81864 4.92927 0.03945 4.65748 25 G - - > 1.38629 1.38629 1.38629 1.38629 0.02036 4.59769 4.59769 1.46634 0.26236 1.09861 0.40547 18 2.78676 3.19380 0.75749 0.84741 26 g - - > 1.38629 1.38629 1.38629 1.38629 0.53341 0.88334 * 0.71040 0.67618 0.00000 * //