INFERNAL1/a [1.1 | October 2013] NAME twist_up STATES 67 NODES 18 CLEN 21 W 34 ALPH RNA RF no CONS yes MAP yes DATE Mon Jun 2 18:14:39 2014 COM [1] cmbuild -F CM SEED COM [2] cmcalibrate 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 893920814 NULL 0.000 0.000 0.000 0.000 GA 19.00 EFP7GF -5.1213 0.76707 ECMLC 0.65578 -4.46762 4.81782 1600000 529307 0.002267 ECMGC 0.44060 -10.79449 4.06678 1600000 279093 0.001433 ECMLI 0.70130 -2.57370 5.88587 1600000 452620 0.002651 ECMGI 0.47055 -9.11382 4.62863 1600000 257293 0.001555 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 34 53 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 IL 1 1 2 1 6 1 1 36 55 -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 35 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 1 21 C G - - MP 3 2 3 7 6 2 3 34 53 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -7.711 -7.873 -6.752 -4.112 -5.106 -6.752 3.948 -6.386 -7.185 -4.086 -6.790 -6.091 -2.188 -7.607 -3.187 -5.989 ML 4 2 3 7 6 1 1 33 52 -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 33 51 -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 30 49 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 7 7 5 7 6 1 1 34 53 -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 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 2 20 C G - - MP 9 8 6 13 6 2 3 32 51 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -4.857 -4.626 -4.748 -0.602 -3.587 -5.404 3.133 -4.288 -4.687 1.584 -5.114 -2.329 1.299 -4.989 -1.143 -3.456 ML 10 8 6 13 6 1 1 31 50 -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 31 50 -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 29 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 6 1 1 32 51 -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 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 3 19 G C - - MP 15 14 6 19 6 2 3 30 49 -9.928 -9.867 -0.012 -8.644 -8.924 -9.319 -4.630 -3.225 -4.498 1.223 -5.434 -4.982 0.667 -5.077 -4.733 3.369 -5.012 -0.865 -0.869 -4.337 -2.592 -3.437 ML 16 14 6 19 6 1 1 30 49 -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 30 49 -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 28 47 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 30 49 -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 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 4 18 a u - - MP 21 20 6 25 4 2 2 28 47 -8.537 -8.744 -0.192 -3.066 -4.440 -3.638 -4.490 2.845 -4.516 -5.538 -0.112 -4.585 -4.453 1.518 -4.963 -1.232 1.957 -4.766 -2.117 -3.344 ML 22 20 6 25 4 1 1 30 48 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 4 1 1 29 48 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 24 20 6 25 4 0 0 28 47 -4.568 -4.250 -2.265 -0.520 IL 25 25 5 25 4 1 1 31 50 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 26 26 6 26 3 1 1 30 49 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - U - - - ML 27 26 6 29 3 1 1 26 44 -9.315 -0.008 -7.969 -0.705 -0.021 -2.186 1.125 D 28 26 6 29 3 0 0 25 43 -8.138 -0.281 -2.530 IL 29 29 3 29 3 1 1 29 48 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - C - - - ML 30 29 3 32 3 1 1 25 43 -9.483 -0.007 -8.137 -3.203 1.713 -4.108 -0.852 D 31 29 3 32 3 0 0 24 43 -6.174 -1.687 -0.566 IL 32 32 3 32 3 1 1 28 47 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - C - - - ML 33 32 3 35 3 1 1 23 42 -9.810 -0.007 -8.128 -2.431 1.250 -3.425 0.425 D 34 32 3 35 3 0 0 22 41 -5.620 -0.734 -1.403 IL 35 35 3 35 3 1 1 24 43 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 17 - C - - MR 36 35 3 38 3 1 1 22 41 -9.810 -0.007 -8.128 -4.701 1.950 -5.271 -3.778 D 37 35 3 38 3 0 0 21 40 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 23 42 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 16 - A - - MR 39 38 3 41 3 1 1 21 40 -9.810 -0.007 -8.128 1.529 -2.462 -2.612 -0.378 D 40 38 3 41 3 0 0 20 39 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 22 41 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 15 - A - - MR 42 41 3 44 5 1 1 20 39 -8.487 -0.015 -8.302 -8.514 -9.406 1.961 -5.109 -4.553 -4.815 D 43 41 3 44 5 0 0 20 39 -5.352 -0.707 -2.978 -4.409 -2.404 IR 44 44 3 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 11 ] 8 14 C G - - MP 45 44 3 49 4 2 2 19 38 -8.537 -8.744 -0.017 -7.158 -7.711 -7.873 -6.752 -4.112 -5.106 -6.752 3.948 -6.386 -7.185 -4.086 -6.790 -6.091 -2.188 -7.607 -3.187 -5.989 ML 46 44 3 49 4 1 1 21 40 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 47 44 3 49 4 1 1 21 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 48 44 3 49 4 0 0 20 38 -4.568 -4.250 -2.265 -0.520 IL 49 49 5 49 4 1 1 23 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 50 50 6 50 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 9 - A - - - ML 51 50 6 53 3 1 1 16 35 -9.483 -0.007 -8.137 1.369 -3.420 0.269 -3.069 D 52 50 6 53 3 0 0 17 35 -6.174 -1.687 -0.566 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 13 ] 10 - U - - - ML 54 53 3 56 3 1 1 15 34 -9.483 -0.464 -1.870 -4.138 -3.769 -4.938 1.940 D 55 53 3 56 3 0 0 15 34 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 11 - u - - - ML 57 56 3 59 3 1 1 14 32 -9.029 -0.010 -7.683 -0.764 0.161 0.014 0.359 D 58 56 3 59 3 0 0 13 31 -9.201 -0.127 -3.593 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 15 ] 12 - C - - - ML 60 59 3 62 3 1 1 12 30 -9.483 -0.007 -8.137 -3.210 1.716 -4.113 -0.863 D 61 59 3 62 3 0 0 13 32 -6.174 -1.687 -0.566 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 16 ] 13 - C - - - ML 63 62 3 65 2 1 1 1 1 * 0.000 -1.038 1.445 -3.008 -0.586 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 17 ] - - - - - - E 66 65 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME twist_up LENG 21 MAXL 81 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jun 2 18:14:39 2014 COM [1] cmbuild -F CM SEED NSEQ 9 EFFN 7.642090 CKSUM 893920814 STATS LOCAL MSV -6.9813 0.76707 STATS LOCAL VITERBI -7.1411 0.76707 STATS LOCAL FORWARD -2.6062 0.76707 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.62700 0.95566 1.51063 1.61870 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 0.00000 * 1 4.95268 0.04435 4.84223 3.56042 1 C - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 2 2.86375 0.61837 1.58742 1.61108 2 C - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 3 1.82355 2.24479 0.39761 2.80226 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 0.83949 2.50398 1.49808 1.33654 4 a - - < 1.38629 1.38629 1.38629 1.38629 0.13253 4.71850 2.16115 1.46634 0.26236 1.09861 0.40547 5 1.83429 1.40880 2.78991 0.62659 5 U - - - 1.38629 1.38629 1.38629 1.38629 0.02018 4.60615 4.60615 1.46634 0.26236 0.14412 2.00832 6 3.43270 0.21359 4.06434 1.94597 6 C - - - 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 7 2.90943 0.54012 3.58276 1.09358 7 C - - - 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 8 4.85071 0.04627 4.77990 3.54047 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 9 0.45263 3.54069 1.21421 3.26722 9 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 10 4.05132 3.81356 4.60155 0.05077 10 U - - _ 1.38629 1.38629 1.38629 1.38629 0.32813 4.71850 1.30637 1.46634 0.26236 1.09861 0.40547 11 1.84506 1.29660 1.39583 1.13663 11 u - - _ 1.38629 1.38629 1.38629 1.38629 0.02449 4.41486 4.41486 1.46634 0.26236 0.06386 2.78284 12 3.43764 0.21206 4.06836 1.95309 12 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 13 2.07083 0.40800 3.33139 1.75334 13 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 14 3.83005 4.95942 0.03865 4.69036 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 15 0.03321 4.72314 4.34552 4.52691 15 A - - - 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 16 0.34822 2.94748 3.04057 1.64104 16 A - - - 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 17 4.46629 0.04172 4.89111 3.82300 17 C - - - 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 18 1.40615 1.61823 2.32848 0.77822 18 u - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 19 3.06664 0.44162 2.14632 1.64241 19 C - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 20 1.76852 1.65039 0.57210 2.61592 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.01802 4.71850 4.71850 1.46634 0.26236 1.09861 0.40547 21 3.85169 5.00086 0.03745 4.73464 21 G - - > 1.38629 1.38629 1.38629 1.38629 0.00905 4.70953 * 1.46634 0.26236 0.00000 * //