INFERNAL1/a [1.1 | October 2013] NAME k-turn-2 DESC Kink turn, 5' bulge STATES 160 NODES 39 CLEN 52 W 351 ALPH RNA RF no CONS yes MAP yes DATE Fri May 30 14:50:14 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/k-turn-2/CM /share/data/people/ppg15/motifs/k-turn-2/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/k-turn-2/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 1010404883 NULL 0.000 0.000 0.000 0.000 GA 18.00 EFP7GF -2.9604 0.75302 ECMLC 0.66157 -4.48963 3.72108 1600000 274309 0.004375 ECMGC 0.49351 -8.89016 2.94245 1600000 137442 0.002910 ECMLI 0.70364 -1.81130 5.41808 1600000 194256 0.006177 ECMGI 0.54425 -6.15071 4.15998 1600000 109432 0.003655 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 351 717 -9.095 -9.302 -0.694 -1.401 IL 1 1 2 1 4 1 8 353 719 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 7 353 719 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 5 - u - - - ML 3 2 3 5 3 1 8 351 718 -9.368 -0.008 -8.022 -1.485 -2.056 0.656 0.869 D 4 2 3 5 3 0 3 346 712 -10.101 -3.206 -0.167 IL 5 5 3 5 3 1 7 352 718 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 6 - G - - - ML 6 5 3 8 3 1 7 350 717 -9.773 -0.082 -4.204 -1.320 -0.940 1.172 -0.278 D 7 5 3 8 3 0 2 346 712 -8.763 -1.919 -0.448 IL 8 8 3 8 3 1 7 351 717 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 98 - c - - MR 9 8 3 11 3 1 11 350 716 -9.854 -0.007 -8.171 0.001 0.334 -0.401 -0.027 D 10 8 3 11 3 0 2 344 710 -9.792 -2.852 -0.217 IR 11 11 3 11 3 1 7 350 716 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 97 - G - - MR 12 11 3 14 5 1 10 349 715 -8.595 -0.014 -8.411 -8.623 -9.514 0.620 -3.465 1.170 -3.041 D 13 11 3 14 5 0 2 343 709 -7.871 -1.807 -5.497 -6.928 -0.557 IR 14 14 3 14 5 1 7 349 715 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 7 96 u a - - MP 15 14 3 19 6 2 10 348 714 -10.078 -10.017 -0.011 -8.793 -9.073 -9.468 -4.524 -3.930 1.051 -0.315 -4.187 -5.310 0.142 -4.548 -4.565 2.351 -5.015 -1.674 2.559 -4.698 -1.846 -3.439 ML 16 14 3 19 6 1 5 345 711 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 17 14 3 19 6 1 4 345 711 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 18 14 3 19 6 0 1 340 706 -11.837 -10.536 -1.885 -7.015 -7.032 -0.488 IL 19 19 5 19 6 1 6 347 713 -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 6 347 713 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 8 95 c g - - MP 21 20 6 25 6 2 8 346 712 -10.153 -10.092 -0.010 -8.869 -9.149 -9.544 -3.737 -3.705 -3.840 1.133 -3.229 -4.671 1.801 -3.768 -3.820 0.094 -4.355 1.285 1.461 -4.002 1.719 -2.774 ML 22 20 6 25 6 1 5 344 710 -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 4 343 709 -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 1 337 703 -11.406 -10.105 -5.902 -6.584 -6.601 -0.057 IL 25 25 5 25 6 1 5 345 711 -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 6 345 711 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 9 94 C G - - MP 27 26 6 31 6 2 6 344 710 -10.153 -10.092 -0.010 -8.869 -9.149 -9.544 -4.576 -4.334 -4.581 1.101 -3.545 -5.393 3.010 -4.184 -4.478 0.743 -4.981 -1.998 1.525 -4.771 -1.059 -3.249 ML 28 26 6 31 6 1 4 342 708 -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 3 341 707 -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 1 337 703 -11.406 -10.105 -5.902 -6.584 -6.601 -0.057 IL 31 31 5 31 6 1 5 343 709 -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 5 343 709 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 10 93 u a - - MP 33 32 6 37 4 2 4 342 708 -8.870 -0.937 -2.360 -1.833 -4.581 -4.351 -4.585 0.606 -3.540 -5.394 2.432 -4.183 -4.481 0.608 -4.984 -2.018 2.659 -4.777 -1.056 -3.253 ML 34 32 6 37 4 1 4 341 707 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 4 1 2 339 705 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 36 32 6 37 4 0 0 337 703 -6.848 -6.529 -4.545 -0.093 IL 37 37 5 37 4 1 5 342 708 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 38 38 6 38 3 1 6 341 707 -3.835 -0.122 -6.535 0.000 0.000 0.000 0.000 [ MATL 9 ] 11 - c - - - ML 39 38 6 41 3 1 5 340 706 -9.355 -0.008 -8.009 -0.352 0.466 0.098 -0.387 D 40 38 6 41 3 0 0 337 703 -10.122 -5.635 -0.031 IL 41 41 3 41 3 1 4 341 707 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 12 - G - - - ML 42 41 3 44 3 1 5 339 705 -9.355 -0.008 -8.009 -0.143 -2.410 1.307 -1.214 D 43 41 3 44 3 0 0 337 703 -10.122 -2.966 -0.199 IL 44 44 3 44 3 1 4 340 706 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 13 - A - - - ML 45 44 3 47 3 1 4 338 704 -9.779 -0.101 -3.914 1.237 -2.086 -2.240 0.257 D 46 44 3 47 3 0 0 336 702 -8.753 -1.298 -0.759 IL 47 47 3 47 3 1 4 339 705 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 91 - u - - MR 48 47 3 50 3 1 4 337 703 -9.944 -0.095 -4.003 -0.309 0.479 -2.214 0.664 D 49 47 3 50 3 0 0 335 701 -9.568 -2.380 -0.310 IR 50 50 3 50 3 1 4 338 704 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 90 - a - - MR 51 50 3 53 5 1 4 336 702 -8.613 -0.014 -8.428 -8.640 -9.532 0.719 -1.635 -0.559 0.436 D 52 50 3 53 5 0 0 335 701 -7.827 -0.104 -5.453 -6.884 -4.878 IR 53 53 3 53 5 1 1 336 702 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 14 89 g u - - MP 54 53 3 58 6 2 5 335 701 -10.314 -10.253 -0.009 -9.030 -9.310 -9.705 -4.374 -4.041 -4.412 -0.253 -3.697 -5.186 1.614 -4.243 -4.387 1.448 -4.872 2.195 1.422 -4.544 0.651 -3.223 ML 55 53 3 58 6 1 1 333 699 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 56 53 3 58 6 1 1 333 699 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 57 53 3 58 6 0 0 329 695 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 334 700 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 59 59 6 59 5 1 1 334 700 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 15 88 C G - - MP 60 59 6 64 6 2 4 333 699 -10.314 -10.253 -0.009 -9.030 -9.310 -9.705 -5.789 -5.283 -5.532 -1.519 -4.456 -0.153 3.010 -5.163 -5.584 2.458 -5.886 -3.069 -0.738 -5.741 -2.066 -4.372 ML 61 59 6 64 6 1 1 332 698 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 6 1 1 331 697 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 63 59 6 64 6 0 0 328 694 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 6 1 1 333 699 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 65 65 6 65 5 1 1 332 698 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 16 87 C G - - MP 66 65 6 70 4 2 3 331 698 -9.095 -2.380 -0.320 -7.716 -5.918 -5.762 -5.646 -1.728 -4.284 -6.132 3.430 -5.065 -5.618 1.477 -5.953 -3.508 0.610 -5.979 -1.880 -4.381 ML 67 65 6 70 4 1 1 330 696 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 68 65 6 70 4 1 1 329 695 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 69 65 6 70 4 0 0 328 694 -4.568 -4.250 -2.265 -0.520 IL 70 70 5 70 4 1 1 331 697 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 71 71 6 71 3 1 1 329 695 -2.937 -1.268 -1.139 0.000 0.000 0.000 0.000 [ MATL 17 ] 17 - c - - - ML 72 71 6 74 3 1 2 330 696 -9.835 -0.006 -8.489 -0.028 0.366 -0.544 0.064 D 73 71 6 74 3 0 0 327 693 -8.728 -4.241 -0.082 IL 74 74 3 74 3 1 1 330 696 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 18 - u - - - ML 75 74 3 77 3 1 1 329 695 -9.835 -0.111 -3.778 0.076 -1.754 -0.146 0.804 D 76 74 3 77 3 0 0 326 693 -8.728 -4.241 -0.082 IL 77 77 3 77 3 1 1 329 695 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 19 - a - - - ML 78 77 3 80 3 1 1 328 694 -9.730 -0.006 -8.384 0.378 -0.325 -0.588 0.307 D 79 77 3 80 3 0 0 326 692 -9.217 -0.126 -3.609 IL 80 80 3 80 3 1 1 328 694 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 20 - G - - - ML 81 80 3 83 3 1 1 327 693 -10.029 -0.005 -8.683 -4.745 -6.356 1.974 -5.481 D 82 80 3 83 3 0 0 324 690 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 327 693 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 21 - A - - - ML 84 83 3 86 3 1 1 326 692 -1.744 -0.517 -8.683 1.977 -5.890 -5.301 -5.534 D 85 83 3 86 3 0 0 323 689 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 326 692 -2.219 -0.372 -6.307 0.000 0.000 0.000 0.000 [ MATL 22 ] 24 - A - - - ML 87 86 3 89 3 1 1 324 690 -10.346 -0.005 -8.663 1.866 -4.476 -1.951 -4.322 D 88 86 3 89 3 0 0 322 688 -5.620 -0.734 -1.403 IL 89 89 3 89 3 1 1 324 690 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 85 - A - - MR 90 89 3 92 3 1 1 323 689 -10.346 -0.005 -8.663 1.977 -5.890 -5.301 -5.534 D 91 89 3 92 3 0 0 321 687 -6.390 -1.568 -0.620 IR 92 92 3 92 3 1 1 323 690 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 84 - G - - MR 93 92 3 95 3 1 1 322 688 -10.346 -0.005 -8.663 -4.745 -6.356 1.974 -5.481 D 94 92 3 95 3 0 0 320 686 -6.390 -1.568 -0.620 IR 95 95 3 95 3 1 1 322 689 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 83 - G - - MR 96 95 3 98 5 1 1 321 687 -9.011 -0.010 -8.826 -9.039 -9.930 -2.601 0.326 1.290 -2.884 D 97 95 3 98 5 0 0 319 685 -5.352 -0.707 -2.978 -4.409 -2.404 IR 98 98 3 98 5 1 1 321 687 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 25 82 g u - - MP 99 98 3 103 6 2 2 320 686 -10.314 -10.253 -0.071 -9.030 -9.310 -4.543 -5.070 -3.721 -4.987 1.365 -6.220 -5.867 -0.080 -5.489 -5.163 2.539 -5.542 2.560 -1.593 -5.058 -3.347 -3.861 ML 100 98 3 103 6 1 1 318 684 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 101 98 3 103 6 1 1 318 684 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 102 98 3 103 6 0 0 315 681 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 103 103 5 103 6 1 1 320 686 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 104 104 6 104 5 1 1 319 685 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 26 81 C G - - MP 105 104 6 109 6 2 2 318 685 -10.253 -10.192 -0.010 -8.968 -9.248 -9.643 -5.431 -5.222 -5.276 -1.147 -4.018 -5.888 3.238 -4.750 -5.210 1.461 -5.614 -2.905 1.360 -5.545 -1.573 -3.964 ML 106 104 6 109 6 1 1 316 682 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 107 104 6 109 6 1 1 317 683 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 108 104 6 109 6 0 0 314 680 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 109 109 5 109 6 1 1 318 684 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 110 110 6 110 5 1 1 317 684 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 28 ] 27 80 c g - - MP 111 110 6 115 6 2 2 316 683 -10.253 -10.192 -0.010 -8.968 -9.248 -9.643 -4.997 -4.796 -4.942 0.988 -3.835 -5.663 2.977 -4.513 -4.862 0.319 -5.323 -2.503 0.203 -5.170 1.662 -3.646 ML 112 110 6 115 6 1 1 314 680 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 113 110 6 115 6 1 1 315 681 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 114 110 6 115 6 0 0 314 680 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 115 115 5 115 6 1 1 316 682 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 116 116 6 116 5 1 1 316 682 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 28 79 G C - - MP 117 116 6 121 6 2 2 314 681 -10.253 -10.192 -0.010 -8.968 -9.248 -9.643 -4.453 -3.205 -4.306 0.978 -5.095 -4.929 0.994 -4.881 -4.679 3.036 -4.966 0.509 -0.604 -4.194 0.295 -3.262 ML 118 116 6 121 6 1 1 312 678 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 119 116 6 121 6 1 1 314 680 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 120 116 6 121 6 0 0 314 680 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 121 121 5 121 6 1 1 314 680 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 122 122 6 122 5 1 1 314 680 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 29 78 G C - - MP 123 122 6 127 6 2 2 312 679 -10.253 -10.192 -0.010 -8.968 -9.248 -9.643 -4.475 -3.240 -4.327 0.390 -5.024 -4.948 0.368 -4.868 -4.691 3.030 -4.980 1.202 0.638 -4.219 -0.240 -3.275 ML 124 122 6 127 6 1 1 310 676 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 125 122 6 127 6 1 1 313 679 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 126 122 6 127 6 0 0 314 680 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 127 127 5 127 6 1 1 312 678 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 128 128 6 128 5 1 1 312 678 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 30 77 c g - - MP 129 128 6 133 6 2 2 310 677 -10.253 -10.192 -0.074 -8.968 -4.465 -9.643 -0.471 -2.412 -0.354 0.942 -2.464 -3.302 1.445 -2.810 1.108 1.381 -3.097 0.805 0.609 -2.590 -0.695 -1.712 ML 130 128 6 133 6 1 1 306 672 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 131 128 6 133 6 1 1 313 679 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 132 128 6 133 6 0 0 314 680 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 133 133 5 133 6 1 1 310 676 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 134 134 6 134 5 1 1 310 676 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 32 ] 31 76 c g - - MP 135 134 6 139 6 2 2 308 674 -10.188 -10.128 -0.010 -8.904 -9.184 -9.579 -4.936 -4.331 -4.928 2.266 -4.266 -5.830 2.786 -4.710 -4.851 1.307 -5.338 -1.920 -0.189 -5.198 -1.806 -3.670 ML 136 134 6 139 6 1 1 298 664 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 137 134 6 139 6 1 1 314 680 -8.068 -6.797 -2.706 -6.776 -0.334 -4.989 -0.623 -1.662 1.352 -1.051 D 138 134 6 139 6 0 0 315 681 -10.443 -9.142 -4.939 -5.621 -5.638 -0.113 IL 139 139 5 139 6 1 1 308 674 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 140 140 6 140 5 1 1 308 674 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 33 ] 32 75 c g - - MP 141 140 6 145 4 2 2 306 672 -1.492 -9.127 -0.650 -7.541 -4.400 -4.364 -4.426 -0.618 -0.770 -5.171 2.237 -4.206 -4.399 -0.473 -4.887 1.775 1.118 -4.626 1.717 -3.303 ML 142 140 6 145 4 1 1 274 640 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 143 140 6 145 4 1 1 315 681 -0.791 -5.030 -2.898 -1.959 -0.623 -1.662 1.352 -1.051 D 144 140 6 145 4 0 0 315 681 -0.689 -5.584 -3.600 -1.855 IL 145 145 5 145 4 1 1 325 691 -0.073 -9.883 -4.511 -7.907 0.000 0.000 0.000 0.000 IR 146 146 6 146 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 71 - g - - - ML 147 146 6 149 3 1 1 15 33 -9.975 -0.005 -8.629 -1.474 0.022 0.627 0.112 D 148 146 6 149 3 0 0 15 33 -7.452 -0.482 -1.844 IL 149 149 3 149 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 35 ] 72 - a - - - ML 150 149 3 152 3 1 1 13 32 -10.029 -0.005 -8.683 0.514 -0.657 -0.841 0.464 D 151 149 3 152 3 0 0 15 33 -6.174 -1.687 -0.566 IL 152 152 3 152 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 73 - g - - - ML 153 152 3 155 3 1 1 12 30 -10.029 -0.005 -8.683 0.165 -0.721 0.580 -0.364 D 154 152 3 155 3 0 0 13 32 -6.174 -1.687 -0.566 IL 155 155 3 155 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 74 - a - - - ML 156 155 3 158 2 1 1 1 1 * 0.000 0.667 -0.082 -0.202 -0.742 D 157 155 3 158 2 0 0 0 0 * 0.000 IL 158 158 3 158 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 38 ] - - - - - - E 159 158 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME k-turn-2 DESC Kink turn, 5' bulge LENG 52 MAXL 457 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri May 30 14:50:14 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/k-turn-2/CM /share/data/people/ppg15/motifs/k-turn-2/SEED NSEQ 14 EFFN 14.000000 CKSUM 1010404883 STATS LOCAL MSV -8.6997 0.75302 STATS LOCAL VITERBI -9.7110 0.75302 STATS LOCAL FORWARD -2.4386 0.75302 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.47467 1.47409 1.11565 1.53965 1.38629 1.38629 1.38629 1.38629 0.25386 1.54178 4.58526 1.38872 0.28687 0.00000 * 1 2.41542 2.81144 0.93193 0.78360 5 u - - : 1.38629 1.38629 1.38629 1.38629 0.01947 4.64165 4.64165 1.46634 0.26236 1.09861 0.40547 2 2.30152 2.03774 0.57378 1.57902 6 G - - : 1.38629 1.38629 1.38629 1.38629 0.01848 4.69320 4.69320 1.46634 0.26236 1.09861 0.40547 3 1.67214 2.55456 1.07367 0.93477 7 u - - < 1.38629 1.38629 1.38629 1.38629 0.01553 4.86598 4.86598 1.46634 0.26236 1.09861 0.40547 4 1.88158 1.46433 1.48519 0.94172 8 u - - < 1.38629 1.38629 1.38629 1.38629 0.01444 4.93823 4.93823 1.46634 0.26236 1.09861 0.40547 5 1.93931 0.67063 2.07329 1.51849 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.01444 4.93823 4.93823 1.46634 0.26236 1.09861 0.40547 6 2.25309 1.06007 2.15181 0.83882 10 u - - < 1.38629 1.38629 1.38629 1.38629 0.32498 4.93823 1.30826 1.46634 0.26236 1.09861 0.40547 7 1.63019 1.06337 1.31811 1.65455 11 c - - - 1.38629 1.38629 1.38629 1.38629 0.01964 4.63289 4.63289 1.46634 0.26236 3.68164 0.02550 8 1.48534 3.05655 0.48008 2.22756 12 G - - - 1.38629 1.38629 1.38629 1.38629 0.01964 4.63289 4.63289 1.46634 0.26236 3.68164 0.02550 9 0.52857 2.83233 2.93923 1.20807 13 A - - - 1.38629 1.38629 1.38629 1.38629 0.01841 4.69718 4.69718 1.46634 0.26236 0.05168 2.98849 10 2.74544 1.60411 0.77681 1.29156 14 g - - < 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 11 3.58280 0.57630 1.04331 2.84832 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 3.72860 0.39039 1.70405 2.14359 16 C - - < 1.38629 1.38629 1.38629 1.38629 0.14580 5.08760 2.04411 1.46634 0.26236 1.09861 0.40547 13 1.40593 1.13289 1.76341 1.34208 17 c - - - 1.38629 1.38629 1.38629 1.38629 0.01418 4.95598 4.95598 1.46634 0.26236 3.13455 0.04449 14 1.33330 2.60203 1.48771 0.82924 18 u - - - 1.38629 1.38629 1.38629 1.38629 0.08616 4.95598 2.58346 1.46634 0.26236 3.13455 0.04449 15 1.12433 1.61163 1.79388 1.17359 19 a - - - 1.38629 1.38629 1.38629 1.38629 0.01523 4.88505 4.88505 1.46634 0.26236 0.06311 2.79431 16 4.67556 5.79226 0.01813 5.18575 20 G - - - 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 17 0.01608 5.46922 5.06084 5.22189 21 A - - - 1.38629 1.38629 1.38629 1.38629 0.36202 1.21215 5.08760 0.21934 1.62479 1.09861 0.40547 18 0.09254 4.48848 2.73885 4.38198 24 A - - - 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 19 1.77157 2.76686 0.31022 3.38758 25 G - - < 1.38629 1.38629 1.38629 1.38629 0.06951 5.08760 2.79727 1.46634 0.26236 1.09861 0.40547 20 3.37847 0.51882 1.69541 1.67583 26 C - - < 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 21 2.03148 0.69510 2.37139 1.28561 27 c - - < 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 22 1.98796 2.03378 0.50467 2.05196 28 G - - < 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 23 2.34566 2.43746 0.42127 1.82871 29 G - - < 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 24 1.48543 1.62577 0.88466 1.80801 30 g - - < 1.38629 1.38629 1.38629 1.38629 0.07390 5.03123 2.73798 1.46634 0.26236 2.47471 0.08794 25 1.17779 0.82920 1.74205 2.51972 31 c - - < 1.38629 1.38629 1.38629 1.38629 0.01397 4.97130 4.97130 1.46634 0.26236 0.10117 2.34110 26 2.96770 1.09244 1.33279 1.05142 32 u - - < 1.38629 1.38629 1.38629 1.38629 0.40447 1.11933 5.08760 3.31259 0.03710 1.09861 0.40547 27 2.40802 1.37109 0.95183 1.30880 71 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 28 1.02977 1.84150 1.96912 1.06493 72 a - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 29 1.27163 1.88576 0.98445 1.63853 73 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 30 0.92379 1.44314 1.52624 1.90080 74 a - - _ 1.38629 1.38629 1.38629 1.38629 0.06951 5.08760 2.79727 1.46634 0.26236 1.09861 0.40547 31 1.72844 2.92930 0.67212 1.35333 75 G - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 32 2.69992 1.85440 0.77258 1.15702 76 g - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 33 1.24947 1.65418 1.32886 1.35745 77 a - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 34 2.24750 0.65264 1.97218 1.45023 78 C - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 35 3.00176 0.64823 1.57801 1.50984 79 C - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 36 2.50629 2.48054 0.36893 1.94309 80 G - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 2.47471 0.08794 37 1.78380 1.73617 0.49076 3.13163 81 G - - > 1.38629 1.38629 1.38629 1.38629 0.01315 5.03123 5.03123 1.46634 0.26236 0.18437 1.78156 38 3.65434 0.99293 2.67427 0.62610 82 U - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 39 3.18891 1.16000 0.49197 3.38508 83 G - - - 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 40 4.67556 5.79226 0.01813 5.18575 84 G - - - 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 41 0.01608 5.46922 5.06084 5.22189 85 A - - - 1.38629 1.38629 1.38629 1.38629 0.21778 1.66325 5.08760 0.06391 2.78200 1.09861 0.40547 42 2.28295 1.73128 0.37022 3.49409 87 G - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 43 3.12229 0.91296 0.65486 3.34976 88 G - - > 1.38629 1.38629 1.38629 1.38629 0.01242 5.08760 5.08760 1.46634 0.26236 1.09861 0.40547 44 1.72121 1.72175 1.22359 1.05491 89 u - - > 1.38629 1.38629 1.38629 1.38629 0.19520 4.98599 1.76905 1.46634 0.26236 1.09861 0.40547 45 0.88798 2.51948 1.77362 1.08383 90 a - - - 1.38629 1.38629 1.38629 1.38629 0.01746 4.74988 4.74988 1.46634 0.26236 1.18766 0.36375 46 1.60082 1.05456 2.92075 0.92627 91 u - - - 1.38629 1.38629 1.38629 1.38629 0.87218 0.55544 4.81047 0.02815 3.58433 0.10686 2.28916 47 0.90437 2.27547 0.99195 2.10702 93 a - - > 1.38629 1.38629 1.38629 1.38629 0.01444 4.93823 4.93823 1.46634 0.26236 1.09861 0.40547 48 1.65287 2.18904 0.62357 1.82977 94 G - - > 1.38629 1.38629 1.38629 1.38629 0.01444 4.93823 4.93823 1.46634 0.26236 1.09861 0.40547 49 1.66745 2.54412 0.84446 1.19422 95 g - - > 1.38629 1.38629 1.38629 1.38629 0.01553 4.86598 4.86598 1.46634 0.26236 1.09861 0.40547 50 0.97596 1.12037 1.52416 2.53567 96 a - - > 1.38629 1.38629 1.38629 1.38629 0.01668 4.79489 4.79489 1.46634 0.26236 1.09861 0.40547 51 0.95634 3.78801 0.57502 3.49431 97 G - - : 1.38629 1.38629 1.38629 1.38629 0.01748 4.74844 4.74844 1.46634 0.26236 1.09861 0.40547 52 1.38579 1.15458 1.66426 1.40506 98 c - - : 1.38629 1.38629 1.38629 1.38629 0.68830 0.69801 * 1.86987 0.16741 0.00000 * //