INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR4 ACC RF01317 DESC CRISPR RNA direct repeat element STATES 88 NODES 25 CLEN 28 W 40 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 12:12:47 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01317/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 33 EFFN 33.000000 CKSUM 2839651052 NULL 0.000 0.000 0.000 0.000 GA 35.00 TC 35.00 NC 34.90 EFP7GF -13.3930 0.72986 ECMLC 0.70113 -4.25190 4.81171 1600000 690295 0.001738 ECMGC 0.54544 -13.83552 -0.64421 1600000 533144 0.000750 ECMLI 0.70862 -3.09750 5.60086 1600000 570316 0.002104 ECMGI 0.56135 -12.38754 0.25379 1600000 482977 0.000828 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 40 58 -10.244 -10.451 -0.005 -8.865 IL 1 1 2 1 4 1 1 46 65 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 45 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - G - - - ML 3 2 3 5 3 1 2 40 58 -11.165 -0.002 -9.819 -1.434 -1.317 1.658 -3.789 D 4 2 3 5 3 0 0 40 58 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 44 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - U - - - ML 6 5 3 8 3 1 1 39 57 -11.165 -0.002 -9.819 -6.836 -6.192 -7.760 1.990 D 7 5 3 8 3 0 0 39 57 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 43 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - U - - - ML 9 8 3 11 3 1 1 38 56 -11.165 -0.002 -9.819 -4.332 -4.178 -1.920 1.860 D 10 8 3 11 3 0 0 38 56 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 42 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - C - - - ML 12 11 3 14 3 1 1 36 55 -11.165 -0.002 -9.819 -2.103 1.764 -5.085 -1.546 D 13 11 3 14 3 0 0 37 55 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 41 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - A - - - ML 15 14 3 17 3 1 1 35 54 -11.469 -0.002 -9.786 1.797 -2.286 -2.584 -2.708 D 16 14 3 17 3 0 0 34 53 -5.620 -0.734 -1.403 IL 17 17 3 17 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 28 - A - - MR 18 17 3 20 3 1 1 34 53 -11.469 -0.002 -9.786 1.682 -4.143 -1.736 -1.203 D 19 17 3 20 3 0 0 33 51 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 27 - A - - MR 21 20 3 23 3 1 1 33 52 -11.469 -0.002 -9.786 1.802 -4.303 -2.757 -1.669 D 22 20 3 23 3 0 0 32 50 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 26 - A - - MR 24 23 3 26 3 1 1 32 51 -11.469 -0.002 -9.786 1.865 -5.710 -1.662 -5.570 D 25 23 3 26 3 0 0 31 49 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 25 - G - - MR 27 26 3 29 3 1 1 31 50 -11.469 -0.002 -9.786 -2.051 -1.992 1.732 -2.440 D 28 26 3 29 3 0 0 30 48 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 24 - A - - MR 30 29 3 32 3 1 1 30 49 -11.469 -0.002 -9.786 1.908 -5.330 -5.455 -2.322 D 31 29 3 32 3 0 0 29 47 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 23 - U - - MR 33 32 3 35 3 1 1 29 48 -11.469 -0.002 -9.786 -0.953 -1.102 -4.441 1.571 D 34 32 3 35 3 0 0 28 46 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 22 - U - - MR 36 35 3 38 3 1 1 28 47 -11.469 -0.002 -9.786 -1.848 -1.943 -4.787 1.776 D 37 35 3 38 3 0 0 27 45 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 21 - C - - MR 39 38 3 41 5 1 1 27 46 -10.120 -0.005 -9.936 -10.148 -11.039 -5.411 1.784 -6.166 -0.948 D 40 38 3 41 5 0 0 26 45 -5.352 -0.707 -2.978 -4.409 -2.404 IR 41 41 3 41 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 6 20 C G - - MP 42 41 3 46 6 2 2 26 45 -11.234 -11.173 -0.005 -9.950 -10.230 -10.625 -10.468 -10.703 -8.109 -7.207 -6.375 -7.735 3.992 -9.311 -10.131 -7.145 -7.767 -9.224 -5.132 -10.463 -6.111 -8.924 ML 43 41 3 46 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 3 46 6 1 1 25 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 3 46 6 0 0 23 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 26 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 7 19 U A - - MP 48 47 6 52 6 2 2 24 43 -11.234 -11.173 -0.005 -9.950 -10.230 -10.625 -8.070 -8.332 -7.393 -4.567 -5.749 -7.543 1.008 -6.661 -7.494 -4.541 -7.617 -6.702 3.779 -7.910 -3.451 -6.297 ML 49 47 6 52 6 1 1 23 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 51 47 6 52 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 24 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 8 18 G C - - MP 54 53 6 58 6 2 2 22 41 -11.234 -11.173 -0.005 -9.950 -10.230 -10.625 -8.794 -5.787 -10.084 -0.236 -10.525 -7.070 -5.022 -9.933 -7.132 3.903 -7.366 -3.650 -5.342 -7.478 -7.383 -8.866 ML 55 53 6 58 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 56 53 6 58 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 57 53 6 58 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 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 59 59 6 59 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 9 17 C G - - MP 60 59 6 64 6 2 2 20 39 -11.234 -11.173 -0.005 -9.950 -10.230 -10.625 -8.078 -8.354 -7.396 -4.590 -5.748 -7.542 3.894 -6.664 -7.500 -4.563 -7.620 -6.748 -2.481 -7.914 -0.347 -6.302 ML 61 59 6 64 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 62 59 6 64 6 1 1 22 40 -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 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 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 65 65 6 65 5 1 1 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 10 16 C G - - MP 66 65 6 70 4 2 2 18 37 -10.244 -10.451 -0.005 -8.865 -8.061 -8.331 -7.387 -4.557 -5.742 -7.537 3.785 -6.655 -7.488 -4.522 -7.612 -6.708 -0.135 -7.900 0.183 -6.289 ML 67 65 6 70 4 1 1 21 40 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 68 65 6 70 4 1 1 21 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 69 65 6 70 4 0 0 20 38 -4.568 -4.250 -2.265 -0.520 IL 70 70 5 70 4 1 1 23 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 71 71 6 71 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 11 - G - - - ML 72 71 6 74 3 1 1 15 34 -11.165 -0.002 -9.819 -2.357 -6.833 1.919 -6.077 D 73 71 6 74 3 0 0 17 35 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 12 - c - - - ML 75 74 3 77 3 1 1 14 32 -11.165 -0.002 -9.819 -0.829 0.675 -1.521 0.577 D 76 74 3 77 3 0 0 16 34 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 13 - A - - - ML 78 77 3 80 3 1 1 13 31 -11.165 -0.002 -9.819 1.836 -5.639 -1.366 -5.515 D 79 77 3 80 3 0 0 15 33 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 14 - C - - - ML 81 80 3 83 3 1 1 11 29 -11.165 -0.002 -9.819 -4.713 1.395 -5.785 0.394 D 82 80 3 83 3 0 0 13 32 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 15 - A - - - ML 84 83 3 86 2 1 1 1 1 * 0.000 1.991 -7.278 -6.595 -6.755 D 85 83 3 86 2 0 0 0 0 * 0.000 IL 86 86 3 86 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 24 ] - - - - - - E 87 86 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR4 ACC RF01317 DESC CRISPR RNA direct repeat element LENG 28 MAXL 83 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 12:12:47 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01317/CM NSEQ 33 EFFN 32.786499 CKSUM 2839651052 STATS LOCAL MSV -6.3904 0.72986 STATS LOCAL VITERBI -6.4929 0.72986 STATS LOCAL FORWARD -3.4739 0.72986 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.26553 1.37369 1.37407 1.55275 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 0.00000 * 1 2.37926 2.29964 0.23712 4.00711 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 2 6.11434 5.66945 6.75374 0.00685 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 3 4.38296 4.27576 2.71730 0.09700 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 4 2.84374 0.16408 4.90525 2.45679 4 C - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 5 0.14084 2.96989 3.17659 3.26134 5 A - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 6 6.71827 0.00572 6.71303 5.72099 6 C - - < 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 7 5.50832 2.05562 5.43157 0.14669 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 8 2.90116 5.84056 0.06277 5.81894 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 9 5.48915 0.07308 5.42611 2.78153 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 10 5.46423 0.14860 5.39896 2.04541 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 11 3.02045 6.11406 0.05628 5.59070 11 G - - _ 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 12 1.96021 0.91872 2.43971 0.98629 12 c - - _ 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 13 0.11379 5.28783 2.33314 5.20135 13 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 14 4.64347 0.41975 5.38640 1.11296 14 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 15 0.00657 6.42414 5.95115 6.06251 15 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 16 2.82445 5.53161 0.07106 5.24108 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 17 4.29243 5.56001 0.02295 5.26538 17 G - - > 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 18 5.88073 0.06680 5.75643 2.83599 18 C - - > 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 19 0.15227 5.57396 2.02230 5.27883 19 A - - > 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 20 5.80490 6.87364 0.00512 6.85048 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 21 5.12831 0.14965 5.65265 2.04368 21 C - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 22 2.66682 2.73235 4.69837 0.15508 22 U - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 23 2.04662 2.14985 4.45763 0.29741 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 24 0.06399 5.07333 5.16002 2.99611 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 25 2.80590 2.76663 0.18569 3.07607 25 G - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 26 0.09335 5.33698 2.53819 5.23955 26 A - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 27 0.13739 4.36334 3.29597 2.54336 27 A - - : 1.38629 1.38629 1.38629 1.38629 0.00570 5.86363 5.86363 1.46634 0.26236 1.09861 0.40547 28 0.22059 4.25153 2.58891 2.21997 28 A - - : 1.38629 1.38629 1.38629 1.38629 0.00285 5.86079 * 1.46634 0.26236 0.00000 * //