INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR3 ACC RF01316 DESC CRISPR RNA direct repeat element STATES 94 NODES 28 CLEN 30 W 42 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 6 02:03:38 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/RF01316/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 20 EFFN 20.000000 CKSUM 2897682762 NULL 0.000 0.000 0.000 0.000 GA 41.00 TC 41.00 NC 40.90 EFP7GF -14.7621 0.72622 ECMLC 0.41713 -11.62791 4.26016 1600000 906661 0.001324 ECMGC 0.40579 -19.29798 -1.00313 1600000 670146 0.000597 ECMLI 0.42211 -10.31268 5.07149 1600000 793254 0.001513 ECMGI 0.41894 -17.21569 0.30689 1600000 616862 0.000648 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 42 61 -9.564 -9.771 -0.009 -8.186 IL 1 1 2 1 4 1 1 48 67 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 47 66 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - A - - - ML 3 2 3 5 3 1 3 42 61 -10.492 -0.004 -9.146 1.613 -3.684 -0.756 -1.884 D 4 2 3 5 3 0 0 42 61 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 46 65 -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 2 41 60 -10.492 -0.004 -9.146 -3.999 -0.750 -4.753 1.725 D 7 5 3 8 3 0 0 41 60 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 45 64 -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 2 40 59 -10.492 -0.004 -9.146 -5.705 -5.198 -6.559 1.979 D 10 8 3 11 3 0 0 40 59 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 44 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - U - - - ML 12 11 3 14 3 1 2 39 58 -10.492 -0.004 -9.146 -5.705 -5.198 -6.559 1.979 D 13 11 3 14 3 0 0 39 58 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 43 61 -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 38 56 -10.492 -0.004 -9.146 1.845 -1.782 -4.254 -3.946 D 16 14 3 17 3 0 0 38 57 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 42 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - A - - - ML 18 17 3 20 3 1 1 37 55 -10.492 -0.004 -9.146 1.984 -6.495 -5.869 -6.068 D 19 17 3 20 3 0 0 37 55 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 41 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - A - - - ML 21 20 3 23 3 1 1 36 54 -10.492 -0.004 -9.146 1.984 -6.495 -5.869 -6.068 D 22 20 3 23 3 0 0 36 54 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 1 40 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - U - - - ML 24 23 3 26 3 1 1 35 53 -10.802 -0.003 -9.120 -5.705 -5.198 -6.559 1.979 D 25 23 3 26 3 0 0 34 52 -5.620 -0.734 -1.403 IL 26 26 3 26 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 30 - C - - MR 27 26 3 29 3 1 1 34 52 -10.802 -0.003 -9.120 -4.739 1.829 -5.459 -1.370 D 28 26 3 29 3 0 0 32 51 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 29 - A - - MR 30 29 3 32 3 1 1 33 51 -10.802 -0.003 -9.120 1.856 -4.282 -4.455 -1.819 D 31 29 3 32 3 0 0 31 50 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 28 - A - - MR 33 32 3 35 3 1 1 32 50 -10.802 -0.003 -9.120 1.984 -6.495 -5.869 -6.068 D 34 32 3 35 3 0 0 30 49 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 27 - C - - MR 36 35 3 38 3 1 1 31 49 -10.802 -0.003 -9.120 -4.425 1.750 -5.282 -0.829 D 37 35 3 38 3 0 0 29 48 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 26 - U - - MR 39 38 3 41 3 1 1 30 48 -10.802 -0.003 -9.120 -5.705 -5.198 -6.559 1.979 D 40 38 3 41 3 0 0 28 47 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 25 - U - - MR 42 41 3 44 3 1 1 29 47 -10.802 -0.003 -9.120 -5.705 -5.198 -6.559 1.979 D 43 41 3 44 3 0 0 27 46 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 24 - G - - MR 45 44 3 47 3 1 1 28 46 -10.802 -0.003 -9.120 -1.908 -4.114 1.777 -2.002 D 46 44 3 47 3 0 0 26 45 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 23 - U - - MR 48 47 3 50 3 1 1 27 45 -10.802 -0.003 -9.120 -1.577 -2.897 -0.219 1.417 D 49 47 3 50 3 0 0 25 44 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 1 28 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 22 - A - - MR 51 50 3 53 3 1 1 26 44 -10.802 -0.003 -9.120 1.248 -1.134 -2.836 0.042 D 52 50 3 53 3 0 0 24 43 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 1 27 45 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 21 - A - - MR 54 53 3 56 3 1 1 25 43 -10.802 -0.003 -9.120 1.984 -6.495 -5.869 -6.068 D 55 53 3 56 3 0 0 23 42 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 1 26 44 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 20 - U - - MR 57 56 3 59 5 1 1 24 42 -9.460 -0.007 -9.276 -9.488 -10.380 -4.105 -1.870 -4.838 1.861 D 58 56 3 59 5 0 0 22 41 -5.352 -0.707 -2.978 -4.409 -2.404 IR 59 59 3 59 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 9 19 A U - - MP 60 59 3 64 6 2 2 23 41 -10.672 -10.611 -0.007 -9.388 -9.668 -10.063 -8.155 -6.928 -6.015 3.976 -9.681 -10.613 -5.550 -5.867 -7.949 -3.579 -8.542 -4.030 -5.739 -9.456 -7.356 -5.648 ML 61 59 3 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 3 64 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 63 59 3 64 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 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 65 65 6 65 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 10 18 C G - - MP 66 65 6 70 6 2 2 21 39 -10.672 -10.611 -0.007 -9.388 -9.668 -10.063 -9.428 -9.648 -7.762 -5.998 -6.056 -7.518 3.984 -8.138 -8.958 -5.968 -7.556 -8.031 -3.960 -9.346 -4.936 -7.758 ML 67 65 6 70 6 1 1 20 39 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 68 65 6 70 6 1 1 20 39 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 69 65 6 70 6 0 0 19 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 6 1 1 21 39 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 71 71 6 71 5 1 1 20 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 11 17 A U - - MP 72 71 6 76 6 2 2 19 37 -10.672 -10.611 -0.007 -9.388 -9.668 -10.063 -8.155 -6.928 -6.015 3.976 -9.681 -10.613 -5.550 -5.867 -7.949 -3.579 -8.542 -4.030 -5.739 -9.456 -7.356 -5.648 ML 73 71 6 76 6 1 1 20 38 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 74 71 6 76 6 1 1 20 38 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 75 71 6 76 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 6 1 1 19 38 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 77 77 6 77 5 1 1 19 37 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 12 16 U A - - MP 78 77 6 82 4 2 2 17 35 -9.564 -9.771 -0.009 -8.186 -6.716 -5.718 -6.601 2.380 -6.012 -7.745 -1.677 -6.254 -6.375 -2.282 -6.835 -3.105 3.316 -7.475 -3.663 -5.320 ML 79 77 6 82 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 80 77 6 82 4 1 1 19 37 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 81 77 6 82 4 0 0 18 36 -4.568 -4.250 -2.265 -0.520 IL 82 82 5 82 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 83 83 6 83 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 13 - C - - - ML 84 83 6 86 3 1 1 13 31 -10.492 -0.004 -9.146 -1.157 1.471 -3.890 -0.489 D 85 83 6 86 3 0 0 15 33 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 14 - U - - - ML 87 86 3 89 3 1 1 11 30 -10.492 -0.004 -9.146 -3.829 0.539 -4.761 1.287 D 88 86 3 89 3 0 0 13 32 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 15 - C - - - ML 90 89 3 92 2 1 1 1 1 * 0.000 -3.747 1.382 -4.807 0.359 D 91 89 3 92 2 0 0 0 0 * 0.000 IL 92 92 3 92 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 27 ] - - - - - - E 93 92 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR3 ACC RF01316 DESC CRISPR RNA direct repeat element LENG 30 MAXL 88 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 6 02:03:38 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/RF01316/CM NSEQ 20 EFFN 18.520508 CKSUM 2897682762 STATS LOCAL MSV -6.5948 0.72622 STATS LOCAL VITERBI -6.6056 0.72622 STATS LOCAL FORWARD -3.5899 0.72622 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.06303 1.77898 2.46265 0.91486 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 0.00000 * 1 0.27187 3.85983 1.91089 2.67322 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 2 4.07761 1.90847 4.60063 0.19274 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 3 5.22697 4.88719 5.81349 0.01603 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 4 5.22697 4.88719 5.81349 0.01603 4 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 5 0.10994 2.62267 4.26092 4.05151 5 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 6 0.01177 5.80010 5.37195 5.51459 6 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 7 0.01177 5.80010 5.37195 5.51459 7 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 8 5.22697 4.88719 5.81349 0.01603 8 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 9 0.01825 5.74651 4.50150 5.57231 9 A - - < 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 10 5.96503 0.01325 5.97536 4.82092 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 11 0.01883 5.69687 4.48544 5.51430 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 12 1.11881 3.71281 3.74204 0.46966 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 13 2.18089 0.37226 4.01427 1.71575 13 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 14 3.94117 1.01631 4.58499 0.49685 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 15 3.88899 0.43159 4.62190 1.13872 15 C - - _ 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 16 0.47720 4.10951 3.54440 1.09608 16 A - - > 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 17 5.83988 4.94031 5.58096 0.01393 17 U - - > 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 18 5.02337 6.13416 0.01145 5.93729 18 G - - > 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 19 5.97488 4.97037 5.64885 0.01309 19 U - - > 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 20 4.15828 2.67504 4.66635 0.09866 20 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 21 0.01177 5.80010 5.37195 5.51459 21 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 22 0.52876 2.15993 3.27871 1.35613 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 23 2.44462 3.31849 1.54447 0.41006 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 24 2.69169 4.17537 0.15772 2.76815 24 G - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 25 5.22697 4.88719 5.81349 0.01603 25 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 26 5.22697 4.88719 5.81349 0.01603 26 U - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 27 4.35981 0.17547 4.96025 1.95794 27 C - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 28 0.01177 5.80010 5.37195 5.51459 28 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 29 0.10199 4.28089 4.39585 2.64782 29 A - - : 1.38629 1.38629 1.38629 1.38629 0.00905 5.40268 5.40268 1.46634 0.26236 1.09861 0.40547 30 4.58176 0.12049 5.08978 2.33181 30 C - - : 1.38629 1.38629 1.38629 1.38629 0.00454 5.39816 * 1.46634 0.26236 0.00000 * //