INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR38 ACC RF01348 DESC CRISPR RNA direct repeat element STATES 109 NODES 34 CLEN 35 W 49 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 15:18:59 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/RF01348/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 5 EFFN 5.000000 CKSUM 2664565337 NULL 0.000 0.000 0.000 0.000 GA 44.00 TC 50.20 NC 42.10 EFP7GF -8.8427 0.73180 ECMLC 0.50172 -10.29934 2.39573 1600000 700402 0.001713 ECMGC 0.42226 -15.25759 0.48854 1600000 308802 0.001295 ECMLI 0.49252 -8.63807 3.37887 1600000 446276 0.002689 ECMGI 0.43658 -12.78694 1.88148 1600000 241693 0.001655 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 49 68 -7.853 -8.060 -0.028 -6.474 IL 1 1 2 1 4 1 3 54 73 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 2 53 72 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - c - - - ML 3 2 3 5 3 1 4 49 68 -8.820 -0.011 -7.474 0.067 0.577 -0.345 -0.571 D 4 2 3 5 3 0 0 48 67 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 2 52 71 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - A - - - ML 6 5 3 8 3 1 4 48 67 -8.820 -0.011 -7.474 1.047 -1.463 -1.610 0.315 D 7 5 3 8 3 0 0 47 66 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 51 70 -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 3 47 66 -8.820 -0.011 -7.474 -1.785 -0.301 -2.567 1.449 D 10 8 3 11 3 0 0 46 65 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 50 69 -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 3 46 65 -8.820 -0.011 -7.474 -1.548 0.484 -2.389 1.048 D 13 11 3 14 3 0 0 45 64 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 48 68 -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 2 45 64 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 16 14 3 17 3 0 0 44 63 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 47 67 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 2 44 63 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 19 17 3 20 3 0 0 43 62 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 46 66 -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 2 43 62 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 22 20 3 23 3 0 0 42 61 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 1 45 65 -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 42 61 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 25 23 3 26 3 0 0 41 60 -6.174 -1.687 -0.566 IL 26 26 3 26 3 1 1 44 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 9 - C - - - ML 27 26 3 29 3 1 1 41 59 -8.820 -0.011 -7.474 -3.685 1.899 -4.419 -2.783 D 28 26 3 29 3 0 0 40 59 -6.174 -1.687 -0.566 IL 29 29 3 29 3 1 1 43 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 10 - U - - - ML 30 29 3 32 3 1 1 40 58 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 31 29 3 32 3 0 0 39 58 -6.174 -1.687 -0.566 IL 32 32 3 32 3 1 1 42 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 11 - u - - - ML 33 32 3 35 3 1 1 38 57 -8.820 -0.011 -7.474 0.433 -1.371 -1.632 0.956 D 34 32 3 35 3 0 0 38 56 -6.174 -1.687 -0.566 IL 35 35 3 35 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 12 - A - - - ML 36 35 3 38 3 1 1 37 56 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 37 35 3 38 3 0 0 36 55 -6.174 -1.687 -0.566 IL 38 38 3 38 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - U - - - ML 39 38 3 41 3 1 1 36 55 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 40 38 3 41 3 0 0 35 54 -6.174 -1.687 -0.566 IL 41 41 3 41 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 14 - U - - - ML 42 41 3 44 3 1 1 35 54 -8.820 -0.011 -7.474 -1.785 -0.301 -2.567 1.449 D 43 41 3 44 3 0 0 34 53 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 15 - G - - - ML 45 44 3 47 3 1 1 34 53 -8.820 -0.011 -7.474 -3.201 -4.609 1.920 -3.943 D 46 44 3 47 3 0 0 33 52 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 16 - C - - - ML 48 47 3 50 3 1 1 33 52 -8.820 -0.011 -7.474 -3.685 1.899 -4.419 -2.783 D 49 47 3 50 3 0 0 32 51 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 36 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 17 - A - - - ML 51 50 3 53 3 1 1 32 50 -9.168 -0.011 -7.485 1.917 -4.036 -3.527 -3.736 D 52 50 3 53 3 0 0 31 49 -5.620 -0.734 -1.403 IL 53 53 3 53 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 35 - C - - MR 54 53 3 56 3 1 1 31 49 -9.168 -0.011 -7.485 -0.375 1.368 -2.447 -1.104 D 55 53 3 56 3 0 0 29 48 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 34 - A - - MR 57 56 3 59 3 1 1 30 48 -9.168 -0.011 -7.485 1.405 -1.796 -1.895 -0.331 D 58 56 3 59 3 0 0 28 47 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 33 - A - - MR 60 59 3 62 3 1 1 29 47 -9.168 -0.011 -7.485 1.405 -1.796 -1.895 -0.331 D 61 59 3 62 3 0 0 27 46 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 32 - A - - MR 63 62 3 65 3 1 1 28 46 -9.168 -0.011 -7.485 1.917 -4.036 -3.527 -3.736 D 64 62 3 65 3 0 0 26 45 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 31 - G - - MR 66 65 3 68 3 1 1 27 45 -9.168 -0.011 -7.485 -3.201 -4.609 1.920 -3.943 D 67 65 3 68 3 0 0 25 44 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 1 28 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 30 - U - - MR 69 68 3 71 3 1 1 26 44 -9.168 -0.011 -7.485 -3.083 -2.826 -3.864 1.877 D 70 68 3 71 3 0 0 24 43 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 1 27 45 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 29 - U - - MR 72 71 3 74 3 1 1 25 43 -9.168 -0.011 -7.485 -3.083 -2.826 -3.864 1.877 D 73 71 3 74 3 0 0 23 42 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 1 26 44 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 28 - A - - MR 75 74 3 77 3 1 1 24 42 -9.168 -0.011 -7.485 1.917 -4.036 -3.527 -3.736 D 76 74 3 77 3 0 0 22 41 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 1 25 43 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 27 - G - - MR 78 77 3 80 5 1 1 23 41 -7.865 -0.023 -7.680 -7.892 -8.784 -0.209 -2.713 1.467 -2.197 D 79 77 3 80 5 0 0 22 40 -5.352 -0.707 -2.978 -4.409 -2.404 IR 80 80 3 80 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 18 26 C G - - MP 81 80 3 85 6 2 2 22 40 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -6.436 -6.502 -5.772 -2.678 -4.205 -5.936 3.874 -5.224 -5.962 -2.604 -5.938 -4.563 -0.969 -6.377 -2.038 -4.766 ML 82 80 3 85 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 83 80 3 85 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 84 80 3 85 6 0 0 19 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 1 22 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 86 86 6 86 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 28 ] 19 25 U A - - MP 87 86 6 91 6 2 2 20 38 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -4.232 -3.824 -4.180 -0.050 -3.352 -4.933 1.086 -3.913 -4.133 1.576 -4.580 -1.535 3.075 -4.463 -0.975 -2.995 ML 88 86 6 91 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 89 86 6 91 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 90 86 6 91 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 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 92 92 6 92 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 20 24 C G - - MP 93 92 6 97 4 2 2 18 36 -7.853 -8.060 -0.028 -6.474 -6.436 -6.502 -5.772 -2.678 -4.205 -5.936 3.874 -5.224 -5.962 -2.604 -5.938 -4.563 -0.969 -6.377 -2.038 -4.766 ML 94 92 6 97 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 96 92 6 97 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 97 97 5 97 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 98 98 6 98 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 21 - A - - - ML 99 98 6 101 3 1 1 14 33 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 100 98 6 101 3 0 0 15 33 -6.174 -1.687 -0.566 IL 101 101 3 101 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 22 - U - - - ML 102 101 3 104 3 1 1 12 31 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 103 101 3 104 3 0 0 13 32 -6.174 -1.687 -0.566 IL 104 104 3 104 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 23 - a - - - ML 105 104 3 107 2 1 1 1 1 * 0.000 0.905 -1.359 -0.264 -0.144 D 106 104 3 107 2 0 0 0 0 * 0.000 IL 107 107 3 107 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 33 ] - - - - - - E 108 107 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR38 ACC RF01348 DESC CRISPR RNA direct repeat element LENG 35 MAXL 104 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 15:18:59 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/RF01348/CM NSEQ 5 EFFN 4.194336 CKSUM 2664565337 STATS LOCAL MSV -6.6297 0.73180 STATS LOCAL VITERBI -7.3043 0.73180 STATS LOCAL FORWARD -3.3458 0.73180 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.15815 1.63310 1.71930 1.16662 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 0.00000 * 1 1.32790 1.02338 1.62960 1.71713 1 c - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 2 0.69125 2.30690 2.40879 1.17261 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 3 2.46708 1.58780 3.00527 0.41360 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 4 2.31907 1.07755 2.89084 0.68186 4 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 5 0.07239 3.95753 3.61923 3.73301 5 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 6 3.30174 3.15459 3.83896 0.10646 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 7 0.07239 3.95753 3.61923 3.73301 7 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 8 3.30174 3.15459 3.83896 0.10646 8 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 9 3.69428 0.08845 4.23309 3.09486 9 C - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 10 3.30174 3.15459 3.83896 0.10646 10 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 11 1.09777 2.24349 2.42580 0.75101 11 u - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 12 0.07239 3.95753 3.61923 3.73301 12 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 13 3.30174 3.15459 3.83896 0.10646 13 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 14 2.46708 1.58780 3.00527 0.41360 14 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 15 3.39960 4.35584 0.06853 3.91107 15 G - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 16 3.69428 0.08845 4.23309 3.09486 16 C - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 17 0.07239 3.95753 3.61923 3.73301 17 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 18 3.97459 0.11124 3.82932 2.73704 18 C - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 19 2.46876 1.80723 1.52054 0.62997 19 U - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 20 3.96851 0.11153 3.82590 2.73586 20 C - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 21 0.07239 3.95753 3.61923 3.73301 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 22 3.30174 3.15459 3.83896 0.10646 22 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 23 0.78122 2.25935 1.57019 1.47084 23 a - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 24 3.02061 3.99351 0.09518 3.74725 24 G - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 25 0.69295 1.62068 1.64474 2.21574 25 A - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 26 3.02951 4.00842 0.09398 3.76364 26 G - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 27 1.51209 3.11785 0.39864 2.74786 27 G - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 28 0.07239 3.95753 3.61923 3.73301 28 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 29 3.30174 3.15459 3.83896 0.10646 29 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 30 3.30174 3.15459 3.83896 0.10646 30 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 31 3.39960 4.35584 0.06853 3.91107 31 G - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 32 0.07239 3.95753 3.61923 3.73301 32 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 33 0.44545 2.51968 2.58050 1.59334 33 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 34 0.44545 2.51968 2.58050 1.59334 34 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 35 1.61287 0.48672 2.91332 2.02685 35 C - - : 1.38629 1.38629 1.38629 1.38629 0.01418 4.26268 * 1.46634 0.26236 0.00000 * //