INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR40 ACC RF01349 DESC CRISPR RNA direct repeat element STATES 94 NODES 22 CLEN 30 W 44 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 9 20:09:41 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/RF01349/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 3 EFFN 3.000000 CKSUM 3421319488 NULL 0.000 0.000 0.000 0.000 GA 42.00 TC 49.80 NC 41.40 EFP7GF -4.7621 0.74459 ECMLC 0.53739 -4.76366 6.09646 1600000 410928 0.002920 ECMGC 0.45180 -9.78686 5.18040 1600000 345818 0.001157 ECMLI 0.54610 -3.21799 7.05861 1600000 328456 0.003653 ECMGI 0.46851 -7.44295 6.33834 1600000 254789 0.001570 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 44 63 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 49 68 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 48 67 -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 1 44 63 -8.693 -0.015 -7.010 0.346 -1.879 1.038 -1.307 D 4 2 3 5 3 0 0 43 62 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 1 45 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 30 - C - - MR 6 5 3 8 5 1 1 43 62 -7.411 -0.031 -7.227 -7.439 -8.330 -2.619 1.795 -3.443 -1.863 D 7 5 3 8 5 0 0 42 61 -5.352 -0.707 -2.978 -4.409 -2.404 IR 8 8 3 8 5 1 1 44 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 2 29 U A - - MP 9 8 3 13 6 2 2 42 61 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 10 8 3 13 6 1 1 41 60 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 11 8 3 13 6 1 1 41 60 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 12 8 3 13 6 0 0 38 57 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 13 13 5 13 6 1 1 42 61 -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 42 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 3 28 U A - - MP 15 14 6 19 6 2 2 40 59 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 16 14 6 19 6 1 1 39 58 -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 39 58 -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 36 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 40 59 -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 40 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 4 27 U A - - MP 21 20 6 25 6 2 2 38 57 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 22 20 6 25 6 1 1 37 56 -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 1 37 56 -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 0 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 38 57 -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 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 5 26 A U - - MP 27 26 6 31 6 2 2 36 55 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.476 -3.353 -4.422 3.642 -5.136 -6.285 -0.788 -4.416 -4.312 0.335 -4.892 -0.734 -1.200 -5.339 -2.725 -3.234 ML 28 26 6 31 6 1 1 36 55 -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 1 35 55 -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 0 34 53 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 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 32 32 6 32 5 1 1 36 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 25 A U - - MP 33 32 6 37 4 2 2 34 53 -7.331 -7.538 -0.041 -5.952 -4.476 -3.353 -4.422 3.642 -5.136 -6.285 -0.788 -4.416 -4.312 0.335 -4.892 -0.734 -1.200 -5.339 -2.725 -3.234 ML 34 32 6 37 4 1 1 35 54 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 4 1 1 35 54 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 36 32 6 37 4 0 0 34 53 -4.568 -4.250 -2.265 -0.520 IL 37 37 5 37 4 1 1 36 56 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 38 38 6 38 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 7 - C - - - ML 39 38 6 41 3 1 1 32 50 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 40 38 6 41 3 0 0 31 50 -6.174 -1.687 -0.566 IL 41 41 3 41 3 1 1 34 53 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 8 - U - - - ML 42 41 3 44 3 1 1 30 49 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 43 41 3 44 3 0 0 29 48 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 9 - U - - - ML 45 44 3 47 3 1 1 29 48 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 46 44 3 47 3 0 0 28 47 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 32 51 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 10 - C - - - ML 48 47 3 50 3 1 1 28 47 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 49 47 3 50 3 0 0 27 46 -5.620 -0.734 -1.403 IL 50 50 3 50 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 24 - U - - MR 51 50 3 53 5 1 1 27 46 -7.411 -0.031 -7.227 -7.439 -8.330 -2.168 -2.049 -2.929 1.767 D 52 50 3 53 5 0 0 26 45 -5.352 -0.707 -2.978 -4.409 -2.404 IR 53 53 3 53 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 11 23 U A - - MP 54 53 3 58 6 2 2 26 45 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 ML 55 53 3 58 6 1 1 25 43 -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 25 43 -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 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 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 59 59 6 59 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 12 22 A U - - MP 60 59 6 64 6 2 2 24 43 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.476 -3.353 -4.422 3.642 -5.136 -6.285 -0.788 -4.416 -4.312 0.335 -4.892 -0.734 -1.200 -5.339 -2.725 -3.234 ML 61 59 6 64 6 1 1 23 41 -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 23 41 -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 24 43 -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 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 13 21 C G - - MP 66 65 6 70 6 2 2 22 41 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.152 -4.099 -3.966 -0.265 -2.771 -4.487 3.005 -3.521 -3.968 -0.066 -4.330 -2.034 2.146 -4.261 -0.424 -2.806 ML 67 65 6 70 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 68 65 6 70 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 69 65 6 70 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 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 71 71 6 71 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 14 20 A U - - MP 72 71 6 76 6 2 2 20 39 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.476 -3.353 -4.422 3.642 -5.136 -6.285 -0.788 -4.416 -4.312 0.335 -4.892 -0.734 -1.200 -5.339 -2.725 -3.234 ML 73 71 6 76 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 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 20 39 -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 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 15 19 U A - - MP 78 77 6 82 4 2 2 18 37 -7.331 -7.538 -0.041 -5.952 -5.110 -4.948 -4.841 -1.191 -3.607 -5.317 0.730 -4.359 -4.839 -1.044 -5.166 -2.820 3.636 -5.217 -1.262 -3.547 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 38 -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 37 -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 18 ] 16 - U - - - ML 84 83 6 86 3 1 1 15 33 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 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 19 ] 17 - A - - - ML 87 86 3 89 3 1 1 13 31 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 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 20 ] 18 - g - - - ML 90 89 3 92 2 1 1 1 1 * 0.000 -0.692 -1.393 0.948 0.098 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 21 ] - - - - - - E 93 92 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR40 ACC RF01349 DESC CRISPR RNA direct repeat element LENG 30 MAXL 101 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 9 20:09:41 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/RF01349/CM NSEQ 3 EFFN 2.862305 CKSUM 3421319488 STATS LOCAL MSV -7.5438 0.74459 STATS LOCAL VITERBI -7.6616 0.74459 STATS LOCAL FORWARD -2.6034 0.74459 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.17974 1.75779 2.04295 0.94015 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 1.14656 2.65766 0.67784 2.25906 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 3.25435 2.11473 3.03043 0.23265 2 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 3 3.25309 2.11463 3.02982 0.23276 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 3.25140 2.11450 3.02901 0.23291 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 0.25634 3.06967 2.04536 2.98867 5 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 0.25647 3.06901 2.04521 2.98776 6 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 3.13235 0.15190 3.70614 2.62083 7 C - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 2.83404 2.76044 3.35951 0.17054 8 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 2.83404 2.76044 3.35951 0.17054 9 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 10 3.13235 0.15190 3.70614 2.62083 10 C - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 3.25083 2.11445 3.02873 0.23296 11 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 0.25624 3.07024 2.04549 2.98946 12 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 2.69253 0.67014 2.45050 1.09541 13 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 14 0.25641 3.06931 2.04528 2.98817 14 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 3.24754 2.11419 3.02715 0.23326 15 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.83404 2.76044 3.35951 0.17054 16 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 0.12017 3.47572 3.17722 3.20423 17 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 1.84389 2.32796 0.74239 1.31554 18 g - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 0.26445 3.21614 1.95084 2.99358 19 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 3.21339 2.36738 2.87925 0.21087 20 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 1.23019 2.61847 0.59975 2.45454 21 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 3.22064 2.36845 2.88223 0.21018 22 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 23 0.26318 3.22445 1.95203 3.00310 23 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 2.83404 2.76044 3.35951 0.17054 24 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 3.21161 2.36712 2.87851 0.21104 25 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 3.21405 2.36748 2.87952 0.21081 26 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 27 0.26394 3.21948 1.95132 2.99741 27 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 28 0.26358 3.22183 1.95165 3.00009 28 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 29 0.26308 3.22512 1.95212 3.00387 29 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 30 3.13235 0.15190 3.70614 2.62083 30 C - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //