INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR17 ACC RF01328 DESC CRISPR RNA direct repeat element STATES 79 NODES 21 CLEN 25 W 39 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 5 21:11:00 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/RF01328/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 261809117 NULL 0.000 0.000 0.000 0.000 GA 42.00 TC 42.30 NC 40.40 EFP7GF -3.9047 0.75385 ECMLC 0.61185 -6.21588 4.69541 1600000 951856 0.001261 ECMGC 0.50153 -10.66384 4.27120 1600000 716259 0.000558 ECMLI 0.61450 -4.88118 5.46871 1600000 693903 0.001729 ECMGI 0.52791 -8.68235 5.25151 1600000 626084 0.000639 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 39 58 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 44 63 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 42 62 -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 1 39 58 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 4 2 3 5 3 0 0 38 57 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 41 61 -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 38 57 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 7 5 3 8 3 0 0 37 56 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 40 60 -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 37 56 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 10 8 3 11 3 0 0 36 55 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 39 58 -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 1 36 54 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 13 11 3 14 3 0 0 35 54 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - C - - - ML 15 14 3 17 3 1 1 34 53 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 16 14 3 17 3 0 0 33 52 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 37 56 -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 1 33 52 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 19 17 3 20 3 0 0 32 51 -5.620 -0.734 -1.403 IL 20 20 3 20 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 25 - C - - MR 21 20 3 23 3 1 1 32 51 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 22 20 3 23 3 0 0 31 49 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 24 - u - - MR 24 23 3 26 3 1 1 31 50 -8.693 -0.015 -7.010 0.192 -1.054 -1.371 0.992 D 25 23 3 26 3 0 0 30 49 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 23 - U - - MR 27 26 3 29 5 1 1 30 49 -7.411 -0.031 -7.227 -7.439 -8.330 -2.168 -2.049 -2.929 1.767 D 28 26 3 29 5 0 0 29 48 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 5 1 1 31 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 7 22 A U - - MP 30 29 3 34 6 2 2 29 48 -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 31 29 3 34 6 1 1 28 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 32 29 3 34 6 1 1 28 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 3 34 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 1 29 48 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 35 35 6 35 5 1 1 29 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 8 21 A U - - MP 36 35 6 40 6 2 2 27 46 -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 37 35 6 40 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 38 35 6 40 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 39 35 6 40 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 27 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 41 41 6 41 5 1 1 27 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 9 20 U A - - MP 42 41 6 46 6 2 2 25 44 -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 43 41 6 46 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 6 46 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 25 44 -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 25 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 10 19 C G - - MP 48 47 6 52 6 2 2 23 42 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 49 47 6 52 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 50 47 6 52 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 51 47 6 52 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 23 42 -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 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 11 18 C G - - MP 54 53 6 58 6 2 2 21 40 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 55 53 6 58 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 56 53 6 58 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 57 53 6 58 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 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 59 59 6 59 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 12 17 C G - - MP 60 59 6 64 4 2 2 19 38 -7.331 -7.538 -0.041 -5.952 -5.348 -5.320 -4.896 -1.500 -3.462 -5.201 3.738 -4.352 -4.984 -1.348 -5.146 -3.290 -0.044 -5.361 -1.200 -3.801 ML 61 59 6 64 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 63 59 6 64 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 64 64 5 64 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 65 65 6 65 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 13 - U - - - ML 66 65 6 68 3 1 1 16 34 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 67 65 6 68 3 0 0 16 34 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 14 - U - - - ML 69 68 3 71 3 1 1 15 33 -8.323 -0.016 -6.977 -1.065 0.139 -1.849 1.100 D 70 68 3 71 3 0 0 15 33 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 15 - U - - - ML 72 71 3 74 3 1 1 13 31 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 73 71 3 74 3 0 0 13 32 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 16 - U - - - ML 75 74 3 77 2 1 1 1 1 * 0.000 -2.168 -2.049 -2.929 1.767 D 76 74 3 77 2 0 0 0 0 * 0.000 IL 77 77 3 77 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 20 ] - - - - - - E 78 77 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR17 ACC RF01328 DESC CRISPR RNA direct repeat element LENG 25 MAXL 94 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 5 21:11:00 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/RF01328/CM NSEQ 3 EFFN 2.551758 CKSUM 261809117 STATS LOCAL MSV -6.8551 0.75385 STATS LOCAL VITERBI -7.5041 0.75385 STATS LOCAL FORWARD -2.2914 0.75385 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.83017 1.34594 1.82358 0.87258 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 2.96673 0.17868 3.54293 2.48615 1 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 2.70344 2.65159 3.22446 0.19515 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 2.70344 2.65159 3.22446 0.19515 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 2.70344 2.65159 3.22446 0.19515 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 2.96673 0.17868 3.54293 2.48615 5 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 2.70344 2.65159 3.22446 0.19515 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 0.30326 2.89422 1.91944 2.82068 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 0.30311 2.89491 1.91958 2.82164 8 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 3.08397 1.98795 2.84591 0.27554 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 3.29812 0.21686 3.08481 2.18691 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 3.29699 0.21697 3.08426 2.18671 11 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 3.29587 0.21708 3.08370 2.18651 12 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 2.70344 2.65159 3.22446 0.19515 13 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 14 2.03243 1.30494 2.56931 0.65161 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 2.70344 2.65159 3.22446 0.19515 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 2.70344 2.65159 3.22446 0.19515 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 2.46471 3.25121 0.18730 3.05665 17 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 2.46539 3.25218 0.18712 3.05780 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 2.46627 3.25342 0.18689 3.05927 19 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 0.31222 3.03376 1.82498 2.83314 20 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 3.05407 2.22617 2.70820 0.25073 21 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 3.05848 2.22676 2.70992 0.25023 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 2.70344 2.65159 3.22446 0.19515 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 1.25190 2.05528 2.27364 0.72764 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 2.96673 0.17868 3.54293 2.48615 25 C - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //