INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR44 ACC RF01353 DESC CRISPR RNA direct repeat element STATES 88 NODES 26 CLEN 28 W 42 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 03:20:24 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/RF01353/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 1035530228 NULL 0.000 0.000 0.000 0.000 GA 35.00 TC 35.10 NC 34.80 EFP7GF -3.0178 0.75518 ECMLC 0.53522 -6.64501 5.30233 1600000 718243 0.001671 ECMGC 0.46114 -8.87320 5.99887 1600000 380635 0.001051 ECMLI 0.56487 -4.18823 6.39501 1600000 473658 0.002533 ECMGI 0.46604 -7.68339 6.62166 1600000 314339 0.001273 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 42 61 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 47 66 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 46 65 -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 42 61 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 4 2 3 5 3 0 0 41 60 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 44 64 -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 41 60 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 7 5 3 8 3 0 0 40 59 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 43 63 -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 40 59 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 10 8 3 11 3 0 0 39 58 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 42 61 -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 39 57 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 13 11 3 14 3 0 0 38 57 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 41 60 -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 38 56 -8.323 -0.016 -6.977 0.290 0.789 -1.512 -0.517 D 16 14 3 17 3 0 0 36 55 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 40 59 -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 36 55 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 19 17 3 20 3 0 0 35 54 -5.620 -0.734 -1.403 IL 20 20 3 20 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 28 - c - - MR 21 20 3 23 3 1 1 35 54 -8.693 -0.015 -7.010 -0.688 0.786 -0.052 -0.534 D 22 20 3 23 3 0 0 34 52 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 27 - A - - MR 24 23 3 26 3 1 1 34 53 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 25 23 3 26 3 0 0 33 51 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 26 - a - - MR 27 26 3 29 3 1 1 33 52 -8.693 -0.015 -7.010 0.956 -1.138 -1.275 0.254 D 28 26 3 29 3 0 0 32 50 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 25 - A - - MR 30 29 3 32 3 1 1 32 51 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 31 29 3 32 3 0 0 31 49 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 24 - u - - MR 33 32 3 35 3 1 1 31 50 -8.693 -0.015 -7.010 0.225 -1.048 -1.357 0.968 D 34 32 3 35 3 0 0 30 48 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 23 - U - - MR 36 35 3 38 3 1 1 30 49 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 37 35 3 38 3 0 0 29 47 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 22 - C - - MR 39 38 3 41 3 1 1 29 48 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 40 38 3 41 3 0 0 28 46 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 21 - U - - MR 42 41 3 44 3 1 1 28 47 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 43 41 3 44 3 0 0 27 45 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 20 - u - - MR 45 44 3 47 3 1 1 27 46 -8.693 -0.015 -7.010 0.200 -1.052 -1.368 0.987 D 46 44 3 47 3 0 0 26 44 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 19 - A - - MR 48 47 3 50 5 1 1 26 45 -7.411 -0.031 -7.227 -7.439 -8.330 1.047 -0.102 -1.377 -0.695 D 49 47 3 50 5 0 0 25 44 -5.352 -0.707 -2.978 -4.409 -2.404 IR 50 50 3 50 5 1 1 27 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 7 18 U A - - MP 51 50 3 55 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 52 50 3 55 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 53 50 3 55 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 54 50 3 55 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 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 56 56 6 56 5 1 1 25 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 8 17 A U - - MP 57 56 6 61 6 2 2 23 42 -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 58 56 6 61 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 59 56 6 61 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 60 56 6 61 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 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 62 62 6 62 5 1 1 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 9 16 C G - - MP 63 62 6 67 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 64 62 6 67 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 65 62 6 67 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 66 62 6 67 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 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 68 68 6 68 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 10 15 U A - - MP 69 68 6 73 4 2 2 19 38 -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 70 68 6 73 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 71 68 6 73 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 72 68 6 73 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 73 73 5 73 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 74 74 6 74 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 11 - A - - - ML 75 74 6 77 3 1 1 16 34 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 D 76 74 6 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 22 ] 12 - u - - - ML 78 77 3 80 3 1 1 15 33 -8.323 -0.016 -6.977 0.200 -1.052 -1.368 0.987 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 23 ] 13 - C - - - ML 81 80 3 83 3 1 1 13 31 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 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 24 ] 14 - U - - - ML 84 83 3 86 2 1 1 1 1 * 0.000 -2.168 -2.049 -2.929 1.767 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 25 ] - - - - - - E 87 86 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR44 ACC RF01353 DESC CRISPR RNA direct repeat element LENG 28 MAXL 98 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 03:20:24 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/RF01353/CM NSEQ 3 EFFN 2.534180 CKSUM 1035530228 STATS LOCAL MSV -7.1209 0.75518 STATS LOCAL VITERBI -7.6743 0.75518 STATS LOCAL FORWARD -2.4702 0.75518 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.17687 1.41344 2.16334 1.09808 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 2.95694 0.18042 3.53318 2.47823 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 2.69579 2.64523 3.21653 0.19671 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 2.69579 2.64523 3.21653 0.19671 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 2.95694 0.18042 3.53318 2.47823 4 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 1.18574 0.88604 2.34664 1.67931 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 0.14040 3.33048 3.04569 3.04380 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 3.07100 1.98058 2.83385 0.27859 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 0.30621 2.88435 1.91223 2.81134 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 3.28976 0.21869 3.07547 2.18041 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 10 3.07341 1.98074 2.83496 0.27833 10 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 0.14040 3.33048 3.04569 3.04380 11 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 1.24693 2.05215 2.26905 0.73242 12 u - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 2.95694 0.18042 3.53318 2.47823 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 2.69579 2.64523 3.21653 0.19671 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 0.31552 3.02177 1.81769 2.82216 15 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.46062 3.24539 0.18824 3.05235 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 3.04392 2.21788 2.69793 0.25339 17 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 0.31460 3.02662 1.81826 2.82793 18 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 0.69457 1.47107 2.26051 1.79135 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 1.24693 2.05215 2.26905 0.73242 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 2.69579 2.64523 3.21653 0.19671 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 2.95694 0.18042 3.53318 2.47823 22 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 23 2.69579 2.64523 3.21653 0.19671 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 1.23040 2.04991 2.26229 0.74451 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 0.14040 3.33048 3.04569 3.04380 25 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 0.75125 2.11616 2.20860 1.21108 26 a - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 27 0.14040 3.33048 3.04569 3.04380 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 1.78063 0.89478 1.43822 1.68512 28 c - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //