INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR28 ACC RF01356 DESC CRISPR RNA direct repeat element STATES 76 NODES 19 CLEN 24 W 38 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 9 07:31:18 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/RF01356/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 1688699847 NULL 0.000 0.000 0.000 0.000 GA 35.00 TC 35.00 NC 34.80 EFP7GF -4.7764 0.75470 ECMLC 0.56429 -7.16072 4.09442 1600000 687823 0.001745 ECMGC 0.49085 -10.95545 3.48525 1600000 479140 0.000835 ECMLI 0.56629 -5.76719 4.69293 1600000 448432 0.002676 ECMGI 0.50407 -9.34167 4.18654 1600000 366085 0.001093 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 38 57 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 42 62 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 41 61 -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 38 57 -8.323 -0.016 -6.977 0.362 -1.873 1.025 -1.300 D 4 2 3 5 3 0 0 37 56 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 40 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - G - - - ML 6 5 3 8 3 1 1 37 56 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 7 5 3 8 3 0 0 36 55 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - C - - - ML 9 8 3 11 3 1 1 36 54 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 10 8 3 11 3 0 0 35 54 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - A - - - ML 12 11 3 14 3 1 1 34 53 -8.323 -0.016 -6.977 1.103 -1.748 0.161 -1.200 D 13 11 3 14 3 0 0 33 52 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 37 56 -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 33 52 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 16 14 3 17 3 0 0 32 51 -5.620 -0.734 -1.403 IL 17 17 3 17 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 24 - A - - MR 18 17 3 20 5 1 1 32 51 -7.411 -0.031 -7.227 -7.439 -8.330 1.837 -3.097 -2.659 -2.714 D 19 17 3 20 5 0 0 31 50 -5.352 -0.707 -2.978 -4.409 -2.404 IR 20 20 3 20 5 1 1 33 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 23 a u - - MP 21 20 3 25 6 2 2 31 50 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -3.116 -2.620 1.229 2.799 -3.395 -4.303 0.425 -3.444 -3.212 1.069 -3.764 -0.390 0.133 -3.539 -1.318 -2.254 ML 22 20 3 25 6 1 1 30 49 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 3 25 6 1 1 30 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 3 25 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 31 50 -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 31 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 7 22 G C - - MP 27 26 6 31 6 2 2 29 48 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 28 26 6 31 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 29 26 6 31 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 30 26 6 31 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 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 32 32 6 32 5 1 1 29 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 8 21 C G - - MP 33 32 6 37 6 2 2 27 46 -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 34 32 6 37 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 35 32 6 37 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 36 32 6 37 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 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 38 38 6 38 5 1 1 27 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 9 20 C G - - MP 39 38 6 43 6 2 2 25 44 -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 40 38 6 43 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 41 38 6 43 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 42 38 6 43 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 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 44 44 6 44 5 1 1 25 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 10 19 C G - - MP 45 44 6 49 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 46 44 6 49 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 47 44 6 49 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 48 44 6 49 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 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 50 50 6 50 5 1 1 23 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 11 18 G C - - MP 51 50 6 55 6 2 2 21 40 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -5.440 -3.434 -5.640 -0.286 -6.206 -4.955 -1.397 -5.907 -4.753 3.769 -5.047 -1.169 -1.766 -4.916 -3.477 -4.506 ML 52 50 6 55 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 53 50 6 55 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 54 50 6 55 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 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 56 56 6 56 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 12 17 C G - - MP 57 56 6 61 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 58 56 6 61 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 60 56 6 61 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 61 61 5 61 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 62 62 6 62 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 13 - C - - - ML 63 62 6 65 3 1 1 16 34 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 64 62 6 65 3 0 0 16 34 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 14 - U - - - ML 66 65 3 68 3 1 1 15 33 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 67 65 3 68 3 0 0 15 33 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 15 - G - - - ML 69 68 3 71 3 1 1 13 31 -8.323 -0.016 -6.977 -2.322 -3.642 1.847 -3.026 D 70 68 3 71 3 0 0 13 32 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 16 - C - - - ML 72 71 3 74 2 1 1 1 1 * 0.000 -2.619 1.795 -3.443 -1.863 D 73 71 3 74 2 0 0 0 0 * 0.000 IL 74 74 3 74 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 18 ] - - - - - - E 75 74 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR28 ACC RF01356 DESC CRISPR RNA direct repeat element LENG 24 MAXL 93 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 9 07:31:18 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/RF01356/CM NSEQ 3 EFFN 2.516602 CKSUM 1688699847 STATS LOCAL MSV -7.5847 0.75470 STATS LOCAL VITERBI -7.3802 0.75470 STATS LOCAL FORWARD -2.5769 0.75470 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.69247 1.09292 1.06233 2.00209 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 1.13696 2.57258 0.71633 2.16869 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 2.78529 3.67455 0.13451 3.24975 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 3 2.94709 0.18219 3.52337 2.47028 3 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 0.65286 2.48870 1.29412 2.10138 4 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 0.14164 3.32236 3.03835 3.03483 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 0.62014 2.13579 1.56411 2.00465 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 2.64016 3.32592 0.15722 3.26515 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 3.28346 0.22033 3.06712 2.17426 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 3.28222 0.22045 3.06651 2.17404 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 3.28088 0.22059 3.06586 2.17380 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 2.63806 3.32333 0.15766 3.26157 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 3.27852 0.22083 3.06471 2.17338 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 2.94709 0.18219 3.52337 2.47028 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 2.68812 2.63885 3.20857 0.19829 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 2.78529 3.67455 0.13451 3.24975 15 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 2.94709 0.18219 3.52337 2.47028 16 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 2.45116 3.23200 0.19062 3.03908 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 3.46035 0.18702 3.15991 2.33586 18 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 2.45243 3.23379 0.19028 3.04121 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 2.45334 3.23506 0.19003 3.04271 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 2.45451 3.23671 0.18972 3.04467 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 3.47512 0.18581 3.16652 2.33865 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 2.23537 1.78066 1.37029 0.75399 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 0.14164 3.32236 3.03835 3.03483 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //