INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR41 ACC RF01350 DESC CRISPR RNA direct repeat element STATES 91 NODES 23 CLEN 29 W 43 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 12 14:13:35 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/RF01350/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 2 EFFN 2.000000 CKSUM 3400681714 NULL 0.000 0.000 0.000 0.000 GA 36.00 TC 46.20 NC 35.60 EFP7GF -2.5883 0.76609 ECMLC 0.64247 -4.59541 4.58447 1600000 437093 0.002745 ECMGC 0.47398 -9.27020 4.63551 1600000 291424 0.001373 ECMLI 0.66621 -2.89380 5.66492 1600000 359337 0.003339 ECMGI 0.51715 -6.77346 5.49541 1600000 227828 0.001756 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 43 62 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 48 67 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 47 66 -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 43 63 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 4 2 3 5 3 0 0 42 61 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 1 44 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 29 - C - - MR 6 5 3 8 5 1 1 42 62 -7.117 -0.038 -6.932 -7.144 -8.036 -1.806 1.641 -2.632 -1.207 D 7 5 3 8 5 0 0 41 60 -5.352 -0.707 -2.978 -4.409 -2.404 IR 8 8 3 8 5 1 1 43 62 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 2 28 U A - - MP 9 8 3 13 6 2 2 41 61 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 10 8 3 13 6 1 1 40 59 -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 40 59 -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 41 60 -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 41 60 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 3 27 U A - - MP 15 14 6 19 6 2 2 39 58 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 16 14 6 19 6 1 1 38 57 -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 38 57 -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 39 58 -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 39 58 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 4 26 U A - - MP 21 20 6 25 6 2 2 37 56 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 22 20 6 25 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 23 20 6 25 6 1 1 36 55 -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 34 53 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 37 56 -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 37 56 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 5 25 C G - - MP 27 26 6 31 6 2 2 35 54 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 28 26 6 31 6 1 1 35 54 -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 54 -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 33 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 35 54 -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 35 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 24 C G - - MP 33 32 6 37 4 2 2 33 52 -6.977 -7.184 -0.052 -5.598 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 34 32 6 37 4 1 1 34 53 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 4 1 1 34 53 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 36 32 6 37 4 0 0 33 52 -4.568 -4.250 -2.265 -0.520 IL 37 37 5 37 4 1 1 35 55 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 38 38 6 38 3 1 1 34 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 7 - A - - - ML 39 38 6 41 3 1 1 31 50 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 40 38 6 41 3 0 0 30 49 -6.174 -1.687 -0.566 IL 41 41 3 41 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 8 - C - - - ML 42 41 3 44 3 1 1 30 48 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 43 41 3 44 3 0 0 28 47 -5.620 -0.734 -1.403 IL 44 44 3 44 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 23 - C - - MR 45 44 3 47 3 1 1 29 47 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 46 44 3 47 3 0 0 27 46 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 22 - A - - MR 48 47 3 50 3 1 1 28 46 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 49 47 3 50 3 0 0 26 45 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 21 - U - - MR 51 50 3 53 3 1 1 27 45 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 52 50 3 53 3 0 0 25 44 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 1 27 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 20 - C - - MR 54 53 3 56 3 1 1 26 44 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 55 53 3 56 3 0 0 24 43 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 1 26 45 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 19 - U - - MR 57 56 3 59 5 1 1 25 43 -7.117 -0.038 -6.932 -7.144 -8.036 -1.535 -1.523 -2.271 1.632 D 58 56 3 59 5 0 0 23 42 -5.352 -0.707 -2.978 -4.409 -2.404 IR 59 59 3 59 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 9 18 A U - - MP 60 59 3 64 6 2 2 24 42 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -3.842 -2.861 -3.857 3.364 -4.221 -5.288 0.082 -3.896 -3.747 1.023 -4.297 -0.328 -0.335 -4.467 -1.858 -2.688 ML 61 59 3 64 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 62 59 3 64 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 63 59 3 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 23 42 -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 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 10 17 C G - - MP 66 65 6 70 6 2 2 22 40 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 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 40 -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 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 11 16 U A - - MP 72 71 6 76 4 2 2 20 38 -6.977 -7.184 -0.052 -5.598 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 73 71 6 76 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 74 71 6 76 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 75 71 6 76 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 76 76 5 76 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 77 77 6 77 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 12 - A - - - ML 78 77 6 80 3 1 1 16 35 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 79 77 6 80 3 0 0 16 34 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 13 - u - - - ML 81 80 3 83 3 1 1 15 33 -7.991 -0.020 -6.645 -0.727 0.473 -1.508 0.728 D 82 80 3 83 3 0 0 15 33 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 14 - U - - - ML 84 83 3 86 3 1 1 13 31 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 85 83 3 86 3 0 0 13 32 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 15 - u - - - ML 87 86 3 89 2 1 1 1 1 * 0.000 0.557 -0.859 -1.066 0.585 D 88 86 3 89 2 0 0 0 0 * 0.000 IL 89 89 3 89 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 22 ] - - - - - - E 90 89 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR41 ACC RF01350 DESC CRISPR RNA direct repeat element LENG 29 MAXL 103 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 12 14:13:35 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/RF01350/CM NSEQ 2 EFFN 1.769531 CKSUM 3400681714 STATS LOCAL MSV -6.8368 0.76609 STATS LOCAL VITERBI -8.2499 0.76609 STATS LOCAL FORWARD -2.5082 0.76609 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.34852 1.25935 1.74065 1.26894 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.48930 0.29029 3.05665 2.10422 1 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.66141 1.68086 2.37357 0.42957 2 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.66289 1.68087 2.37412 0.42933 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.66307 1.68087 2.37419 0.42930 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.90448 0.32460 2.63910 1.89062 5 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.90375 0.32471 2.63879 1.89050 6 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 0.21448 2.94347 2.69707 2.61798 7 A - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.48930 0.29029 3.05665 2.10422 8 C - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 0.48595 2.43102 1.59003 2.37493 9 A - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.90141 0.32506 2.63780 1.89014 10 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 2.66154 1.68086 2.37362 0.42955 11 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 0.21448 2.94347 2.69707 2.61798 12 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 1.84121 1.08255 2.37615 0.89224 13 u - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.33713 2.34863 2.84142 0.28828 14 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 1.00967 1.95263 2.09392 0.99275 15 u - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 0.48843 2.55290 1.51757 2.41564 16 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 2.16676 2.80748 0.28056 2.66302 17 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.61319 1.85145 2.24920 0.40916 18 U - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 2.33713 2.34863 2.84142 0.28828 19 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.48930 0.29029 3.05665 2.10422 20 C - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.33713 2.34863 2.84142 0.28828 21 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 0.21448 2.94347 2.69707 2.61798 22 A - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.48930 0.29029 3.05665 2.10422 23 C - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 2.16529 2.80572 0.28114 2.66074 24 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.16584 2.80638 0.28092 2.66160 25 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 26 0.48830 2.55330 1.51757 2.41619 26 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 27 0.48808 2.55398 1.51757 2.41712 27 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 28 0.48780 2.55483 1.51757 2.41828 28 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 29 2.48930 0.29029 3.05665 2.10422 29 C - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //