INFERNAL1/a [1.1.5 | Sep 2023] NAME CRISPR-DR39 ACC RF01358 DESC CRISPR RNA direct repeat element STATES 97 NODES 29 CLEN 31 W 45 ALPH RNA RF no CONS yes MAP yes DATE Wed Jul 10 18:24:15 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/RF01358/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 230842909 NULL 0.000 0.000 0.000 0.000 GA 39.00 TC 39.20 NC 38.40 EFP7GF -3.5982 0.74956 ECMLC 0.51605 -6.67773 5.21403 1600000 555045 0.002162 ECMGC 0.51419 -8.85429 4.03767 1600000 302661 0.001322 ECMLI 0.52350 -4.64152 6.43020 1600000 394790 0.003040 ECMGI 0.52912 -7.26489 5.14050 1600000 283613 0.001410 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 45 64 -7.331 -7.538 -0.041 -5.952 IL 1 1 2 1 4 1 1 50 69 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 49 68 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - A - - - ML 3 2 3 5 3 1 2 45 64 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 D 4 2 3 5 3 0 0 44 63 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 48 67 -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 44 63 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 7 5 3 8 3 0 0 43 62 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 46 66 -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 43 62 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 10 8 3 11 3 0 0 42 61 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 45 65 -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 42 61 -8.323 -0.016 -6.977 -2.168 -2.049 -2.929 1.767 D 13 11 3 14 3 0 0 41 60 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 44 63 -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 41 59 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 16 14 3 17 3 0 0 40 59 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 43 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - C - - - ML 18 17 3 20 3 1 1 40 58 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 19 17 3 20 3 0 0 39 57 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 42 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - A - - - ML 21 20 3 23 3 1 1 38 57 -8.323 -0.016 -6.977 1.837 -3.097 -2.659 -2.714 D 22 20 3 23 3 0 0 37 56 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - U - - - ML 24 23 3 26 3 1 1 37 56 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 25 23 3 26 3 0 0 36 55 -5.620 -0.734 -1.403 IL 26 26 3 26 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 31 - u - - MR 27 26 3 29 3 1 1 36 55 -8.693 -0.015 -7.010 0.324 0.027 -1.172 0.363 D 28 26 3 29 3 0 0 35 53 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 30 - a - - MR 30 29 3 32 3 1 1 35 54 -8.693 -0.015 -7.010 0.999 -0.026 -1.366 -0.663 D 31 29 3 32 3 0 0 34 52 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 29 - A - - MR 33 32 3 35 3 1 1 34 53 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 34 32 3 35 3 0 0 33 51 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 28 - U - - MR 36 35 3 38 3 1 1 33 52 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 37 35 3 38 3 0 0 32 50 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 27 - U - - MR 39 38 3 41 3 1 1 32 51 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 40 38 3 41 3 0 0 31 49 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 26 - U - - MR 42 41 3 44 3 1 1 31 50 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 43 41 3 44 3 0 0 30 48 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 25 - U - - MR 45 44 3 47 3 1 1 30 49 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 46 44 3 47 3 0 0 29 47 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 24 - A - - MR 48 47 3 50 3 1 1 29 48 -8.693 -0.015 -7.010 1.837 -3.097 -2.659 -2.714 D 49 47 3 50 3 0 0 28 46 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 23 - g - - MR 51 50 3 53 3 1 1 28 47 -8.693 -0.015 -7.010 -0.716 -1.430 0.995 0.037 D 52 50 3 53 3 0 0 27 45 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 22 - U - - MR 54 53 3 56 3 1 1 27 46 -8.693 -0.015 -7.010 -2.168 -2.049 -2.929 1.767 D 55 53 3 56 3 0 0 26 44 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 21 - C - - MR 57 56 3 59 3 1 1 26 45 -8.693 -0.015 -7.010 -2.619 1.795 -3.443 -1.863 D 58 56 3 59 3 0 0 25 43 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 1 27 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 20 - U - - MR 60 59 3 62 5 1 1 25 44 -7.411 -0.031 -7.227 -7.439 -8.330 -2.168 -2.049 -2.929 1.767 D 61 59 3 62 5 0 0 24 43 -5.352 -0.707 -2.978 -4.409 -2.404 IR 62 62 3 62 5 1 1 26 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 9 19 c g - - MP 63 62 3 67 6 2 2 24 43 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.136 -4.082 -3.955 -0.250 -2.768 -4.481 2.969 -3.516 -3.957 -0.051 -4.321 -2.017 2.202 -4.247 -0.421 -2.796 ML 64 62 3 67 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 65 62 3 67 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 66 62 3 67 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 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 68 68 6 68 5 1 1 24 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 10 18 C G - - MP 69 68 6 73 6 2 2 22 41 -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 70 68 6 73 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 71 68 6 73 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 72 68 6 73 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 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 74 74 6 74 5 1 1 22 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 11 17 u a - - MP 75 74 6 79 6 2 2 20 39 -9.266 -9.205 -0.019 -7.982 -8.261 -8.656 -4.077 -4.028 -3.912 -0.221 -2.759 -4.453 2.526 -3.497 -3.917 -0.022 -4.289 -1.979 2.724 -4.199 -0.419 -2.766 ML 76 74 6 79 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 77 74 6 79 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 78 74 6 79 6 0 0 18 37 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 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 80 80 6 80 5 1 1 20 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 24 ] 12 16 C G - - MP 81 80 6 85 4 2 2 18 37 -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 82 80 6 85 4 1 1 19 38 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 4 1 1 19 38 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 84 80 6 85 4 0 0 18 37 -4.568 -4.250 -2.265 -0.520 IL 85 85 5 85 4 1 1 21 39 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 86 86 6 86 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 13 - C - - - ML 87 86 6 89 3 1 1 15 33 -8.323 -0.016 -6.977 -2.619 1.795 -3.443 -1.863 D 88 86 6 89 3 0 0 15 33 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 14 - A - - - ML 90 89 3 92 3 1 1 13 31 -8.323 -0.016 -6.977 1.067 -1.741 0.223 -1.189 D 91 89 3 92 3 0 0 13 32 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 27 ] 15 - A - - - ML 93 92 3 95 2 1 1 1 1 * 0.000 1.837 -3.097 -2.659 -2.714 D 94 92 3 95 2 0 0 0 0 * 0.000 IL 95 95 3 95 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 28 ] - - - - - - E 96 95 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME CRISPR-DR39 ACC RF01358 DESC CRISPR RNA direct repeat element LENG 31 MAXL 103 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Jul 10 18:24:15 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/RF01358/CM NSEQ 3 EFFN 2.270508 CKSUM 230842909 STATS LOCAL MSV -7.4229 0.74956 STATS LOCAL VITERBI -7.9013 0.74956 STATS LOCAL FORWARD -2.6372 0.74956 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.37449 1.40748 1.84071 1.06837 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 0.16084 3.20491 2.93237 2.90524 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 2 2.57778 2.54724 3.09385 0.22260 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 2.57778 2.54724 3.09385 0.22260 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 2.57778 2.54724 3.09385 0.22260 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 2.80462 0.20998 3.38025 2.35564 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 2.80462 0.20998 3.38025 2.35564 6 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 0.16084 3.20491 2.93237 2.90524 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 2.57778 2.54724 3.09385 0.22260 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 2.54047 0.73649 2.28594 1.07675 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 3.16004 0.24913 2.93098 2.08144 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 2.51384 0.99021 2.25711 0.81443 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 3.16076 0.24904 2.93132 2.08156 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 2.80462 0.20998 3.38025 2.35564 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 0.69507 2.42815 1.26554 2.03505 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 0.16084 3.20491 2.93237 2.90524 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 2.35948 3.09987 0.21496 2.92064 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 0.92522 2.42371 0.88513 2.27983 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 2.36157 3.10268 0.21433 2.92406 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 1.22333 2.45476 0.65296 2.30897 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 2.57778 2.54724 3.09385 0.22260 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 2.80462 0.20998 3.38025 2.35564 21 C - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 2.57778 2.54724 3.09385 0.22260 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 1.76069 2.24454 0.77672 1.33871 23 g - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 0.16084 3.20491 2.93237 2.90524 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 2.57778 2.54724 3.09385 0.22260 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 2.57778 2.54724 3.09385 0.22260 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 2.57778 2.54724 3.09385 0.22260 27 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 28 2.57778 2.54724 3.09385 0.22260 28 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 29 0.16084 3.20491 2.93237 2.90524 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 0.74684 1.43188 2.20926 1.72880 30 a - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 31 1.17065 1.39350 2.12698 1.13186 31 u - - : 1.38629 1.38629 1.38629 1.38629 0.01980 3.93183 * 1.46634 0.26236 0.00000 * //