INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-clpP ACC RF04331 DESC Plastid-clpP 5UTR RNA STATES 216 NODES 62 CLEN 69 W 86 ALPH RNA RF no CONS yes MAP yes DATE Tue Sep 2 22:48:31 2025 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/15.1/Chloroplasts/fixed/GOOD/NC_008457.1/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 343 EFFN 2.049019 CKSUM 1817873414 NULL 0.000 0.000 0.000 0.000 GA 55.00 TC 55.00 NC 54.90 EFP7GF -7.9860 0.71893 ECMLC 0.52399 -10.80634 1.40441 1600000 720986 0.001664 ECMGC 0.39442 -14.94554 -1.29474 1600000 87169 0.004589 ECMLI 0.49834 -8.68873 3.31368 1600000 475118 0.002526 ECMGI 0.43183 -9.78178 2.02070 1600000 65388 0.006117 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 86 107 -6.996 -7.203 -0.305 -2.507 IL 1 1 2 1 4 3 28 90 111 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 2 28 89 110 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 2 - A - - - ML 3 2 3 5 3 2 26 86 107 -7.784 -0.023 -6.438 1.584 -1.898 -1.489 -1.408 D 4 2 3 5 3 0 25 85 106 -7.425 -0.970 -1.047 IL 5 5 3 5 3 2 27 88 109 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 3 - A - - - ML 6 5 3 8 3 1 25 85 106 -8.328 -0.266 -2.599 1.397 -1.561 -0.920 -1.003 D 7 5 3 8 3 0 24 84 105 -5.987 -0.780 -1.315 IL 8 8 3 8 3 2 26 86 107 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 140 - G - - MR 9 8 3 11 2 1 25 84 105 -8.057 -0.005 -0.559 -1.756 1.358 -1.113 D 10 8 3 11 2 0 24 83 104 -5.769 -0.027 IR 11 11 3 11 2 1 25 85 106 -1.823 -0.479 0.000 0.000 0.000 0.000 [ BIF 4 ] - - - - - - B 12 11 3 13 75 0 24 83 104 [ BEGL 5 ] - - - - - - S 13 12 1 14 4 0 0 35 56 -0.061 -6.858 -5.350 -6.905 [ MATP 6 ] 4 53 u g - - MP 14 13 1 18 6 2 2 35 56 -9.113 -8.149 -0.023 -7.829 -8.109 -8.504 -2.474 -2.507 -2.441 0.826 -2.217 -3.392 1.768 -2.699 -2.634 1.041 -2.693 -0.776 1.479 -2.585 1.824 -1.451 ML 15 13 1 18 6 1 1 35 55 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 16 13 1 18 6 1 1 34 55 -7.128 -5.857 -1.695 -5.835 -0.764 -4.049 0.280 -0.513 0.091 0.029 D 17 13 1 18 6 0 0 33 53 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 18 18 5 18 6 1 1 35 56 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 19 19 6 19 5 1 1 35 56 -2.205 -0.545 -5.989 -4.156 -5.262 0.000 0.000 0.000 0.000 [ MATP 7 ] 5 47 U A - - MP 20 19 6 24 4 2 2 33 54 -6.969 -6.843 -0.055 -5.590 -3.147 -3.166 -3.260 0.260 -2.595 -4.064 1.270 -3.313 -3.282 0.460 -3.813 -1.369 3.111 -2.825 -0.378 -2.019 ML 21 19 6 24 4 1 1 34 54 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 22 19 6 24 4 1 1 33 54 -4.946 -3.975 -1.815 -0.690 0.644 -0.574 -0.277 -0.090 D 23 19 6 24 4 0 0 32 53 -4.568 -4.250 -2.265 -0.520 IL 24 24 5 24 4 1 1 35 56 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 25 25 6 25 3 1 1 34 55 -1.410 -0.816 -4.170 0.000 0.000 0.000 0.000 [ MATL 8 ] 6 - c - - - ML 26 25 6 28 3 1 1 31 52 -8.374 -0.018 -6.692 -0.331 0.696 -1.287 0.233 D 27 25 6 28 3 0 0 30 51 -5.752 -0.652 -1.535 IL 28 28 3 28 3 1 1 32 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 41 - A - - MR 29 28 3 31 5 1 1 30 51 -6.682 -0.061 -6.948 -5.640 -8.052 1.589 -1.854 -1.500 -1.467 D 30 28 3 31 5 0 0 29 49 -5.352 -0.707 -2.978 -4.409 -2.404 IR 31 31 3 31 5 1 1 30 51 -2.248 -0.534 -5.973 -4.141 -5.247 0.000 0.000 0.000 0.000 [ MATP 10 ] 7 35 U A - - MP 32 31 3 36 6 2 2 29 50 -9.117 -7.243 -0.028 -7.833 -8.113 -8.508 -2.943 -3.369 -3.503 0.079 -3.057 -4.311 1.042 -3.551 -2.929 0.315 -4.050 -1.519 3.279 -3.659 -0.833 -2.464 ML 33 31 3 36 6 1 1 27 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 34 31 3 36 6 1 1 27 48 -7.089 -5.818 -1.704 -5.796 -0.766 -4.010 0.494 -0.566 -0.028 -0.097 D 35 31 3 36 6 0 0 25 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 36 36 5 36 6 1 1 28 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 37 37 6 37 5 1 1 28 49 -2.449 -0.480 -5.960 -4.128 -5.233 0.000 0.000 0.000 0.000 [ MATP 11 ] 8 33 G C - - MP 38 37 6 42 6 2 2 27 48 -9.118 -8.605 -0.022 -7.833 -8.113 -8.508 -3.910 -2.485 -3.886 0.793 -4.345 -4.252 0.314 -4.315 -3.920 3.353 -4.259 -0.394 -0.107 -3.260 -1.782 -2.855 ML 39 37 6 42 6 1 1 25 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 40 37 6 42 6 1 1 25 46 -7.082 -5.811 -1.640 -5.789 -0.880 -3.437 0.426 -0.282 -0.333 0.058 D 41 37 6 42 6 0 0 23 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 42 42 5 42 6 1 1 27 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 43 43 6 43 5 1 1 26 47 -2.340 -0.512 -5.943 -4.111 -5.217 0.000 0.000 0.000 0.000 [ MATP 12 ] 9 28 U A - - MP 44 43 6 48 6 2 2 25 46 -9.120 -8.736 -0.022 -7.836 -8.116 -8.511 -4.226 -4.110 -4.058 -0.400 -2.973 -4.601 1.356 -3.689 -4.073 -0.146 -4.441 -2.061 3.343 -4.356 -0.550 -2.890 ML 45 43 6 48 6 1 1 23 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 46 43 6 48 6 1 1 23 44 -7.012 -5.741 -1.650 -5.719 -0.810 -3.933 0.460 -0.450 -0.187 0.020 D 47 43 6 48 6 0 0 21 42 -9.115 -7.813 -3.610 -4.292 -4.310 -0.303 IL 48 48 5 48 6 1 1 25 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 49 49 6 49 5 1 1 24 45 -2.395 -0.499 -5.928 -4.095 -5.201 0.000 0.000 0.000 0.000 [ MATP 13 ] 10 25 U A - - MP 50 49 6 54 6 2 2 23 44 -9.120 -9.059 -0.030 -6.545 -8.116 -8.511 -4.225 -4.110 -4.058 -0.400 -2.972 -4.600 1.356 -3.688 -4.073 -0.146 -4.441 -2.062 3.343 -4.355 -0.548 -2.889 ML 51 49 6 54 6 1 1 22 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 52 49 6 54 6 1 1 22 43 -7.012 -5.741 -1.650 -5.719 -0.810 -3.933 0.460 -0.450 -0.187 0.020 D 53 49 6 54 6 0 0 20 41 -9.115 -7.813 -3.610 -4.292 -4.310 -0.303 IL 54 54 5 54 6 1 1 23 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 55 55 6 55 5 1 1 22 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 11 24 c g - - MP 56 55 6 60 4 2 2 21 42 -6.628 -7.164 -0.056 -5.578 -3.469 -3.423 -2.929 0.253 -2.477 -4.041 2.928 -3.150 -3.423 0.489 -3.847 -1.451 1.306 -3.643 0.884 -2.325 ML 57 55 6 60 4 1 1 21 42 -3.846 -4.029 -0.471 -2.758 0.222 -0.021 -0.437 0.150 MR 58 55 6 60 4 1 1 21 41 -4.838 -3.867 -1.734 -0.747 0.397 -0.481 -0.019 -0.030 D 59 55 6 60 4 0 0 20 40 -4.630 -4.312 -2.327 -0.494 IL 60 60 5 60 4 1 1 22 43 -1.699 -2.382 -1.102 -4.868 0.000 0.000 0.000 0.000 IR 61 61 6 61 3 1 1 22 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 13 - G - - - ML 62 61 6 64 3 1 1 18 39 -7.543 -0.022 -6.649 -0.435 -1.564 1.291 -1.072 D 63 61 6 64 3 0 0 17 38 -6.306 -1.671 -0.571 IL 64 64 3 64 3 1 1 20 41 -1.447 -0.794 -4.147 0.000 0.000 0.000 0.000 [ MATL 16 ] 15 - U - - - ML 65 64 3 67 3 1 1 17 38 -6.172 -0.035 -6.654 -0.967 -1.026 -1.653 1.422 D 66 64 3 67 3 0 0 16 37 -6.261 -1.774 -0.526 IL 67 67 3 67 3 1 1 21 42 -1.250 -0.917 -4.320 0.000 0.000 0.000 0.000 [ MATL 17 ] 22 - A - - - ML 68 67 3 70 3 1 1 13 31 -8.000 -0.020 -6.654 1.616 -1.917 -1.622 -1.537 D 69 67 3 70 3 0 0 13 32 -6.261 -1.774 -0.526 IL 70 70 3 70 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 23 - G - - - ML 71 70 3 73 2 1 1 1 1 * 0.000 0.030 -1.426 1.055 -0.917 D 72 70 3 73 2 0 0 0 0 * 0.000 IL 73 73 3 73 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 19 ] - - - - - - E 74 73 3 -1 0 0 0 0 0 [ BEGR 20 ] - - - - - - S 75 12 1 76 3 0 7 62 82 -7.076 -0.025 -6.663 IL 76 76 2 76 3 1 7 65 86 -1.394 -0.825 -4.190 0.000 0.000 0.000 0.000 [ MATL 21 ] 58 - A - - - ML 77 76 2 79 3 1 8 62 82 -8.009 -0.020 -6.663 1.399 -1.269 -1.161 -0.997 D 78 76 2 79 3 0 2 61 81 -6.174 -1.687 -0.566 IL 79 79 3 79 3 1 6 64 84 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 59 - G - - - ML 80 79 3 82 3 1 7 61 81 -8.009 -0.020 -6.663 -0.787 -1.898 1.427 -1.107 D 81 79 3 82 3 0 1 60 80 -6.174 -1.687 -0.566 IL 82 82 3 82 3 1 6 63 83 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 60 - A - - - ML 83 82 3 85 3 1 6 60 80 -8.009 -0.020 -6.663 1.738 -2.462 -2.085 -2.014 D 84 82 3 85 3 0 0 59 79 -6.174 -1.687 -0.566 IL 85 85 3 85 3 1 5 62 82 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 61 - A - - - ML 86 85 3 88 3 1 6 59 79 -8.009 -0.020 -6.663 1.684 -2.263 -1.763 -1.814 D 87 85 3 88 3 0 0 58 78 -6.174 -1.687 -0.566 IL 88 88 3 88 3 1 4 61 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 62 - G - - - ML 89 88 3 91 3 1 5 58 78 -8.009 -0.020 -6.663 -0.346 -1.839 1.335 -1.282 D 90 88 3 91 3 0 0 56 77 -6.174 -1.687 -0.566 IL 91 91 3 91 3 1 4 60 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 63 - C - - - ML 92 91 3 94 3 1 4 57 77 -7.668 -0.031 -5.922 -1.401 1.512 -2.110 -0.894 D 93 91 3 94 3 0 0 55 75 -6.174 -1.687 -0.566 IL 94 94 3 94 3 1 3 59 79 -1.421 -0.809 -4.160 0.000 0.000 0.000 0.000 [ MATL 27 ] 69 - A - - - ML 95 94 3 97 3 1 4 56 76 -8.000 -0.020 -6.654 1.656 -2.147 -1.696 -1.668 D 96 94 3 97 3 0 0 54 74 -6.262 -1.775 -0.525 IL 97 97 3 97 3 1 2 58 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 28 ] 70 - G - - - ML 98 97 3 100 3 1 4 55 75 -8.000 -0.020 -6.654 -0.567 -2.022 1.433 -1.400 D 99 97 3 100 3 0 0 53 73 -6.262 -1.775 -0.525 IL 100 100 3 100 3 1 2 57 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 29 ] 71 - A - - - ML 101 100 3 103 3 1 3 54 74 -8.000 -0.020 -6.654 1.597 -2.012 -1.376 -1.546 D 102 100 3 103 3 0 0 52 72 -6.262 -1.775 -0.525 IL 103 103 3 103 3 1 2 56 76 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 72 - U - - - ML 104 103 3 106 3 1 3 53 72 -8.000 -0.020 -6.654 -1.433 -1.371 -2.168 1.595 D 105 103 3 106 3 0 0 51 71 -6.262 -1.775 -0.525 IL 106 106 3 106 3 1 1 55 75 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 73 - c - - - ML 107 106 3 109 3 1 2 52 71 -5.656 -0.044 -6.654 -0.614 0.582 -1.437 0.566 D 108 106 3 109 3 0 0 50 70 -6.262 -1.775 -0.525 IL 109 109 3 109 3 1 1 53 73 -1.495 -0.759 -4.196 0.000 0.000 0.000 0.000 [ MATL 32 ] 75 - U - - - ML 110 109 3 112 3 1 2 50 70 -6.882 -0.027 -6.654 -1.551 -1.536 -2.288 1.637 D 111 109 3 112 3 0 0 49 69 -6.262 -1.775 -0.525 IL 112 112 3 112 3 1 1 52 72 -1.457 -0.786 -4.157 0.000 0.000 0.000 0.000 [ MATL 33 ] 77 - A - - - ML 113 112 3 115 3 1 2 49 69 -8.000 -0.020 -6.654 1.734 -2.443 -2.068 -1.992 D 114 112 3 115 3 0 0 48 68 -6.262 -1.775 -0.525 IL 115 115 3 115 3 1 1 51 71 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 78 - U - - - ML 116 115 3 118 3 1 2 48 68 -7.647 -0.022 -6.654 -1.551 -1.536 -2.288 1.637 D 117 115 3 118 3 0 0 47 67 -6.262 -1.775 -0.525 IL 118 118 3 118 3 1 1 50 70 -1.420 -0.810 -4.160 0.000 0.000 0.000 0.000 [ MATL 35 ] 84 - U - - - ML 119 118 3 121 3 1 1 47 67 -8.000 -0.020 -6.654 -1.551 -1.536 -2.288 1.637 D 120 118 3 121 3 0 0 46 65 -6.262 -1.775 -0.525 IL 121 121 3 121 3 1 1 49 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 85 - C - - - ML 122 121 3 124 3 1 1 46 66 -8.000 -0.020 -6.654 -1.116 1.263 -1.940 -0.187 D 123 121 3 124 3 0 0 45 64 -6.262 -1.775 -0.525 IL 124 124 3 124 3 1 1 48 68 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 86 - U - - - ML 125 124 3 127 3 1 1 45 65 -7.284 -0.024 -6.654 -1.551 -1.536 -2.288 1.637 D 126 124 3 127 3 0 0 44 63 -6.262 -1.775 -0.525 IL 127 127 3 127 3 1 1 47 67 -1.394 -0.825 -4.184 0.000 0.000 0.000 0.000 [ MATL 38 ] 92 - A - - - ML 128 127 3 130 3 1 1 44 63 -7.502 -0.026 -6.370 1.734 -2.443 -2.068 -1.992 D 129 127 3 130 3 0 0 43 62 -6.262 -1.775 -0.525 IL 130 130 3 130 3 1 1 46 66 -1.410 -0.816 -4.169 0.000 0.000 0.000 0.000 [ MATL 39 ] 98 - U - - - ML 131 130 3 133 3 1 1 43 62 -7.650 -0.022 -6.650 -0.832 -0.812 -1.405 1.317 D 132 130 3 133 3 0 0 42 61 -6.290 -1.711 -0.553 IL 133 133 3 133 3 1 1 45 65 -1.369 -0.841 -4.192 0.000 0.000 0.000 0.000 [ MATL 40 ] 113 - A - - - ML 134 133 3 136 5 1 1 42 61 -7.124 -0.103 -4.287 -7.152 -8.043 1.734 -2.443 -2.068 -1.992 D 135 133 3 136 5 0 0 40 60 -5.010 -0.854 -4.271 -2.646 -2.293 IL 136 136 3 136 5 1 1 42 61 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 41 ] 114 139 c g - - MP 137 136 3 141 6 2 2 41 60 -9.092 -9.031 -0.021 -7.808 -8.088 -8.483 -2.898 -2.922 -2.790 0.531 -2.206 -3.494 2.935 -2.072 -3.013 0.692 -3.520 -1.114 1.213 -3.163 -0.024 -1.987 ML 138 136 3 141 6 1 1 39 59 -6.601 -6.947 -0.910 -1.356 -6.797 -4.327 0.016 0.304 -0.677 0.175 MR 139 136 3 141 6 1 1 39 59 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 140 136 3 141 6 0 0 37 56 -9.116 -7.814 -3.611 -4.293 -4.311 -0.303 IL 141 141 5 141 6 1 1 40 60 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 142 142 6 142 5 1 1 40 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 115 138 c g - - MP 143 142 6 147 6 2 2 39 58 -9.122 -9.061 -0.021 -7.838 -8.118 -8.513 -3.551 -3.558 -3.459 0.098 -1.897 -4.045 2.787 -3.160 -3.478 0.275 -3.880 -1.640 1.175 -3.714 1.639 -2.385 ML 144 142 6 147 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 145 142 6 147 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 146 142 6 147 6 0 0 36 55 -9.116 -7.814 -3.611 -4.293 -4.311 -0.303 IL 147 147 5 147 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 148 148 6 148 5 1 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 116 137 C G - - MP 149 148 6 153 4 2 2 37 56 -6.986 -7.193 -0.052 -5.607 -4.200 -4.130 -3.316 -0.488 -3.288 -4.777 3.548 -3.991 -4.198 -0.216 -4.100 -2.156 0.371 -4.394 -0.924 -3.115 ML 150 148 6 153 4 1 1 37 57 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 151 148 6 153 4 1 1 37 56 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 152 148 6 153 4 0 0 36 55 -4.631 -4.312 -2.328 -0.494 IL 153 153 5 153 4 1 1 39 58 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 154 154 6 154 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 44 ] 117 - G - - - ML 155 154 6 157 3 1 1 34 53 -8.000 -0.020 -6.654 -0.499 -1.875 1.372 -1.210 D 156 154 6 157 3 0 0 33 52 -6.262 -1.775 -0.525 IL 157 157 3 157 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 45 ] 118 - A - - - ML 158 157 3 160 3 1 1 33 52 -8.000 -0.020 -6.654 1.734 -2.443 -2.068 -1.992 D 159 157 3 160 3 0 0 32 51 -6.262 -1.775 -0.525 IL 160 160 3 160 3 1 1 35 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 119 - U - - - ML 161 160 3 163 3 1 1 32 51 -8.000 -0.020 -6.654 -1.014 -1.090 -1.622 1.438 D 162 160 3 163 3 0 0 31 50 -6.262 -1.775 -0.525 IL 163 163 3 163 3 1 1 34 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 120 - A - - - ML 164 163 3 166 3 1 1 31 50 -8.000 -0.020 -6.654 1.658 -2.114 -1.716 -1.695 D 165 163 3 166 3 0 0 30 49 -6.262 -1.775 -0.525 IL 166 166 3 166 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 48 ] 121 - A - - - ML 167 166 3 169 3 1 1 30 48 -8.388 -0.018 -6.705 1.636 -1.919 -1.774 -1.580 D 168 166 3 169 3 0 0 28 47 -5.674 -0.788 -1.317 IL 169 169 3 169 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 49 ] - 136 - U - - MR 170 169 3 172 3 1 1 29 47 -8.388 -0.018 -6.705 -1.551 -1.536 -2.288 1.637 D 171 169 3 172 3 0 0 27 46 -6.465 -1.643 -0.581 IR 172 172 3 172 3 1 1 29 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 50 ] - 135 - A - - MR 173 172 3 175 3 1 1 28 46 -8.388 -0.018 -6.705 1.734 -2.443 -2.068 -1.992 D 174 172 3 175 3 0 0 26 45 -6.465 -1.643 -0.581 IR 175 175 3 175 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 51 ] - 134 - A - - MR 176 175 3 178 3 1 1 27 45 -8.388 -0.018 -6.705 1.734 -2.443 -2.068 -1.992 D 177 175 3 178 3 0 0 25 44 -6.465 -1.643 -0.581 IR 178 178 3 178 3 1 1 27 46 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 52 ] - 133 - C - - MR 179 178 3 181 3 1 1 26 44 -8.388 -0.018 -6.705 -1.827 1.647 -2.654 -1.223 D 180 178 3 181 3 0 0 24 43 -6.465 -1.643 -0.581 IR 181 181 3 181 3 1 1 26 45 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 53 ] - 132 - G - - MR 182 181 3 184 5 1 1 25 43 -7.124 -0.038 -6.940 -7.152 -8.043 -1.656 -2.888 1.740 -2.275 D 183 181 3 184 5 0 0 23 42 -5.394 -0.749 -3.021 -4.452 -2.235 IR 184 184 3 184 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 54 ] 122 131 G C - - MP 185 184 3 189 6 2 2 24 42 -9.122 -9.061 -0.021 -7.838 -8.118 -8.513 -4.180 -2.273 -4.206 0.631 -4.863 -4.494 -0.262 -4.611 -4.057 3.456 -4.415 0.048 -0.546 -4.016 -2.253 -3.131 ML 186 184 3 189 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 187 184 3 189 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 188 184 3 189 6 0 0 20 39 -9.116 -7.814 -3.611 -4.293 -4.311 -0.303 IL 189 189 5 189 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 190 190 6 190 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 55 ] 123 130 U A - - MP 191 190 6 195 6 2 2 22 40 -9.122 -9.061 -0.021 -7.838 -8.118 -8.513 -2.949 -3.195 -3.291 0.142 -2.870 -4.118 0.998 -3.419 -2.719 0.318 -3.867 -1.467 3.256 -3.260 -0.785 -2.312 ML 192 190 6 195 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 193 190 6 195 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 194 190 6 195 6 0 0 19 38 -9.116 -7.814 -3.611 -4.293 -4.311 -0.303 IL 195 195 5 195 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 196 196 6 196 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 56 ] 124 129 A U - - MP 197 196 6 201 4 2 2 20 38 -6.986 -7.193 -0.052 -5.607 -3.553 -2.883 -3.190 3.329 -3.747 -4.598 0.255 -3.068 -3.687 0.955 -4.210 -0.799 -0.034 -3.845 -1.578 -2.616 ML 198 196 6 201 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 199 196 6 201 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 200 196 6 201 4 0 0 19 38 -4.631 -4.312 -2.328 -0.494 IL 201 201 5 201 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 202 202 6 202 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 57 ] 125 - C - - - ML 203 202 6 205 3 1 1 16 35 -8.000 -0.020 -6.654 -1.029 1.179 -1.850 -0.046 D 204 202 6 205 3 0 0 16 34 -6.262 -1.775 -0.525 IL 205 205 3 205 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 58 ] 126 - C - - - ML 206 205 3 208 3 1 1 15 33 -8.000 -0.020 -6.654 -1.591 1.556 -2.418 -0.889 D 207 205 3 208 3 0 0 15 33 -6.262 -1.775 -0.525 IL 208 208 3 208 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 59 ] 127 - A - - - ML 209 208 3 211 3 1 1 13 31 -8.000 -0.020 -6.654 1.670 -2.214 -1.701 -1.762 D 210 208 3 211 3 0 0 13 32 -6.262 -1.775 -0.525 IL 211 211 3 211 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 60 ] 128 - A - - - ML 212 211 3 214 2 1 1 1 1 * 0.000 1.734 -2.443 -2.068 -1.992 D 213 211 3 214 2 0 0 0 0 * 0.000 IL 214 214 3 214 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 61 ] - - - - - - E 215 214 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-clpP ACC RF04331 DESC Plastid-clpP 5UTR RNA LENG 69 MAXL 155 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Sep 2 22:48:31 2025 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/15.1/Chloroplasts/fixed/GOOD/NC_008457.1/CM NSEQ 343 EFFN 2.629967 CKSUM 1817873414 STATS LOCAL MSV -8.4640 0.71893 STATS LOCAL VITERBI -9.0320 0.71893 STATS LOCAL FORWARD -3.5016 0.71893 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.05429 1.69067 1.55393 1.36356 1.38629 1.38629 1.38629 1.38629 0.65430 0.82072 3.21699 0.11261 2.23963 0.00000 * 1 0.22825 2.91139 2.59116 2.59376 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.04486 3.81971 3.81971 1.46634 0.26236 0.82352 0.57783 2 0.36754 2.59699 2.08752 2.21576 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.03957 3.94251 3.94251 1.46634 0.26236 1.09861 0.40547 3 1.96319 1.46342 1.74909 0.78918 4 u - - < 1.38629 1.38629 1.38629 1.38629 0.03819 3.97732 3.97732 1.46634 0.26236 1.09861 0.40547 4 2.53914 1.97565 2.34541 0.37602 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.03804 3.98122 3.98122 1.46634 0.26236 1.09861 0.40547 5 1.67664 0.84006 2.37922 1.24240 6 c - - - 1.38629 1.38629 1.38629 1.38629 0.03799 3.98243 3.98243 1.46634 0.26236 1.09861 0.40547 6 2.73131 2.23021 2.51710 0.29214 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.03792 3.98432 3.98432 1.46634 0.26236 1.09861 0.40547 7 2.09162 2.54545 0.33442 2.49714 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.03787 3.98555 3.98555 1.46634 0.26236 1.09861 0.40547 8 3.10789 1.96015 2.87405 0.27708 9 U - - < 1.38629 1.38629 1.38629 1.38629 0.03770 3.98997 3.98997 1.46634 0.26236 1.09861 0.40547 9 3.10719 1.95955 2.87355 0.27726 10 U - - < 1.38629 1.38629 1.38629 1.38629 0.03770 3.98997 3.98997 1.46634 0.26236 1.09861 0.40547 10 2.42261 0.65687 2.22720 1.25524 11 C - - < 1.38629 1.38629 1.38629 1.38629 0.03995 3.87924 3.98997 1.33212 0.30641 1.09861 0.40547 11 1.77507 2.57864 0.42832 2.27256 13 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03943 3.90406 3.98997 1.36093 0.29628 1.09861 0.40547 12 2.21519 2.21859 2.69007 0.33655 15 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04948 3.51162 3.99405 1.59983 0.22556 1.09861 0.40547 13 0.21597 2.88407 2.67350 2.66893 22 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03755 3.99405 3.99405 1.46634 0.26236 1.09861 0.40547 14 1.40016 2.47887 0.59120 2.15468 23 G - - _ 1.38629 1.38629 1.38629 1.38629 0.05577 3.99405 3.32916 1.46634 0.26236 1.09861 0.40547 15 1.78250 2.39554 0.45546 2.23959 24 G - - > 1.38629 1.38629 1.38629 1.38629 0.03822 3.97650 3.97650 1.46634 0.26236 0.70738 0.67912 16 0.32052 3.04128 1.77748 2.85788 25 A - - > 1.38629 1.38629 1.38629 1.38629 0.03887 3.92730 3.99405 1.40917 0.28017 1.09861 0.40547 17 0.32108 3.03733 1.77791 2.85282 28 A - - > 1.38629 1.38629 1.38629 1.38629 0.03952 3.89588 3.99405 1.45499 0.26579 1.09861 0.40547 18 2.72787 0.38502 2.37304 1.82628 33 C - - > 1.38629 1.38629 1.38629 1.38629 0.05072 3.46837 4.00159 0.92951 0.50211 1.09861 0.40547 19 0.32419 2.70431 2.03523 2.53429 35 A - - > 1.38629 1.38629 1.38629 1.38629 0.04082 3.82984 4.00159 1.50230 0.25182 1.09861 0.40547 20 0.23544 2.82803 2.56607 2.60626 41 A - - - 1.38629 1.38629 1.38629 1.38629 0.03919 3.90460 4.00159 1.48842 0.25583 1.09861 0.40547 21 0.44040 2.47022 1.76316 2.30106 47 A - - > 1.38629 1.38629 1.38629 1.38629 0.04179 3.78802 4.00159 1.50911 0.24988 1.09861 0.40547 22 1.57608 1.91970 0.75146 1.74362 53 g - - > 1.38629 1.38629 1.38629 1.38629 0.04149 3.80058 4.00159 1.44530 0.26876 1.09861 0.40547 23 0.36494 2.34479 2.28976 2.22008 58 A - - - 1.38629 1.38629 1.38629 1.38629 0.03726 4.00159 4.00159 1.46634 0.26236 1.09861 0.40547 24 2.06589 2.87190 0.33491 2.28967 59 G - - - 1.38629 1.38629 1.38629 1.38629 0.03726 4.00159 4.00159 1.46634 0.26236 1.09861 0.40547 25 0.13397 3.37411 3.08515 3.09199 60 A - - - 1.38629 1.38629 1.38629 1.38629 0.03726 4.00159 4.00159 1.46634 0.26236 1.09861 0.40547 26 0.16978 3.19517 2.79759 2.91440 61 A - - - 1.38629 1.38629 1.38629 1.38629 0.03726 4.00159 4.00159 1.46634 0.26236 1.09861 0.40547 27 1.69850 2.81611 0.39892 2.45158 62 G - - - 1.38629 1.38629 1.38629 1.38629 0.03726 4.00159 4.00159 1.46634 0.26236 1.09861 0.40547 28 2.62598 0.25675 3.09287 2.21918 63 C - - - 1.38629 1.38629 1.38629 1.38629 0.03877 3.93213 3.99378 1.48097 0.25802 1.09861 0.40547 29 0.18867 3.09217 2.73916 2.78205 69 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 30 1.88092 2.97302 0.33127 2.54602 70 G - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 31 0.22860 2.97975 2.46262 2.68329 71 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 32 2.60974 2.51133 3.12756 0.22132 72 U - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 33 1.90646 0.92633 2.49813 0.98577 73 c - - - 1.38629 1.38629 1.38629 1.38629 0.05676 3.30353 3.99378 0.81294 0.58618 1.09861 0.40547 34 2.72288 2.66777 3.24460 0.19125 75 U - - - 1.38629 1.38629 1.38629 1.38629 0.04303 3.74289 3.99378 1.18155 0.36644 1.09861 0.40547 35 0.13615 3.35908 3.07155 3.07539 77 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 36 2.72288 2.66777 3.24460 0.19125 78 U - - - 1.38629 1.38629 1.38629 1.38629 0.03882 3.92971 3.99378 1.48150 0.25786 1.09861 0.40547 37 2.72288 2.66777 3.24460 0.19125 84 U - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 38 2.34865 0.43428 2.93720 1.59081 85 C - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 39 2.72288 2.66777 3.24460 0.19125 86 U - - - 1.38629 1.38629 1.38629 1.38629 0.04051 3.85049 3.99378 1.49729 0.25326 1.09861 0.40547 40 0.13615 3.35908 3.07155 3.07539 92 A - - - 1.38629 1.38629 1.38629 1.38629 0.04204 3.89904 3.86783 1.48796 0.25597 1.09861 0.40547 41 2.10855 2.04063 2.48308 0.40774 98 U - - - 1.38629 1.38629 1.38629 1.38629 0.03889 3.92864 3.99131 1.66277 0.21024 1.01643 0.44924 42 0.13615 3.35908 3.07155 3.07539 113 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 43 2.13358 0.64767 2.00625 1.49686 114 C - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 44 2.55846 0.74819 2.38284 1.02984 115 c - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 45 3.07102 0.21730 2.90331 2.36343 116 C - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 46 1.82411 2.84812 0.37369 2.38060 117 G - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 47 0.13615 3.35908 3.07155 3.07539 118 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 48 2.26089 2.27735 2.66703 0.32334 119 U - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 49 0.18751 3.05858 2.75467 2.80685 120 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 50 0.20140 2.88732 2.81037 2.71045 121 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 51 2.22641 2.98013 0.24413 2.84878 122 G - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 52 2.65962 2.23760 2.47045 0.30278 123 U - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 53 0.26579 2.83811 2.19697 2.75319 124 A - - < 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 54 2.27197 0.49337 2.85937 1.47394 125 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 55 2.77354 0.23385 3.35407 2.19697 126 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 56 0.17870 3.15423 2.74427 2.87041 127 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 57 0.13615 3.35908 3.07155 3.07539 128 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 58 2.98057 2.39772 2.67833 0.23619 129 U - - > 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 59 0.33092 2.66546 2.05079 2.48246 130 A - - > 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 60 3.08931 0.30973 2.80608 1.83021 131 C - - > 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 61 2.82251 3.71656 0.12894 3.29151 132 G - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 62 2.99158 0.17436 3.56762 2.50626 133 C - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 63 0.13615 3.35908 3.07155 3.07539 134 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 64 0.13615 3.35908 3.07155 3.07539 135 A - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 65 2.72288 2.66777 3.24460 0.19125 136 U - - - 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 66 2.64105 3.10960 0.18293 2.97071 137 G - - > 1.38629 1.38629 1.38629 1.38629 0.03756 3.99378 3.99378 1.46634 0.26236 1.09861 0.40547 67 1.86986 2.56918 0.39030 2.38157 138 G - - > 1.38629 1.38629 1.38629 1.38629 0.04107 3.93728 3.87563 1.46634 0.26236 1.09861 0.40547 68 1.77863 2.16622 0.56035 1.92752 139 G - - > 1.38629 1.38629 1.38629 1.38629 0.06371 3.78497 3.24391 1.46634 0.26236 1.11959 0.39514 69 1.89903 2.78174 0.36899 2.33384 140 G - - : 1.38629 1.38629 1.38629 1.38629 0.08523 2.50471 * 0.97014 0.47647 0.00000 * //