INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-ccsA-ndhD-2 ACC RF04347 DESC Plastid-ccsA-ndhD-2 3UTR RNA STATES 163 NODES 36 CLEN 53 W 71 ALPH RNA RF no CONS yes MAP yes DATE Thu Nov 13 16:34:03 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_031887.1/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 421 EFFN 5.148796 CKSUM 2337396393 NULL 0.000 0.000 0.000 0.000 GA 51.50 TC 51.50 NC 51.40 EFP7GF -13.5349 0.71961 ECMLC 0.64020 -5.29094 3.87312 1600000 423756 0.002832 ECMGC 0.48418 -13.82688 0.70049 1600000 453754 0.000882 ECMLI 0.61121 -4.42447 4.60376 1600000 299003 0.004013 ECMGI 0.49842 -10.66226 2.68891 1600000 310501 0.001288 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 71 96 -7.885 -8.092 -0.491 -1.833 IL 1 1 2 1 4 1 1 74 99 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 73 98 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 5 - U - - - ML 3 2 3 5 3 1 1 71 96 -8.418 -0.015 -7.072 -1.313 -1.272 -1.991 1.552 D 4 2 3 5 3 0 0 69 94 -8.616 -1.843 -0.477 IL 5 5 3 5 3 1 1 72 97 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 6 - U - - - ML 6 5 3 8 3 1 1 70 95 -8.549 -0.014 -7.203 -2.143 -1.745 -2.893 1.740 D 7 5 3 8 3 0 0 68 93 -8.254 -1.778 -0.504 IL 8 8 3 8 3 1 1 71 96 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 7 - U - - - ML 9 8 3 11 3 1 1 69 94 -8.997 -0.426 -1.980 -1.222 -1.519 -1.261 1.488 D 10 8 3 11 3 0 0 67 92 -6.885 -1.582 -0.605 IL 11 11 3 11 3 1 1 70 95 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 112 - g - - MR 12 11 3 14 3 1 1 68 94 -8.627 -0.015 -6.945 0.160 -1.055 0.648 -0.262 D 13 11 3 14 3 0 0 65 91 -8.945 -2.894 -0.212 IR 14 14 3 14 3 1 1 69 94 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 111 - C - - MR 15 14 3 17 5 1 1 67 93 -7.410 -0.048 -7.225 -5.899 -8.329 -0.870 1.157 -1.748 -0.112 D 16 14 3 17 5 0 0 65 91 -7.151 -1.835 -1.073 -3.174 -2.982 IR 17 17 3 17 5 1 1 67 93 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 8 110 g c - - MP 18 17 3 22 6 2 2 66 92 -9.300 -9.240 -0.018 -8.016 -8.296 -8.691 -1.298 -1.565 -1.840 1.111 -1.883 -2.571 1.303 -2.214 0.077 1.725 -1.585 -0.069 1.211 -1.621 -0.078 -1.118 ML 19 17 3 22 6 1 1 64 90 -7.792 -8.138 -1.454 -0.734 -7.988 -5.518 -0.188 -0.610 -0.130 0.635 MR 20 17 3 22 6 1 1 64 90 -7.516 -6.245 -1.156 -6.223 -1.080 -4.437 -0.164 0.593 -0.876 0.076 D 21 17 3 22 6 0 0 62 88 -9.535 -8.233 -2.455 -3.314 -3.517 -0.678 IL 22 22 5 22 6 1 1 65 91 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 23 23 6 23 5 1 1 65 91 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 9 109 c g - - MP 24 23 6 28 6 2 2 64 90 -9.407 -8.367 -0.019 -8.123 -8.402 -8.798 -1.581 -2.058 -2.062 0.984 -0.692 -2.913 1.675 -2.147 -2.014 0.839 -2.566 -0.640 1.612 -2.057 1.312 -1.284 ML 25 23 6 28 6 1 1 63 88 -7.465 -7.811 -0.637 -1.669 -7.661 -5.190 -0.527 -0.496 -1.227 1.118 MR 26 23 6 28 6 1 1 62 88 -7.210 -5.939 -1.268 -5.918 -1.035 -4.131 0.719 -0.662 -0.276 -0.159 D 27 23 6 28 6 0 0 60 85 -9.152 -7.850 -3.461 -3.216 -4.347 -0.422 IL 28 28 5 28 6 1 1 63 89 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 29 29 6 29 5 1 1 63 89 -2.424 -0.490 -5.935 -4.103 -5.209 0.000 0.000 0.000 0.000 [ MATP 8 ] 10 107 G C - - MP 30 29 6 34 6 2 2 62 88 -9.516 -9.455 -0.016 -8.232 -8.511 -8.906 -3.584 -1.145 -3.497 1.083 -4.258 -3.669 0.217 -3.449 -3.839 3.159 -3.173 0.173 -0.031 -3.076 -1.686 -2.146 ML 31 29 6 34 6 1 1 60 86 -6.607 -6.953 -1.012 -1.227 -6.803 -4.332 0.397 -0.547 -0.091 0.085 MR 32 29 6 34 6 1 1 60 86 -6.997 -5.726 -1.606 -5.704 -0.838 -3.918 0.353 -0.337 -0.224 0.104 D 33 29 6 34 6 0 0 58 83 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 1 61 87 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 35 35 6 35 5 1 1 61 87 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 11 106 A U - - MP 36 35 6 40 6 2 2 60 86 -9.535 -9.475 -0.016 -8.251 -8.531 -8.926 -6.447 -6.679 -5.117 3.952 -7.133 -7.892 -3.449 -5.145 -7.123 -2.854 -7.623 -4.262 -3.722 -7.208 -5.165 -4.891 ML 37 35 6 40 6 1 1 58 84 -6.319 -6.665 -1.214 -1.074 -6.515 -4.044 0.277 -0.140 -0.359 0.139 MR 38 35 6 40 6 1 1 58 84 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 39 35 6 40 6 0 0 56 81 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 59 85 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 41 41 6 41 5 1 1 59 85 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 12 105 G C - - MP 42 41 6 46 6 2 2 58 84 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -4.455 -2.302 -4.359 0.579 -5.295 -3.224 -0.479 -4.985 -3.538 3.528 -4.741 -0.541 -0.640 -4.072 -2.483 -3.337 ML 43 41 6 46 6 1 1 56 82 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 56 82 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 6 46 6 0 0 54 79 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 57 83 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 1 57 83 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 13 104 A U - - MP 48 47 6 52 6 2 2 56 82 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -5.393 -4.113 -5.151 3.836 -6.995 -8.096 -2.559 -5.130 -5.175 -0.653 -5.812 -1.143 -2.733 -6.655 -4.450 -4.026 ML 49 47 6 52 6 1 1 54 80 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 6 1 1 54 80 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 51 47 6 52 6 0 0 52 77 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 55 81 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 1 55 81 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 14 103 A U - - MP 54 53 6 58 6 2 2 54 80 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -5.109 -3.520 -4.952 3.756 -6.149 -7.161 -1.132 -4.964 -4.943 -0.057 -5.544 -1.274 -2.041 -6.054 -3.676 -3.812 ML 55 53 6 58 6 1 1 52 78 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 56 53 6 58 6 1 1 52 78 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 57 53 6 58 6 0 0 50 75 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 53 79 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 59 59 6 59 5 1 1 53 79 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 15 102 C G - - MP 60 59 6 64 6 2 2 52 78 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -5.612 -5.672 -5.142 -1.779 -2.935 -5.427 3.727 -4.546 -5.221 -1.641 -5.394 -3.690 0.156 -5.587 -0.838 -4.019 ML 61 59 6 64 6 1 1 50 76 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 62 59 6 64 6 1 1 50 76 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 63 59 6 64 6 0 0 48 73 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 6 1 1 51 77 -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 51 77 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 16 101 C G - - MP 66 65 6 70 6 2 2 50 76 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -5.277 -5.323 -4.849 -1.421 -3.374 -5.169 3.602 -4.226 -4.892 -1.277 -5.125 -3.320 0.783 -5.258 -0.283 -3.689 ML 67 65 6 70 6 1 1 48 74 -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 48 74 -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 46 71 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 6 1 1 50 75 -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 49 75 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 17 100 a u - - MP 72 71 6 76 6 2 2 48 74 -8.704 -9.478 -0.017 -8.255 -8.535 -8.930 -1.747 -1.690 -1.703 1.805 -1.690 -2.735 1.448 -1.937 -2.026 0.978 -2.422 -0.527 1.738 -2.100 -0.135 -0.819 ML 73 71 6 76 6 1 1 46 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 74 71 6 76 6 1 1 46 72 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 75 71 6 76 6 0 0 44 69 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 6 1 1 47 73 -2.599 -2.862 -0.747 -4.517 -5.294 -4.954 0.000 0.000 0.000 0.000 IR 77 77 6 77 5 1 1 47 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 19 99 U A - - MP 78 77 6 82 6 2 2 46 72 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -4.182 -4.103 -4.145 -0.286 -2.805 -4.827 1.353 -3.838 -3.644 0.331 -4.572 -2.013 3.266 -4.366 -0.355 -2.958 ML 79 77 6 82 6 1 1 44 70 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 80 77 6 82 6 1 1 44 70 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 81 77 6 82 6 0 0 42 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 6 1 1 46 71 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 83 83 6 83 5 1 1 45 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 20 98 u a - - MP 84 83 6 88 6 2 2 44 70 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -2.879 -2.759 -2.998 0.851 -2.707 -3.823 1.367 -3.133 -2.965 1.698 -3.572 -0.839 2.487 -1.664 -0.537 -2.046 ML 85 83 6 88 6 1 1 42 68 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 86 83 6 88 6 1 1 42 68 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 87 83 6 88 6 0 0 40 65 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 88 88 5 88 6 1 1 44 69 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 89 89 6 89 5 1 1 43 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 21 97 U A - - MP 90 89 6 94 6 2 2 42 68 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -3.963 -5.400 -5.316 -1.625 -4.219 -5.891 0.225 -4.941 -5.298 -1.455 -5.709 -3.372 3.726 -5.568 -1.112 -3.900 ML 91 89 6 94 6 1 1 40 66 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 92 89 6 94 6 1 1 40 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 93 89 6 94 6 0 0 38 63 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 94 94 5 94 6 1 1 42 67 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 95 95 6 95 5 1 1 41 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 22 96 G C - - MP 96 95 6 100 6 2 2 40 66 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -3.393 -2.082 -3.910 1.019 -4.864 -3.021 -0.026 -4.548 -4.227 3.365 -4.499 -0.395 -0.349 -3.742 -2.068 -2.890 ML 97 95 6 100 6 1 1 38 64 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 98 95 6 100 6 1 1 38 64 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 99 95 6 100 6 0 0 36 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 100 100 5 100 6 1 1 40 65 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 101 101 6 101 5 1 1 39 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 23 95 A U - - MP 102 101 6 106 6 2 2 38 64 -9.539 -9.478 -0.016 -8.255 -8.535 -8.930 -5.384 -4.103 -5.147 3.834 -7.001 -8.093 -2.563 -5.128 -5.166 -0.642 -5.804 -1.107 -2.730 -6.646 -4.453 -4.020 ML 103 101 6 106 6 1 1 36 62 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 104 101 6 106 6 1 1 36 62 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 105 101 6 106 6 0 0 34 59 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 106 106 5 106 6 1 1 38 63 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 107 107 6 107 5 1 1 37 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 24 94 A U - - MP 108 107 6 112 6 2 2 36 62 -8.836 -9.478 -0.017 -8.255 -8.535 -8.930 -5.343 -4.185 -5.075 3.788 -5.764 -7.136 -0.896 -4.977 -5.121 -0.618 -5.687 -1.528 -1.954 -6.294 -3.358 -3.962 ML 109 107 6 112 6 1 1 34 60 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 110 107 6 112 6 1 1 34 60 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 111 107 6 112 6 0 0 32 57 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 112 112 5 112 6 1 1 36 61 -2.379 -2.905 -0.796 -4.561 -5.337 -4.997 0.000 0.000 0.000 0.000 IR 113 113 6 113 5 1 1 35 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 29 93 U A - - MP 114 113 6 118 6 2 2 34 60 -7.670 -9.478 -0.021 -8.071 -8.535 -8.930 -6.937 -6.889 -6.590 -3.089 -5.214 -6.973 -0.885 -6.031 -6.558 -2.963 -6.891 -4.854 3.891 -6.913 -2.492 -4.011 ML 115 113 6 118 6 1 1 33 58 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 116 113 6 118 6 1 1 32 58 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 117 113 6 118 6 0 0 30 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 118 118 5 118 6 1 1 34 59 -1.944 -3.092 -0.899 -4.747 -5.523 -5.184 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 33 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 34 92 C G - - MP 120 119 6 124 6 2 2 32 58 -8.223 -9.031 -0.019 -8.254 -8.534 -8.929 -6.799 -6.840 -5.912 -3.337 -5.116 -6.367 3.945 -6.229 -6.916 -3.232 -6.197 -5.011 -2.549 -7.077 -4.034 -5.908 ML 121 119 6 124 6 1 1 31 56 -6.261 -6.608 -1.322 -0.993 -6.457 -3.987 0.352 -0.334 -0.227 0.105 MR 122 119 6 124 6 1 1 31 56 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 123 119 6 124 6 0 0 29 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 32 57 -2.241 -2.966 -0.821 -4.621 -5.398 -5.058 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 31 57 -2.414 -0.494 -5.926 -4.093 -5.199 0.000 0.000 0.000 0.000 [ MATP 24 ] 41 90 A U - - MP 126 125 6 130 4 2 2 30 56 -6.519 -8.091 -0.043 -6.097 -4.849 -3.832 -4.135 3.825 -5.056 -5.841 -1.487 -3.924 -5.083 -1.064 -5.617 -2.758 -1.748 -5.129 -3.148 -3.593 ML 127 125 6 130 4 1 1 30 55 -3.767 -3.949 -0.503 -2.678 0.411 -0.415 -0.185 0.058 MR 128 125 6 130 4 1 1 29 55 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 129 125 6 130 4 0 0 28 54 -4.568 -4.250 -2.265 -0.520 IL 130 130 5 130 4 1 1 31 57 -1.370 -2.650 -1.233 -5.135 0.000 0.000 0.000 0.000 IR 131 131 6 131 3 1 1 30 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 46 - A - - - ML 132 131 6 134 3 1 1 28 53 -6.462 -0.029 -6.825 1.665 -1.760 -2.120 -1.719 D 133 131 6 134 3 0 0 26 52 -6.257 -1.770 -0.528 IL 134 134 3 134 3 1 1 29 55 -1.471 -0.772 -4.212 0.000 0.000 0.000 0.000 [ MATL 26 ] 50 - G - - - ML 135 134 3 137 3 1 1 27 52 -5.914 -0.049 -5.876 -0.413 -1.904 1.317 -1.027 D 136 134 3 137 3 0 0 25 51 -6.331 -1.664 -0.573 IL 137 137 3 137 3 1 1 31 57 -1.029 -1.094 -4.585 0.000 0.000 0.000 0.000 [ MATL 27 ] 58 - U - - - ML 138 137 3 140 3 1 1 23 43 -6.424 -0.025 -7.482 -1.516 -1.585 -2.373 1.643 D 139 137 3 140 3 0 0 21 41 -6.518 -2.031 -0.426 IL 140 140 3 140 3 1 1 25 45 -1.473 -0.772 -4.213 0.000 0.000 0.000 0.000 [ MATL 28 ] 61 - A - - - ML 141 140 3 143 3 1 1 22 42 -6.001 -0.100 -4.275 1.597 -1.608 -1.877 -1.413 D 142 140 3 143 3 0 0 20 40 -6.518 -1.780 -0.519 IL 143 143 3 143 3 1 1 24 44 -1.390 -0.817 -4.297 0.000 0.000 0.000 0.000 [ MATL 29 ] 64 - g - - - ML 144 143 3 146 3 1 1 20 41 -8.765 -0.021 -6.401 0.169 -1.219 0.782 -0.462 D 145 143 3 146 3 0 0 18 39 -7.163 -2.676 -0.257 IL 146 146 3 146 3 1 1 23 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 65 - U - - - ML 147 146 3 149 3 1 1 19 40 -6.777 -0.033 -6.186 -1.547 -1.329 -2.512 1.625 D 148 146 3 149 3 0 0 18 38 -7.232 -2.000 -0.428 IL 149 149 3 149 3 1 1 22 43 -1.322 -0.867 -4.278 0.000 0.000 0.000 0.000 [ MATL 31 ] 72 - G - - - ML 150 149 3 152 3 1 1 18 38 -6.837 -0.036 -5.988 -0.097 -1.646 1.146 -0.909 D 151 149 3 152 3 0 0 16 37 -7.172 -2.194 -0.369 IL 152 152 3 152 3 1 1 22 42 -1.296 -0.884 -4.292 0.000 0.000 0.000 0.000 [ MATL 32 ] 83 - U - - - ML 153 152 3 155 3 1 1 16 34 -6.339 -0.027 -7.415 -0.905 -1.087 -1.203 1.357 D 154 152 3 155 3 0 0 14 32 -7.196 -2.153 -0.380 IL 155 155 3 155 3 1 1 19 37 -1.438 -0.791 -4.234 0.000 0.000 0.000 0.000 [ MATL 33 ] 87 - A - - - ML 156 155 3 158 3 1 1 13 31 -7.693 -0.015 -7.428 1.546 -1.509 -1.433 -1.478 D 157 155 3 158 3 0 0 13 31 -7.089 -0.796 -1.263 IL 158 158 3 158 3 1 1 17 36 -1.457 -0.787 -4.157 0.000 0.000 0.000 0.000 [ MATL 34 ] 89 - G - - - ML 159 158 3 161 2 1 1 1 1 * 0.000 -0.748 -2.105 1.455 -1.219 D 160 158 3 161 2 0 0 0 0 * 0.000 IL 161 161 3 161 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 35 ] - - - - - - E 162 161 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-ccsA-ndhD-2 ACC RF04347 DESC Plastid-ccsA-ndhD-2 3UTR RNA LENG 53 MAXL 124 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Nov 13 16:34:03 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_031887.1/CM NSEQ 421 EFFN 8.694817 CKSUM 2337396393 STATS LOCAL MSV -7.4553 0.71961 STATS LOCAL VITERBI -8.0900 0.71961 STATS LOCAL FORWARD -4.0988 0.71961 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.26340 1.75235 1.53157 1.11551 1.38629 1.38629 1.38629 1.38629 0.67982 0.75938 3.67555 1.23703 0.34283 0.00000 * 1 2.68833 2.55673 3.12696 0.20998 5 U - - : 1.38629 1.38629 1.38629 1.38629 0.02213 4.51501 4.51501 1.46634 0.26236 1.09861 0.40547 2 3.37867 2.89651 3.89694 0.11610 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.01987 4.62167 4.62167 1.46634 0.26236 1.09861 0.40547 3 2.62850 2.83481 2.36392 0.25485 7 U - - : 1.38629 1.38629 1.38629 1.38629 0.02501 4.69634 4.16225 1.46634 0.26236 1.09861 0.40547 4 1.66965 1.76218 0.99098 1.31377 8 g - - < 1.38629 1.38629 1.38629 1.38629 0.01719 4.76502 4.76502 1.46634 0.26236 1.30992 0.31449 5 1.83599 1.40609 1.88902 0.81142 9 u - - < 1.38629 1.38629 1.38629 1.38629 0.01605 4.83334 4.83334 1.46634 0.26236 0.77584 0.61678 6 1.82642 2.62512 0.38876 2.42268 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.01561 4.86090 4.86090 1.46634 0.26236 1.09861 0.40547 7 0.01980 5.00874 5.16812 4.92969 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 8 2.35628 3.11467 0.20843 3.01639 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 9 0.05998 4.85891 3.22151 4.55075 13 A - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 10 0.09354 3.84949 2.91384 4.28716 14 A - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 11 4.19226 0.12719 4.08353 2.43640 15 C - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 12 4.01088 0.19807 3.87982 1.95960 16 C - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 13 1.19996 1.60339 1.73348 1.13658 17 u - - < 1.38629 1.38629 1.38629 1.38629 0.01774 4.62024 4.86173 1.19105 0.36226 1.09861 0.40547 14 3.17344 1.98608 2.49677 0.30306 19 U - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 15 2.14564 1.92487 1.41110 0.70676 20 u - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 16 4.25690 3.12884 4.35251 0.07344 21 U - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 17 1.98925 2.77478 0.30151 2.79457 22 G - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 18 0.05864 4.94604 3.21508 4.63709 23 A - - < 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 19 0.08032 3.67155 3.32203 4.15674 24 A - - < 1.38629 1.38629 1.38629 1.38629 0.01732 4.66386 4.86173 1.44557 0.26868 1.09861 0.40547 20 5.48481 4.49604 5.57149 0.01929 29 U - - < 1.38629 1.38629 1.38629 1.38629 0.02289 4.20709 4.86173 1.41857 0.27715 1.09861 0.40547 21 5.53028 0.01228 5.67324 5.33777 34 C - - < 1.38629 1.38629 1.38629 1.38629 0.01968 4.44362 4.86173 1.35940 0.29681 1.09861 0.40547 22 0.03181 4.68126 4.41156 4.61455 41 A - - < 1.38629 1.38629 1.38629 1.38629 0.02697 4.20139 4.45345 1.39619 0.28440 1.09861 0.40547 23 0.17567 2.73656 3.21048 2.88285 46 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03007 4.01012 4.46609 0.79611 0.59981 1.25397 0.33599 24 1.77323 2.99932 0.38997 2.26992 50 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04591 3.72618 3.87328 1.70702 0.20017 1.07995 0.41493 25 2.72806 2.77044 3.38996 0.17637 58 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02680 3.98614 4.84380 0.78884 0.60582 1.66723 0.20920 26 0.21284 2.65134 3.00368 2.63726 61 A - - _ 1.38629 1.38629 1.38629 1.38629 0.08674 3.76944 2.81313 0.93757 0.49688 1.25895 0.33401 27 1.29511 2.40517 0.74120 1.83671 64 g - - _ 1.38629 1.38629 1.38629 1.38629 0.02366 4.79443 4.19295 1.46634 0.26236 2.43470 0.09170 28 2.77579 2.51205 3.57689 0.18797 65 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03395 4.12925 4.05768 1.35933 0.29684 1.47728 0.25910 29 1.52254 2.78953 0.49037 2.22569 72 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03583 4.15888 3.93395 1.45015 0.26727 1.71409 0.19861 30 2.26005 2.34089 2.31553 0.35568 83 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02846 3.92448 4.79116 0.89386 0.52606 1.65906 0.21111 31 0.24198 2.57075 2.57528 2.77551 87 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01953 4.49919 4.80146 1.13101 0.38965 0.32634 1.27856 32 2.04081 3.12253 0.30980 2.38124 89 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01571 4.85443 4.85443 1.46634 0.26236 0.76973 0.62202 33 4.88750 4.56861 4.59538 0.02841 90 U - - > 1.38629 1.38629 1.38629 1.38629 0.01665 4.73678 4.86084 1.31693 0.31192 1.13632 0.38713 34 5.25661 5.82879 0.01171 5.65910 92 G - - > 1.38629 1.38629 1.38629 1.38629 0.01561 4.86084 4.86084 1.46634 0.26236 1.02721 0.44317 35 0.02495 5.71985 4.19774 5.06295 93 A - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 36 4.37575 3.72191 3.55863 0.06747 94 U - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 37 4.80073 3.76332 4.74310 0.04097 95 U - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 38 2.99598 0.32346 2.70626 1.83515 96 C - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 39 0.09363 4.51095 2.75190 4.22746 97 A - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 40 0.80929 1.43064 1.75336 1.94854 98 a - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 41 0.35401 2.63150 1.75344 2.93778 99 A - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 42 1.30506 1.87699 1.43521 1.08551 100 u - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 43 2.32023 4.02455 0.14962 3.77914 101 G - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 44 2.74042 4.22597 0.10299 3.97855 102 G - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 45 4.44963 3.20108 3.74370 0.07912 103 U - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 46 4.70125 3.75338 4.67864 0.04271 104 U - - > 1.38629 1.38629 1.38629 1.38629 0.01560 4.86173 4.86173 1.46634 0.26236 1.09861 0.40547 47 3.15008 0.23208 3.07564 2.13618 105 C - - > 1.38629 1.38629 1.38629 1.38629 0.01568 4.85626 4.85626 1.46634 0.26236 1.09861 0.40547 48 5.29789 5.60503 5.33734 0.01358 106 U - - > 1.38629 1.38629 1.38629 1.38629 0.01610 4.82986 4.82986 1.46634 0.26236 1.09861 0.40547 49 2.80210 0.42657 2.47079 1.59922 107 C - - > 1.38629 1.38629 1.38629 1.38629 0.02176 4.39185 4.69414 1.13100 0.38966 1.09861 0.40547 50 1.27325 1.99672 0.92507 1.67241 109 g - - > 1.38629 1.38629 1.38629 1.38629 0.02082 4.57520 4.57520 1.46634 0.26236 1.09861 0.40547 51 1.34222 1.23382 1.48344 1.51094 110 c - - > 1.38629 1.38629 1.38629 1.38629 0.02399 4.43510 4.43510 1.46634 0.26236 1.09861 0.40547 52 2.25516 0.45870 2.91917 1.56514 111 C - - : 1.38629 1.38629 1.38629 1.38629 0.02539 4.37906 4.37906 1.46634 0.26236 1.09861 0.40547 53 1.32054 2.27495 0.81728 1.66827 112 g - - : 1.38629 1.38629 1.38629 1.38629 0.53671 0.87868 * 1.20100 0.35795 0.00000 * //