INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-psbA-4 ACC RF04352 DESC Plastid-psbA-4 3UTR RNA STATES 187 NODES 43 CLEN 61 W 76 ALPH RNA RF no CONS yes MAP yes DATE Wed Nov 19 22:09:55 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/DONE/RF04352/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 633 EFFN 4.863213 CKSUM 3471642664 NULL 0.000 0.000 0.000 0.000 GA 56.80 TC 56.80 NC 56.70 EFP7GF -15.6474 0.71941 ECMLC 0.63221 -5.05095 4.57692 1600000 528023 0.002273 ECMGC 0.43844 -13.27109 0.06040 1600000 138213 0.002894 ECMLI 0.57238 -4.42590 5.60289 1600000 373388 0.003214 ECMGI 0.45584 -9.05434 3.02864 1600000 98655 0.004055 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 76 95 -7.822 -8.029 -0.628 -1.536 IL 1 1 2 1 4 1 10 80 100 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 10 79 99 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 2 - A - - - ML 3 2 3 5 3 1 9 76 95 -8.235 -0.017 -6.889 1.730 -2.465 -1.996 -1.998 D 4 2 3 5 3 0 5 74 93 -8.817 -1.690 -0.540 IL 5 5 3 5 3 1 9 78 98 -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 8 75 94 -8.431 -0.015 -7.085 1.680 -2.078 -1.943 -1.745 D 7 5 3 8 3 0 5 73 92 -8.382 -1.454 -0.662 IL 8 8 3 8 3 1 8 77 97 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 4 - A - - - ML 9 8 3 11 3 1 7 74 93 -8.579 -0.013 -7.233 1.527 -1.771 -1.103 -1.475 D 10 8 3 11 3 0 4 72 91 -7.872 -2.200 -0.362 IL 11 11 3 11 3 1 7 76 96 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 5 - g - - - ML 12 11 3 14 3 1 6 73 92 -8.618 -0.013 -7.273 0.420 -1.222 0.464 -0.228 D 13 11 3 14 3 0 4 71 91 -7.684 -1.266 -0.788 IL 14 14 3 14 3 1 6 75 94 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 6 - U - - - ML 15 14 3 17 3 1 5 72 91 -9.055 -0.441 -1.936 -0.139 -0.892 -1.011 1.040 D 16 14 3 17 3 0 3 70 90 -6.292 -1.069 -0.970 IL 17 17 3 17 3 1 7 73 92 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 124 - u - - MR 18 17 3 20 3 1 8 71 90 -8.660 -0.015 -6.978 -0.604 0.483 -1.432 0.654 D 19 17 3 20 3 0 2 69 89 -8.729 -1.368 -0.713 IR 20 20 3 20 3 1 6 72 91 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 123 - A - - MR 21 20 3 23 5 1 8 70 89 -7.581 -0.033 -7.396 -6.794 -8.500 1.321 -1.311 -1.322 -0.518 D 22 20 3 23 5 0 2 68 88 -6.594 -0.836 -1.917 -4.364 -3.105 IR 23 23 3 23 5 1 5 70 90 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 7 122 a u - - MP 24 23 3 28 6 2 9 69 88 -9.200 -9.373 -0.017 -8.150 -8.429 -8.824 -2.250 -2.026 -2.869 2.976 -2.980 -3.735 0.596 -2.964 -3.008 1.323 -3.535 -0.707 0.494 -3.016 -1.028 -1.522 ML 25 23 3 28 6 1 3 67 87 -6.951 -7.297 -1.137 -1.045 -7.147 -4.676 0.896 -0.833 -0.448 -0.243 MR 26 23 3 28 6 1 3 67 87 -7.130 -5.859 -1.437 -5.837 -0.920 -4.050 0.211 -0.346 -0.407 0.381 D 27 23 3 28 6 0 0 65 84 -9.234 -7.932 -3.729 -2.578 -4.429 -0.504 IL 28 28 5 28 6 1 4 69 88 -2.584 -2.847 -0.757 -4.502 -5.278 -4.939 0.000 0.000 0.000 0.000 IR 29 29 6 29 5 1 4 68 88 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 121 A U - - MP 30 29 6 34 6 2 8 67 86 -9.471 -9.410 -0.016 -8.187 -8.466 -8.861 -3.927 -3.102 -4.078 3.645 -4.455 -5.217 -0.516 -3.931 -4.439 0.138 -4.954 -1.703 -0.841 -4.486 -2.382 -2.979 ML 31 29 6 34 6 1 3 65 85 -6.733 -7.079 -1.329 -0.912 -6.929 -4.458 0.980 -0.846 -0.588 -0.311 MR 32 29 6 34 6 1 3 65 85 -7.016 -5.745 -1.568 -5.723 -0.857 -3.937 0.321 -0.373 -0.244 0.182 D 33 29 6 34 6 0 0 63 82 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 4 67 86 -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 4 66 86 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 10 120 A U - - MP 36 35 6 40 6 2 8 65 84 -8.146 -9.425 -0.019 -8.201 -8.481 -8.876 -3.172 -2.693 -2.918 3.479 -3.539 -4.230 -0.069 -3.364 -3.587 0.399 -4.124 -1.303 -0.289 -3.593 -1.663 -2.455 ML 37 35 6 40 6 1 3 63 83 -6.565 -6.912 -1.053 -1.188 -6.761 -4.291 0.429 -0.176 -0.472 0.067 MR 38 35 6 40 6 1 2 63 83 -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 61 80 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 3 65 84 -2.618 -2.881 -0.734 -4.536 -5.312 -4.973 0.000 0.000 0.000 0.000 IR 41 41 6 41 5 1 3 64 84 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 12 119 G C - - MP 42 41 6 46 6 2 8 63 82 -7.787 -9.441 -0.021 -8.218 -8.497 -8.892 -4.500 -2.159 -4.413 0.620 -5.347 -3.723 -0.525 -5.035 -3.599 3.531 -4.752 -0.432 -0.798 -4.103 -2.533 -3.390 ML 43 41 6 46 6 1 2 61 81 -6.318 -6.664 -1.378 -0.940 -6.514 -4.043 0.279 -0.144 -0.357 0.138 MR 44 41 6 46 6 1 2 61 81 -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 59 78 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 3 62 82 -2.637 -2.900 -0.722 -4.555 -5.331 -4.991 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 3 62 81 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 14 118 G C - - MP 48 47 6 52 6 2 7 61 80 -8.077 -9.441 -0.019 -8.218 -8.497 -8.892 -3.767 -2.566 -3.215 1.207 -4.450 -3.936 0.249 -3.472 -3.663 3.212 -4.304 -0.185 0.124 -3.529 -1.575 -2.617 ML 49 47 6 52 6 1 2 59 79 -6.318 -6.664 -1.378 -0.940 -6.514 -4.043 0.542 -0.505 -0.213 -0.034 MR 50 47 6 52 6 1 2 59 79 -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 57 76 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 3 60 80 -2.622 -2.885 -0.731 -4.540 -5.316 -4.977 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 3 60 79 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 16 117 A U - - MP 54 53 6 58 6 2 7 59 78 -9.502 -9.441 -0.016 -8.218 -8.497 -8.892 -3.868 -2.412 -3.378 3.349 -4.314 -4.921 -0.298 -3.576 -3.999 1.112 -4.506 0.014 -0.361 -4.136 -2.100 -2.902 ML 55 53 6 58 6 1 2 57 77 -6.318 -6.664 -1.378 -0.940 -6.514 -4.043 0.542 -0.505 -0.213 -0.034 MR 56 53 6 58 6 1 2 57 77 -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 55 74 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 3 58 78 -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 3 58 77 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 17 116 G C - - MP 60 59 6 64 6 2 7 57 76 -9.502 -9.441 -0.016 -8.218 -8.497 -8.892 -4.290 -2.209 -4.186 0.891 -5.165 -4.624 -0.329 -4.774 -4.362 3.419 -4.652 -0.153 -0.206 -4.004 -2.338 -3.133 ML 61 59 6 64 6 1 2 55 75 -6.318 -6.664 -1.216 -1.073 -6.514 -4.043 0.542 -0.505 -0.213 -0.034 MR 62 59 6 64 6 1 2 55 75 -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 53 72 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 6 1 2 56 76 -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 2 56 75 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 18 115 C G - - MP 66 65 6 70 6 2 6 55 74 -9.506 -9.445 -0.016 -8.222 -8.501 -8.896 -3.898 -3.810 -3.278 0.252 -2.735 -4.656 3.276 -2.677 -3.878 0.293 -4.354 -1.706 0.936 -4.113 -0.381 -2.751 ML 67 65 6 70 6 1 1 53 73 -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 53 73 -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 51 70 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 6 1 2 54 74 -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 2 54 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 19 114 A U - - MP 72 71 6 76 6 2 6 53 72 -9.506 -9.445 -0.016 -8.222 -8.501 -8.896 -6.879 -5.433 -5.008 3.938 -7.553 -8.306 -3.505 -4.765 -6.879 -2.203 -7.423 -3.266 -3.739 -7.459 -5.331 -4.987 ML 73 71 6 76 6 1 1 51 71 -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 51 71 -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 49 68 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 6 1 2 52 72 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 77 77 6 77 5 1 2 52 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 20 113 A U - - MP 78 77 6 82 6 2 5 51 70 -9.506 -9.445 -0.024 -6.803 -8.501 -8.896 -5.509 -4.000 -4.987 3.824 -6.209 -6.956 -1.908 -4.165 -5.506 -0.713 -6.063 -1.423 -2.295 -6.061 -3.919 -3.781 ML 79 77 6 82 6 1 1 50 69 -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 49 69 -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 47 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 6 1 2 51 70 -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 2 50 70 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 21 112 U A - - MP 84 83 6 88 6 2 4 49 68 -9.027 -9.437 -0.018 -8.213 -8.493 -8.330 -4.152 -4.689 -4.797 -1.047 -3.663 -5.611 0.033 -4.751 -4.774 -0.899 -5.319 -2.782 3.706 -4.811 -1.790 -3.241 ML 85 83 6 88 6 1 1 48 68 -6.385 -6.731 -1.186 -1.140 -5.187 -4.111 0.196 -0.364 -0.384 0.391 MR 86 83 6 88 6 1 1 48 67 -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 46 66 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 88 88 5 88 6 1 1 49 68 -2.589 -2.852 -0.753 -4.507 -5.283 -4.944 0.000 0.000 0.000 0.000 IR 89 89 6 89 5 1 2 48 68 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 23 111 A U - - MP 90 89 6 94 4 2 2 47 66 -7.817 -8.024 -0.043 -5.559 -5.195 -5.134 -4.779 3.889 -5.811 -5.604 -2.273 -4.968 -5.825 -1.468 -6.333 -3.227 -2.464 -5.804 -3.876 -4.278 ML 91 89 6 94 4 1 1 47 67 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 92 89 6 94 4 1 1 47 67 -4.836 -3.865 -1.647 -0.793 0.456 -0.447 -0.187 0.023 D 93 89 6 94 4 0 0 46 66 -4.598 -4.279 -2.158 -0.550 IL 94 94 5 94 4 1 1 49 68 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 95 95 6 95 3 1 1 48 67 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 24 - a - - - ML 96 95 6 98 3 1 1 44 64 -8.548 -0.029 -5.860 0.925 -0.041 -1.097 -0.595 D 97 95 6 98 3 0 0 43 63 -6.378 -1.317 -0.770 IL 98 98 3 98 3 1 1 47 66 -1.424 -0.808 -4.156 0.000 0.000 0.000 0.000 [ MATL 21 ] 31 - C - - - ML 99 98 3 101 3 1 1 43 63 -8.239 -0.088 -4.169 -0.599 1.087 -1.719 -0.133 D 100 98 3 101 3 0 0 42 61 -6.420 -1.388 -0.722 IL 101 101 3 101 3 1 1 46 65 -1.448 -0.793 -4.148 0.000 0.000 0.000 0.000 [ MATL 22 ] 33 - c - - - ML 102 101 3 104 3 1 1 42 61 -9.066 -0.023 -6.161 0.012 0.750 -0.985 -0.314 D 103 101 3 104 3 0 0 41 60 -6.222 -0.439 -2.005 IL 104 104 3 104 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 110 - u - - MR 105 104 3 107 3 1 1 41 60 -6.902 -0.054 -5.140 -0.364 -0.874 0.216 0.600 D 106 104 3 107 3 0 0 40 59 -6.539 -1.313 -0.769 IR 107 107 3 107 3 1 1 42 61 -1.977 -0.531 -4.216 0.000 0.000 0.000 0.000 [ MATR 24 ] - 108 - G - - MR 108 107 3 110 3 1 1 40 59 -7.185 -0.117 -3.815 -0.782 -2.110 1.494 -1.432 D 109 107 3 110 3 0 0 39 58 -6.793 -1.256 -0.805 IR 110 110 3 110 3 1 1 41 60 -1.965 -0.536 -4.203 0.000 0.000 0.000 0.000 [ MATR 25 ] - 106 - u - - MR 111 110 3 113 5 1 1 39 58 -7.284 -0.194 -3.475 -5.349 -7.591 -0.386 -0.543 0.175 0.505 D 112 110 3 113 5 0 0 38 57 -6.005 -0.653 -2.475 -4.367 -3.057 IR 113 113 3 113 5 1 1 40 59 -2.419 -0.492 -5.930 -4.098 -5.204 0.000 0.000 0.000 0.000 [ MATP 26 ] 34 104 a u - - MP 114 113 3 118 6 2 2 38 58 -7.058 -9.336 -0.058 -6.287 -6.057 -8.787 -1.525 -1.184 -1.526 1.961 -1.652 -2.290 1.439 -1.818 -1.800 1.005 -2.463 -0.245 1.214 -1.798 -0.027 -0.875 ML 115 113 3 118 6 1 1 38 57 -7.266 -7.612 -0.540 -1.924 -7.462 -4.991 0.351 -0.329 -0.722 0.403 MR 116 113 3 118 6 1 1 37 57 -7.252 -5.981 -1.249 -5.959 -1.043 -4.173 0.191 -0.263 -0.456 0.374 D 117 113 3 118 6 0 0 36 55 -9.097 -7.795 -3.293 -3.941 -4.292 -0.367 IL 118 118 5 118 6 1 1 39 58 -1.969 -3.123 -0.875 -4.779 -5.555 -5.215 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 38 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 41 103 c g - - MP 120 119 6 124 4 2 2 36 55 -6.566 -7.515 -0.041 -6.378 -0.908 -1.364 -0.134 1.607 -1.706 -2.659 1.623 -1.736 -1.877 0.847 -2.450 -0.285 1.215 -1.950 0.058 -0.786 ML 121 119 6 124 4 1 1 37 56 -3.954 -4.136 -0.432 -2.865 0.449 -0.222 -0.463 0.074 MR 122 119 6 124 4 1 1 36 55 -5.095 -4.124 -1.214 -1.052 0.218 -0.547 0.151 0.060 D 123 119 6 124 4 0 0 35 55 -4.568 -4.250 -2.265 -0.520 IL 124 124 5 124 4 1 1 38 57 -1.750 -2.433 -1.046 -4.919 0.000 0.000 0.000 0.000 IR 125 125 6 125 3 1 1 37 56 -1.450 -0.792 -4.150 0.000 0.000 0.000 0.000 [ MATL 28 ] 43 - U - - - ML 126 125 6 128 3 1 1 34 53 -8.417 -0.020 -6.536 -0.863 0.047 -1.857 1.098 D 127 125 6 128 3 0 0 33 51 -5.620 -0.734 -1.403 IL 128 128 3 128 3 1 1 35 54 -1.935 -0.550 -4.173 0.000 0.000 0.000 0.000 [ MATR 29 ] - 101 - g - - MR 129 128 3 131 5 1 1 33 52 -5.874 -0.042 -7.646 -7.858 -8.750 0.269 -1.696 0.962 -0.893 D 130 128 3 131 5 0 0 31 50 -5.410 -0.672 -3.036 -4.467 -2.462 IR 131 131 3 131 5 1 1 33 52 -2.292 -0.511 -6.050 -4.217 -5.323 0.000 0.000 0.000 0.000 [ MATP 30 ] 45 96 u a - - MP 132 131 3 136 6 2 2 32 51 -9.506 -8.487 -0.022 -7.291 -8.501 -8.896 -2.807 -2.884 -2.940 0.704 -0.505 -3.767 1.838 -3.000 -2.773 0.636 -3.497 -1.135 1.850 -3.099 1.705 -1.953 ML 133 131 3 136 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 134 131 3 136 6 1 1 30 49 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 135 131 3 136 6 0 0 28 47 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 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 137 137 6 137 5 1 1 31 50 -2.171 -0.555 -6.000 -4.167 -5.273 0.000 0.000 0.000 0.000 [ MATP 31 ] 46 89 U A - - MP 138 137 6 142 6 2 2 30 49 -9.501 -9.180 -0.018 -7.873 -8.497 -8.892 -4.600 -5.044 -5.110 -1.454 -4.007 -5.876 -0.119 -5.010 -5.087 -1.309 -5.612 -3.139 3.757 -4.324 -1.784 -3.737 ML 139 137 6 142 6 1 1 28 47 -6.325 -6.671 -1.207 -1.080 -6.521 -4.050 0.361 -0.534 0.106 -0.076 MR 140 137 6 142 6 1 1 28 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 141 137 6 142 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 142 142 5 142 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 143 143 6 143 5 1 1 29 48 -2.345 -0.511 -5.939 -4.107 -5.212 0.000 0.000 0.000 0.000 [ MATP 32 ] 47 82 C G - - MP 144 143 6 148 6 2 2 28 47 -9.504 -8.140 -0.019 -8.220 -8.500 -8.895 -6.257 -6.291 -5.637 -2.767 -4.435 -6.037 3.917 -6.324 -6.366 -2.657 -5.770 -4.443 -1.951 -6.532 -3.459 -5.142 ML 145 143 6 148 6 1 1 26 45 -6.273 -6.619 -1.333 -0.983 -6.469 -3.998 0.337 -0.289 -0.258 0.114 MR 146 143 6 148 6 1 1 26 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 147 143 6 148 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 148 148 5 148 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 149 149 6 149 5 1 1 27 46 -2.164 -0.555 -6.012 -4.180 -5.286 0.000 0.000 0.000 0.000 [ MATP 33 ] 48 77 U A - - MP 150 149 6 154 6 2 2 26 45 -9.504 -9.444 -0.016 -8.220 -8.364 -8.895 -5.768 -6.231 -6.303 -2.817 -5.357 -7.109 -1.780 -6.345 -5.710 -2.726 -6.851 -4.468 3.916 -6.023 -3.276 -4.485 ML 151 149 6 154 6 1 1 25 44 -6.273 -6.619 -1.278 -1.028 -6.469 -3.998 0.335 -0.376 -0.228 0.156 MR 152 149 6 154 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 153 149 6 154 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 154 154 5 154 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 155 155 6 155 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 49 76 U A - - MP 156 155 6 160 6 2 2 24 43 -9.505 -9.445 -0.016 -8.221 -8.501 -8.896 -6.055 -5.989 -5.950 -2.230 -4.888 -6.541 -0.533 -5.600 -5.912 -1.864 -6.351 -3.953 3.837 -4.810 -2.073 -4.280 ML 157 155 6 160 6 1 1 23 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 158 155 6 160 6 1 1 23 42 -6.994 -5.723 -1.631 -5.701 -0.824 -3.914 0.395 -0.404 -0.186 0.071 D 159 155 6 160 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 160 160 5 160 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 161 161 6 161 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 50 75 G C - - MP 162 161 6 166 4 2 2 22 41 -7.499 -7.326 -0.048 -5.554 -3.641 -1.603 -3.546 1.030 -4.338 -2.988 0.183 -3.964 -3.101 3.221 -3.667 0.030 -0.068 -3.008 -1.733 -2.563 ML 163 161 6 166 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 164 161 6 166 4 1 1 22 41 -4.816 -3.845 -1.713 -0.762 0.359 -0.354 -0.213 0.101 D 165 161 6 166 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520 IL 166 166 5 166 4 1 1 24 43 -1.698 -2.382 -1.102 -4.867 0.000 0.000 0.000 0.000 IR 167 167 6 167 3 1 1 23 42 -1.422 -0.808 -4.175 0.000 0.000 0.000 0.000 [ MATL 36 ] 52 - U - - - ML 168 167 6 170 3 1 1 19 37 -8.777 -0.012 -7.431 -0.212 -1.010 -1.486 1.191 D 169 167 6 170 3 0 0 18 37 -6.391 -1.867 -0.486 IL 170 170 3 170 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 53 - U - - - ML 171 170 3 173 3 1 1 17 36 -8.359 -0.013 -7.431 -1.960 -1.520 -2.587 1.691 D 172 170 3 173 3 0 0 17 36 -6.381 -1.894 -0.476 IL 173 173 3 173 3 1 1 21 40 -1.439 -0.799 -4.151 0.000 0.000 0.000 0.000 [ MATL 38 ] 56 - c - - - ML 174 173 3 176 3 1 1 16 35 -8.371 -0.013 -7.431 0.135 0.670 -1.561 -0.041 D 175 173 3 176 3 0 0 16 35 -6.381 -1.500 -0.656 IL 176 176 3 176 3 1 1 20 39 -1.403 -0.820 -4.172 0.000 0.000 0.000 0.000 [ MATL 39 ] 64 - U - - - ML 177 176 3 179 3 1 1 15 33 -8.786 -0.012 -7.440 -0.915 -1.381 -0.910 1.352 D 178 176 3 179 3 0 0 15 33 -6.254 -1.767 -0.529 IL 179 179 3 179 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 40 ] 65 - A - - - ML 180 179 3 182 3 1 1 13 32 -7.606 -0.016 -7.440 1.624 -1.865 -1.534 -1.742 D 181 179 3 182 3 0 0 13 32 -6.254 -1.767 -0.529 IL 182 182 3 182 3 1 1 18 36 -1.430 -0.802 -4.175 0.000 0.000 0.000 0.000 [ MATL 41 ] 68 - U - - - ML 183 182 3 185 2 1 1 1 1 * 0.000 -0.035 -1.120 -1.038 1.055 D 184 182 3 185 2 0 0 0 0 * 0.000 IL 185 185 3 185 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 42 ] - - - - - - E 186 185 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-psbA-4 ACC RF04352 DESC Plastid-psbA-4 3UTR RNA LENG 61 MAXL 128 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Nov 19 22:09:55 2025 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED NSEQ 633 EFFN 7.519386 CKSUM 3471642664 STATS LOCAL MSV -8.0104 0.71941 STATS LOCAL VITERBI -8.4416 0.71941 STATS LOCAL FORWARD -3.7521 0.71941 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.13246 1.75596 1.69541 1.13478 1.38629 1.38629 1.38629 1.38629 1.07295 0.44458 4.07987 0.05194 2.98348 0.00000 * 1 0.12339 3.49580 3.10396 3.19704 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.02297 4.47809 4.47809 1.46634 0.26236 1.09861 0.40547 2 0.16468 3.04249 3.02277 2.89216 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.01936 4.64733 4.64733 1.46634 0.26236 1.09861 0.40547 3 0.26258 2.81440 2.25318 2.71921 4 A - - : 1.38629 1.38629 1.38629 1.38629 0.01709 4.77108 4.77108 1.46634 0.26236 1.09861 0.40547 4 1.08620 2.39646 0.99300 1.60445 5 g - - : 1.38629 1.38629 1.38629 1.38629 0.01653 4.80402 4.80402 1.46634 0.26236 1.09861 0.40547 5 1.51411 2.12572 2.15294 0.60787 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.01542 4.87316 4.87316 1.46634 0.26236 1.09861 0.40547 6 0.52028 2.33720 1.73504 2.02002 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.01528 4.84810 4.91731 1.38071 0.28955 1.09861 0.40547 7 0.09816 3.69691 3.21006 3.56335 9 A - - < 1.38629 1.38629 1.38629 1.38629 0.01438 4.94220 4.94220 1.46634 0.26236 1.09861 0.40547 8 0.18324 3.05966 2.72032 2.90638 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.01886 4.46002 4.94496 0.96846 0.47750 1.09861 0.40547 9 2.26547 3.14069 0.21458 3.07730 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.02108 4.28727 4.94496 0.83590 0.56825 1.09861 0.40547 10 1.86206 2.62559 0.38402 2.39547 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.01931 4.42206 4.94496 0.93770 0.49680 1.09861 0.40547 11 0.29123 3.27940 1.80052 2.99986 16 A - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 12 2.05883 3.05378 0.28231 2.64263 17 G - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 13 2.50254 0.39916 2.42676 1.83938 18 C - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 14 0.01535 5.52657 4.97575 5.43730 19 A - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 15 0.04544 4.71638 3.63260 4.70779 20 A - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 16 3.93702 3.41741 3.85863 0.07623 21 U - - < 1.38629 1.38629 1.38629 1.38629 0.01989 4.79902 4.46921 1.29242 0.32104 1.09861 0.40547 17 0.02297 5.07903 4.69288 4.91682 23 A - - < 1.38629 1.38629 1.38629 1.38629 0.02546 4.94061 4.01795 1.46634 0.26236 0.80774 0.59035 18 0.68268 1.36687 2.27631 1.98653 24 A - - - 1.38629 1.38629 1.38629 1.38629 0.02861 4.87227 3.88492 1.50263 0.25173 0.58496 0.81448 19 1.91474 0.54427 2.79136 1.55583 31 C - - - 1.38629 1.38629 1.38629 1.38629 0.07667 4.77790 2.72741 1.28377 0.32433 0.69500 0.69129 20 1.40975 0.77359 2.14621 1.72869 33 c - - - 1.38629 1.38629 1.38629 1.38629 0.04578 4.88257 3.29229 1.46634 0.26236 0.23983 1.54533 21 1.06384 1.55061 1.67180 1.36710 34 a - - < 1.38629 1.38629 1.38629 1.38629 0.05249 3.93787 3.45306 1.20653 0.35558 0.39202 1.12606 22 1.08958 1.43052 1.72878 1.39855 41 a - - < 1.38629 1.38629 1.38629 1.38629 0.02136 4.28139 4.91831 0.85087 0.55694 0.35496 1.20798 23 2.17360 1.32073 2.95874 0.56668 43 U - - - 1.38629 1.38629 1.38629 1.38629 0.01576 4.76562 4.94496 1.25596 0.33519 1.09861 0.40547 24 2.19810 1.29549 2.12812 0.70085 45 u - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 25 4.28833 3.56429 4.16912 0.05923 46 U - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 26 5.06077 0.02232 5.09424 4.64566 47 C - - < 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 27 5.35151 5.16976 5.43469 0.01490 48 U - - < 1.38629 1.38629 1.38629 1.38629 0.01493 4.94496 4.86718 1.46634 0.26236 1.09861 0.40547 28 4.95695 4.00882 4.73604 0.03455 49 U - - < 1.38629 1.38629 1.38629 1.38629 0.01435 4.94439 4.94439 1.46634 0.26236 1.12522 0.39242 29 1.94672 2.61708 0.35140 2.51903 50 G - - < 1.38629 1.38629 1.38629 1.38629 0.02681 4.78416 4.01247 1.27669 0.32706 1.12522 0.39242 30 1.57259 2.24157 2.59448 0.49181 52 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01451 4.93336 4.93336 1.46634 0.26236 1.45267 0.26650 31 3.11061 2.62760 3.48901 0.15941 53 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01541 4.81662 4.93394 1.36925 0.29343 1.51279 0.24884 32 1.30363 0.83320 2.70656 1.48267 56 c - - _ 1.38629 1.38629 1.38629 1.38629 0.01538 4.82016 4.93394 1.56430 0.23475 0.83268 0.57072 33 2.24923 2.60927 2.05502 0.36695 64 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01440 4.94093 4.94093 1.46634 0.26236 1.27124 0.32918 34 0.20726 2.83840 2.60586 2.90347 65 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01780 4.55701 4.94093 1.19720 0.35959 1.27124 0.32918 35 1.43047 2.34219 2.18408 0.59402 68 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01714 4.62046 4.94093 1.28405 0.32423 0.82318 0.57809 36 2.75469 0.40173 2.49350 1.68963 75 C - - > 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 37 0.04288 4.77220 3.71041 4.70579 76 A - - > 1.38629 1.38629 1.38629 1.38629 0.01627 4.94496 4.70820 1.46634 0.26236 1.09861 0.40547 38 0.01679 5.66186 4.89749 5.16592 77 A - - > 1.38629 1.38629 1.38629 1.38629 0.01889 4.45808 4.94306 1.42633 0.27469 1.18391 0.36540 39 4.74829 5.34134 0.01929 5.17667 82 G - - > 1.38629 1.38629 1.38629 1.38629 0.02151 4.86224 4.30173 1.51257 0.24890 0.94715 0.49077 40 0.06520 4.36333 3.35178 4.17566 89 A - - > 1.38629 1.38629 1.38629 1.38629 0.01735 4.60154 4.93854 1.55765 0.23652 0.71940 0.66757 41 1.20375 2.30947 0.76041 2.01633 96 g - - > 1.38629 1.38629 1.38629 1.38629 0.03698 3.77149 4.32117 0.77630 0.61639 1.09861 0.40547 42 1.21337 2.81517 0.63303 2.18987 101 G - - - 1.38629 1.38629 1.38629 1.38629 0.03820 4.74034 3.54925 1.23562 0.34341 0.89150 0.52770 43 1.58155 1.89062 1.09296 1.17719 103 g - - > 1.38629 1.38629 1.38629 1.38629 0.14876 4.92123 2.03303 1.46634 0.26236 0.58009 0.82063 44 1.63493 1.73699 1.38339 0.97218 104 u - - > 1.38629 1.38629 1.38629 1.38629 0.09480 4.55957 2.52602 1.18200 0.36624 0.29545 1.36334 45 1.77135 1.79584 1.19904 1.01494 106 u - - - 1.38629 1.38629 1.38629 1.38629 0.04303 4.24372 3.58389 0.86990 0.54299 0.24276 1.53460 46 2.04653 3.04736 0.29445 2.54602 108 G - - - 1.38629 1.38629 1.38629 1.38629 0.03276 4.17013 4.08751 0.77417 0.61820 0.34693 1.22710 47 1.74651 2.09198 1.17004 0.93695 110 u - - - 1.38629 1.38629 1.38629 1.38629 0.01662 4.93571 4.67833 1.46634 0.26236 0.62712 0.76384 48 5.14968 4.96989 5.04839 0.01935 111 U - - > 1.38629 1.38629 1.38629 1.38629 0.02647 4.94287 3.96411 1.46634 0.26236 0.93458 0.49882 49 0.08071 4.05596 3.27445 3.79946 112 A - - > 1.38629 1.38629 1.38629 1.38629 0.01451 4.93306 4.93306 1.46634 0.26236 0.56050 0.84611 50 4.98470 4.15167 4.70912 0.03210 113 U - - > 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 51 5.63483 5.34487 5.48180 0.01258 114 U - - > 1.38629 1.38629 1.38629 1.38629 0.01434 4.94496 4.94496 1.46634 0.26236 1.09861 0.40547 52 2.12039 2.59162 0.35204 2.28412 115 G - - > 1.38629 1.38629 1.38629 1.38629 0.01442 4.93917 4.93917 1.46634 0.26236 1.09861 0.40547 53 2.83029 0.33412 2.86498 1.78346 116 C - - > 1.38629 1.38629 1.38629 1.38629 0.01442 4.93917 4.93917 1.46634 0.26236 1.09861 0.40547 54 3.18582 2.18918 3.09427 0.22147 117 U - - > 1.38629 1.38629 1.38629 1.38629 0.01442 4.93917 4.93917 1.46634 0.26236 1.09861 0.40547 55 2.64210 0.44058 2.43510 1.62183 118 C - - > 1.38629 1.38629 1.38629 1.38629 0.01442 4.93917 4.93917 1.46634 0.26236 1.09861 0.40547 56 3.25652 0.24385 3.06327 2.03153 119 C - - > 1.38629 1.38629 1.38629 1.38629 0.01478 4.91510 4.91510 1.46634 0.26236 1.09861 0.40547 57 3.18147 2.89095 2.92643 0.16327 120 U - - > 1.38629 1.38629 1.38629 1.38629 0.01507 4.89597 4.89597 1.46634 0.26236 1.09861 0.40547 58 3.88381 3.40440 3.64145 0.08340 121 U - - > 1.38629 1.38629 1.38629 1.38629 0.01574 4.85260 4.85260 1.46634 0.26236 1.09861 0.40547 59 2.26034 1.84012 2.16474 0.47464 122 U - - > 1.38629 1.38629 1.38629 1.38629 0.01809 4.71463 4.71463 1.46634 0.26236 1.09861 0.40547 60 0.39109 2.47243 2.50305 1.84855 123 A - - : 1.38629 1.38629 1.38629 1.38629 0.02190 4.52528 4.52528 1.46634 0.26236 1.09861 0.40547 61 1.97314 0.96041 2.58143 0.90987 124 u - - : 1.38629 1.38629 1.38629 1.38629 0.47173 0.97797 * 0.71120 0.67541 0.00000 * //