INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-psbA-3 ACC RF04344 DESC Plastid-psbA-3 3UTR RNA STATES 175 NODES 38 CLEN 57 W 73 ALPH RNA RF no CONS yes MAP yes DATE Wed Nov 5 16:02:38 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_036093.1/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 830 EFFN 5.993614 CKSUM 2924302399 NULL 0.000 0.000 0.000 0.000 GA 48.40 TC 48.40 NC 48.30 EFP7GF -15.5711 0.71954 ECMLC 0.63478 -5.16284 4.06395 1600000 419617 0.002860 ECMGC 0.43983 -14.67332 -0.91322 1600000 169998 0.002353 ECMLI 0.58319 -4.52314 4.89256 1600000 291044 0.004123 ECMGI 0.49312 -9.23909 2.10113 1600000 107322 0.003727 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 73 93 -7.907 -9.153 -0.553 -1.678 IL 1 1 2 1 4 1 6 74 95 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 7 75 95 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 110 - U - - MR 3 2 3 5 3 1 8 73 93 -8.874 -0.013 -7.192 -0.825 -1.417 -1.881 1.480 D 4 2 3 5 3 0 3 71 92 -8.910 -0.842 -1.184 IR 5 5 3 5 3 1 6 74 94 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 109 - U - - MR 6 5 3 8 3 1 7 72 92 -9.184 -0.010 -7.502 -1.565 -1.802 -2.510 1.678 D 7 5 3 8 3 0 2 70 91 -7.913 -1.583 -0.595 IR 8 8 3 8 3 1 5 73 93 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 108 - U - - MR 9 8 3 11 3 1 6 71 91 -9.243 -0.010 -7.561 -0.384 -0.400 -1.461 1.079 D 10 8 3 11 3 0 1 69 90 -7.561 -1.314 -0.755 IR 11 11 3 11 3 1 5 72 92 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 107 - u - - MR 12 11 3 14 5 1 6 70 90 -7.988 -0.216 -7.803 -2.957 -8.907 0.396 -0.682 -1.205 0.702 D 13 11 3 14 5 0 1 68 89 -5.820 -0.924 -2.203 -3.634 -2.668 IR 14 14 3 14 5 1 4 70 91 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 2 106 a u - - MP 15 14 3 19 6 2 7 69 90 -9.493 -9.432 -0.016 -8.208 -8.488 -8.883 -1.136 -0.731 -2.305 2.476 -2.353 -3.144 0.982 -2.658 -2.393 1.294 -2.940 -0.469 0.891 -2.353 -0.518 -1.025 ML 16 14 3 19 6 1 2 67 88 -6.534 -6.880 -1.244 -1.009 -6.730 -4.259 0.807 -0.693 -0.416 -0.181 MR 17 14 3 19 6 1 3 67 88 -8.210 -6.939 -1.235 -6.917 -0.925 -5.131 -0.092 -0.348 -0.988 0.826 D 18 14 3 19 6 0 0 65 86 -9.113 -7.811 -2.993 -4.291 -4.308 -0.383 IL 19 19 5 19 6 1 3 69 89 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 3 68 89 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 3 105 A U - - MP 21 20 6 25 6 2 7 67 88 -9.567 -9.506 -0.015 -8.282 -8.562 -8.957 -2.769 0.162 -4.078 3.400 -4.711 -5.390 -0.565 -4.315 -4.023 0.698 -4.587 -0.429 -0.941 -4.503 -2.518 -3.010 ML 22 20 6 25 6 1 2 65 86 -6.396 -6.742 -1.257 -1.022 -6.592 -4.122 0.657 -0.583 -0.286 -0.097 MR 23 20 6 25 6 1 2 65 86 -7.724 -6.453 -1.392 -6.431 -0.859 -4.645 -0.065 -0.498 -0.616 0.751 D 24 20 6 25 6 0 0 63 83 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 3 67 87 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 3 66 87 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 4 104 a u - - MP 27 26 6 31 6 2 7 65 86 -9.599 -9.538 -0.015 -8.315 -8.595 -8.990 -2.069 -0.603 -2.212 2.570 -2.529 -2.809 0.835 -2.643 -2.555 1.433 -3.092 -0.056 0.683 -2.556 -0.674 -1.568 ML 28 26 6 31 6 1 2 63 84 -6.316 -6.662 -1.267 -1.028 -6.512 -4.041 0.539 -0.503 -0.212 -0.032 MR 29 26 6 31 6 1 2 63 84 -7.426 -6.155 -1.301 -6.133 -0.968 -4.347 0.027 -0.405 -0.454 0.581 D 30 26 6 31 6 0 0 61 81 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 2 65 85 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 3 64 85 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 5 103 G C - - MP 33 32 6 37 6 2 6 63 84 -9.622 -9.561 -0.015 -8.337 -8.617 -9.012 -5.840 -3.304 -6.038 -0.221 -7.069 -5.299 -2.034 -6.461 -5.155 3.791 -5.431 -0.977 -2.306 -5.241 -4.134 -4.921 ML 34 32 6 37 6 1 2 61 82 -6.271 -6.618 -1.279 -1.026 -6.467 -3.997 0.399 -0.467 -0.046 -0.015 MR 35 32 6 37 6 1 2 61 82 -7.163 -5.892 -1.777 -5.870 -0.717 -4.084 0.140 0.135 -0.538 0.152 D 36 32 6 37 6 0 0 59 79 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 2 63 83 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 38 38 6 38 5 1 2 62 83 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 6 102 G C - - MP 39 38 6 43 6 2 6 61 82 -9.623 -9.562 -0.015 -8.339 -8.619 -9.014 -3.992 -2.631 -3.841 1.100 -4.818 -3.743 -0.011 -4.488 -3.601 3.312 -4.491 -0.178 -0.124 -2.943 -1.824 -2.817 ML 40 38 6 43 6 1 2 59 80 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 6 1 2 59 80 -7.156 -5.885 -1.439 -5.863 -0.914 -4.077 0.147 0.122 -0.529 0.153 D 42 38 6 43 6 0 0 57 77 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 2 61 81 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 44 44 6 44 5 1 2 60 81 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 7 101 A U - - MP 45 44 6 49 6 2 6 59 80 -9.631 -9.570 -0.015 -8.347 -8.627 -9.022 -6.871 -4.362 -4.889 3.935 -7.588 -8.236 -3.628 -4.873 -6.901 -2.063 -7.437 -3.272 -3.824 -7.401 -5.404 -5.007 ML 46 44 6 49 6 1 1 57 78 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 6 1 1 57 78 -7.035 -5.764 -1.552 -5.742 -0.863 -3.956 0.292 -0.368 -0.277 0.234 D 48 44 6 49 6 0 0 55 75 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 2 59 79 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 50 50 6 50 5 1 2 58 79 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 8 100 G C - - MP 51 50 6 55 6 2 6 57 78 -9.634 -9.573 -0.015 -8.349 -8.629 -9.024 -3.555 -1.119 -3.725 1.029 -4.665 -3.428 0.040 -4.367 -4.114 3.208 -3.382 0.412 -0.178 -3.608 -1.920 -2.502 ML 52 50 6 55 6 1 1 55 76 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 6 1 1 55 76 -6.995 -5.724 -1.610 -5.702 -0.836 -3.916 0.356 -0.346 -0.218 0.103 D 54 50 6 55 6 0 0 53 73 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 2 57 77 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 56 56 6 56 5 1 2 56 77 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 9 99 C G - - MP 57 56 6 61 6 2 5 55 76 -9.634 -9.573 -0.015 -8.350 -8.630 -9.025 -4.008 -4.048 -2.812 -0.465 -3.206 -4.312 3.576 -3.296 -4.130 -0.362 -4.456 -2.212 0.168 -4.290 -1.177 -3.135 ML 58 56 6 61 6 1 1 53 74 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 6 1 1 53 74 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 60 56 6 61 6 0 0 51 71 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 6 1 2 55 75 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 62 62 6 62 5 1 2 54 75 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 10 98 A U - - MP 63 62 6 67 6 2 5 53 74 -9.634 -9.573 -0.015 -8.350 -8.630 -9.025 -8.069 -7.092 -5.160 3.970 -8.709 -9.603 -4.630 -5.048 -7.977 -3.468 -8.496 -4.213 -5.007 -8.852 -6.487 -5.433 ML 64 62 6 67 6 1 1 51 72 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 6 1 1 51 72 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 6 67 6 0 0 49 69 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 53 73 -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 2 52 73 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 11 97 A U - - MP 69 68 6 73 6 2 5 51 72 -9.634 -9.573 -0.015 -8.350 -8.630 -9.025 -5.923 -3.099 -5.387 3.886 -7.635 -8.637 -3.226 -5.341 -5.711 -1.185 -6.347 -1.925 -3.346 -7.185 -5.094 -4.423 ML 70 68 6 73 6 1 1 49 70 -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 49 70 -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 47 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 51 71 -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 50 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 12 96 U A - - MP 75 74 6 79 6 2 5 49 70 -9.634 -7.977 -0.019 -8.350 -8.373 -9.025 -3.241 -4.089 -4.138 -0.787 -3.680 -4.982 -0.062 -4.314 -3.757 -0.761 -4.730 -2.475 3.665 -4.085 -1.724 -2.691 ML 76 74 6 79 6 1 1 47 68 -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 47 68 -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 45 65 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 49 69 -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 48 69 -2.441 -0.483 -5.952 -4.120 -5.226 0.000 0.000 0.000 0.000 [ MATP 16 ] 13 94 A U - - MP 81 80 6 85 6 2 4 47 67 -9.633 -5.928 -0.043 -7.376 -8.121 -9.024 -8.296 -7.587 -5.610 3.976 -8.556 -8.267 -4.868 -5.530 -8.521 -3.746 -8.930 -5.123 -5.115 -8.507 -6.568 -5.474 ML 82 80 6 85 6 1 1 45 66 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 6 1 1 45 66 -6.999 -5.728 -1.601 -5.707 -0.840 -3.920 0.349 -0.325 -0.233 0.107 D 84 80 6 85 6 0 0 43 64 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 1 47 67 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 86 86 6 86 5 1 1 46 67 -2.584 -0.430 -6.095 -4.263 -5.369 0.000 0.000 0.000 0.000 [ MATP 17 ] 14 92 a u - - MP 87 86 6 91 6 2 3 45 65 -7.146 -4.903 -0.120 -6.647 -5.175 -9.019 -1.400 -1.131 -0.706 1.997 -1.874 -2.669 1.490 -1.458 -1.960 0.821 -1.998 -0.138 1.099 -2.056 -0.124 -1.082 ML 88 86 6 91 6 1 1 44 64 -6.329 -6.675 -1.200 -1.084 -6.525 -4.055 0.562 -0.519 -0.223 -0.046 MR 89 86 6 91 6 1 1 43 64 -7.013 -5.742 -1.574 -5.720 -0.854 -3.934 0.423 -0.480 -0.057 -0.028 D 90 86 6 91 6 0 0 42 62 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 45 66 -1.806 -3.130 -0.945 -4.854 -5.630 -5.291 0.000 0.000 0.000 0.000 IR 92 92 6 92 5 1 1 44 65 -2.763 -0.381 -6.274 -4.308 -5.548 0.000 0.000 0.000 0.000 [ MATP 18 ] 21 90 c g - - MP 93 92 6 97 4 2 2 43 63 -7.970 -3.915 -0.291 -3.153 -1.651 -2.096 -0.959 0.890 -1.310 -2.811 2.465 -1.944 -2.152 0.747 -2.390 -0.664 1.175 -2.235 0.211 -1.330 ML 94 92 6 97 4 1 1 42 63 -3.893 -4.075 -0.454 -2.805 0.675 -0.595 -0.319 -0.091 MR 95 92 6 97 4 1 1 42 62 -5.388 -3.994 -1.182 -1.081 0.333 -0.600 0.189 -0.089 D 96 92 6 97 4 0 0 41 61 -4.568 -4.250 -2.265 -0.520 IL 97 97 5 97 4 1 1 44 64 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 98 98 6 98 3 1 1 43 63 -1.648 -0.698 -3.958 0.000 0.000 0.000 0.000 [ MATL 19 ] 22 - c - - - ML 99 98 6 101 3 1 1 40 61 -8.015 -0.175 -3.178 -0.327 0.723 -0.773 -0.049 D 100 98 6 101 3 0 0 39 60 -7.806 -0.835 -1.201 IL 101 101 3 101 3 1 1 42 63 -1.452 -0.790 -4.152 0.000 0.000 0.000 0.000 [ MATL 20 ] 24 - a - - - ML 102 101 3 104 3 1 1 39 60 -8.220 -0.025 -6.193 0.445 -0.258 -0.567 0.173 D 103 101 3 104 3 0 0 38 59 -7.966 -0.365 -2.186 IL 104 104 3 104 3 1 1 41 62 -1.449 -0.793 -4.149 0.000 0.000 0.000 0.000 [ MATL 21 ] 26 - c - - - ML 105 104 3 107 3 1 1 38 59 -8.642 -0.018 -6.695 0.157 0.952 -1.852 -0.569 D 106 104 3 107 3 0 0 37 58 -6.461 -1.320 -0.766 IL 107 107 3 107 3 1 1 40 61 -1.446 -0.795 -4.146 0.000 0.000 0.000 0.000 [ MATL 22 ] 28 - c - - - ML 108 107 3 110 3 1 1 37 58 -8.943 -0.059 -4.711 -0.963 0.749 -2.021 0.642 D 109 107 3 110 3 0 0 36 57 -5.730 -0.705 -1.443 IL 110 110 3 110 3 1 1 38 59 -1.892 -0.566 -4.182 0.000 0.000 0.000 0.000 [ MATR 23 ] - 87 - c - - MR 111 110 3 113 3 1 1 36 57 -3.106 -0.188 -7.389 -0.270 0.294 -0.444 0.274 D 112 110 3 113 3 0 0 35 55 -7.047 -0.799 -1.259 IR 113 113 3 113 3 1 1 36 57 -2.710 -0.295 -4.949 0.000 0.000 0.000 0.000 [ MATR 24 ] - 85 - G - - MR 114 113 3 116 3 1 1 35 56 -5.154 -0.056 -6.692 -0.839 -1.768 1.344 -0.715 D 115 113 3 116 3 0 0 33 54 -6.422 -1.507 -0.652 IR 116 116 3 116 3 1 1 35 56 -2.142 -0.462 -4.399 0.000 0.000 0.000 0.000 [ MATR 25 ] - 82 - G - - MR 117 116 3 119 5 1 1 34 55 -5.463 -0.054 -7.148 -7.719 -8.959 -0.141 -1.980 1.245 -1.094 D 118 116 3 119 5 0 0 33 53 -5.415 -0.691 -2.929 -4.472 -2.467 IR 119 119 3 119 5 1 1 34 55 -2.521 -0.448 -6.066 -4.233 -5.339 0.000 0.000 0.000 0.000 [ MATP 26 ] 33 79 c g - - MP 120 119 3 124 6 2 2 33 54 -9.375 -5.041 -0.058 -8.345 -8.625 -9.020 -2.174 -2.600 -2.640 0.668 0.084 -3.487 2.036 -2.812 -2.571 0.678 -3.231 -0.991 1.539 -2.654 1.435 -1.621 ML 121 119 3 124 6 1 1 31 52 -6.315 -6.661 -1.330 -0.977 -6.510 -4.040 0.279 -0.366 -0.292 0.256 MR 122 119 3 124 6 1 1 31 52 -7.003 -5.732 -1.594 -5.710 -0.844 -3.924 0.431 -0.429 -0.185 0.042 D 123 119 3 124 6 0 0 29 49 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 32 53 -2.513 -2.862 -0.772 -4.517 -5.293 -4.954 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 32 53 -2.729 -0.383 -6.240 -4.408 -5.513 0.000 0.000 0.000 0.000 [ MATP 27 ] 38 77 U A - - MP 126 125 6 130 6 2 2 31 52 -9.631 -8.775 -0.016 -8.347 -8.627 -9.022 -6.929 -6.921 -6.742 -3.145 -4.499 -7.240 -1.157 -6.304 -5.279 -2.995 -7.106 -4.933 3.900 -6.962 -2.486 -4.712 ML 127 125 6 130 6 1 1 29 50 -6.297 -6.643 -1.244 -1.052 -6.493 -4.022 0.302 -0.369 -0.266 0.216 MR 128 125 6 130 6 1 1 29 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 129 125 6 130 6 0 0 27 47 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 30 51 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 131 131 6 131 5 1 1 30 51 -2.393 -0.498 -5.938 -4.106 -5.212 0.000 0.000 0.000 0.000 [ MATP 28 ] 39 74 C G - - MP 132 131 6 136 6 2 2 29 50 -9.634 -9.573 -0.015 -8.350 -8.415 -9.025 -5.952 -5.904 -5.062 -2.109 -3.510 -6.215 3.852 -4.801 -5.907 -1.950 -5.216 -3.846 -1.084 -6.152 -2.088 -4.782 ML 133 131 6 136 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 134 131 6 136 6 1 1 27 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 135 131 6 136 6 0 0 25 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 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 137 137 6 137 5 1 1 28 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 40 73 U A - - MP 138 137 6 142 6 2 2 27 48 -8.426 -9.573 -0.017 -8.349 -8.629 -9.024 -8.051 -8.038 -8.060 -4.476 -6.527 -8.711 -3.025 -7.869 -6.584 -4.340 -8.516 -6.171 3.967 -7.186 -4.232 -5.112 ML 139 137 6 142 6 1 1 26 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 140 137 6 142 6 1 1 25 46 -6.997 -5.726 -1.635 -5.704 -0.821 -3.918 0.410 -0.415 -0.185 0.058 D 141 137 6 142 6 0 0 23 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 142 142 5 142 6 1 1 27 47 -2.135 -2.991 -0.853 -4.646 -5.422 -5.082 0.000 0.000 0.000 0.000 IR 143 143 6 143 5 1 1 26 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 47 72 U A - - MP 144 143 6 148 6 2 2 25 46 -9.633 -9.573 -0.015 -8.233 -8.629 -9.024 -7.083 -7.113 -6.572 -3.325 -5.047 -6.833 -0.744 -5.915 -6.576 -3.261 -6.824 -5.165 3.890 -6.978 -2.320 -4.740 ML 145 143 6 148 6 1 1 24 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 146 143 6 148 6 1 1 24 45 -6.997 -5.726 -1.635 -5.704 -0.821 -3.918 0.410 -0.415 -0.185 0.058 D 147 143 6 148 6 0 0 22 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 148 148 5 148 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 149 149 6 149 5 1 1 24 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 48 71 G C - - MP 150 149 6 154 4 2 2 23 44 -8.053 -8.094 -0.034 -5.998 -3.648 -1.995 -3.380 0.962 -4.147 -3.341 0.156 -3.858 -2.739 3.252 -3.256 -0.145 -0.011 -2.772 -1.759 -2.594 ML 151 149 6 154 4 1 1 23 44 -3.763 -3.946 -0.505 -2.675 0.390 -0.425 -0.124 0.039 MR 152 149 6 154 4 1 1 23 43 -4.821 -3.850 -1.717 -0.759 0.353 -0.335 -0.226 0.105 D 153 149 6 154 4 0 0 22 42 -4.568 -4.250 -2.265 -0.520 IL 154 154 5 154 4 1 1 25 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 155 155 6 155 3 1 1 24 44 -1.422 -0.809 -4.158 0.000 0.000 0.000 0.000 [ MATL 32 ] 49 - u - - - ML 156 155 6 158 3 1 1 21 41 -7.350 -0.016 -7.660 0.153 -0.867 -1.234 0.937 D 157 155 6 158 3 0 0 19 40 -6.339 -1.550 -0.630 IL 158 158 3 158 3 1 1 23 43 -1.470 -0.777 -4.170 0.000 0.000 0.000 0.000 [ MATL 33 ] 51 - U - - - ML 159 158 3 161 3 1 1 19 40 -6.402 -0.024 -7.665 -2.186 -2.045 -2.855 1.765 D 160 158 3 161 3 0 0 18 39 -6.243 -1.598 -0.607 IL 161 161 3 161 3 1 1 23 44 -1.256 -0.908 -4.366 0.000 0.000 0.000 0.000 [ MATL 34 ] 58 - c - - - ML 162 161 3 164 5 1 1 17 35 -7.758 -0.021 -7.860 -8.073 -8.964 0.438 0.492 -1.556 -0.153 D 163 161 3 164 5 0 0 16 35 -4.970 -0.814 -4.231 -2.606 -2.460 IL 164 164 3 164 5 1 1 18 36 -2.415 -0.494 -4.094 -5.926 -5.200 0.000 0.000 0.000 0.000 [ MATP 35 ] 60 64 u u - - MP 165 164 3 169 4 2 2 16 34 -6.459 -7.724 -0.038 -6.675 -0.709 -1.902 -1.776 0.939 -1.804 -2.771 1.215 -2.270 0.249 0.836 -2.399 -0.572 1.158 -1.817 0.250 1.270 ML 166 164 3 169 4 1 1 17 35 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 167 164 3 169 4 1 1 17 35 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 168 164 3 169 4 0 0 16 34 -4.582 -4.263 -2.279 -0.514 IL 169 169 5 169 4 1 1 18 37 -1.786 -2.469 -1.008 -4.954 0.000 0.000 0.000 0.000 IR 170 170 6 170 3 1 1 17 36 -1.452 -0.791 -4.152 0.000 0.000 0.000 0.000 [ MATL 36 ] 62 - A - - - ML 171 170 6 173 2 1 1 1 1 * 0.000 1.696 -2.212 -1.669 -2.120 D 172 170 6 173 2 0 0 0 0 * 0.000 IL 173 173 3 173 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 37 ] - - - - - - E 174 173 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-psbA-3 ACC RF04344 DESC Plastid-psbA-3 3UTR RNA LENG 57 MAXL 124 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Nov 5 16:02:38 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_036093.1/CM NSEQ 830 EFFN 11.192513 CKSUM 2924302399 STATS LOCAL MSV -7.7480 0.71954 STATS LOCAL VITERBI -8.3809 0.71954 STATS LOCAL FORWARD -3.7353 0.71954 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.25982 1.65353 1.64629 1.10215 1.38629 1.38629 1.38629 1.38629 0.51413 1.04886 2.96336 0.06262 2.80188 0.00000 * 1 0.61469 2.15502 1.75258 1.77216 2 A - - < 1.38629 1.38629 1.38629 1.38629 0.01883 4.67474 4.67474 1.46634 0.26236 0.51755 0.90628 2 0.13346 3.83195 2.47872 3.94167 3 A - - < 1.38629 1.38629 1.38629 1.38629 0.01726 4.76125 4.76125 1.46634 0.26236 0.78564 0.60849 3 0.67988 2.10330 1.49478 1.91751 4 A - - < 1.38629 1.38629 1.38629 1.38629 0.01664 4.79750 4.79750 1.46634 0.26236 1.09861 0.40547 4 3.03725 4.56347 0.07251 4.46082 5 G - - < 1.38629 1.38629 1.38629 1.38629 0.01622 4.82301 4.82301 1.46634 0.26236 1.09861 0.40547 5 2.01556 2.87605 0.31260 2.54019 6 G - - < 1.38629 1.38629 1.38629 1.38629 0.01621 4.82363 4.82363 1.46634 0.26236 1.09861 0.40547 6 0.01476 5.62826 4.93581 5.55452 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.01604 4.83368 4.83368 1.46634 0.26236 1.09861 0.40547 7 1.91568 2.83708 0.32032 2.68463 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.01599 4.83679 4.83679 1.46634 0.26236 1.09861 0.40547 8 2.94912 0.21682 2.91529 2.42645 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 9 0.00977 5.82364 5.63042 5.75159 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 10 0.03269 5.33215 3.86861 5.04517 11 A - - < 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 11 3.67101 3.41656 3.63426 0.08848 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.01690 4.83736 4.72980 1.46634 0.26236 1.09861 0.40547 12 0.00825 5.95402 5.91616 5.83359 13 A - - < 1.38629 1.38629 1.38629 1.38629 0.01798 4.83646 4.61669 1.46634 0.26236 1.02820 0.44262 13 0.91167 1.52934 1.70541 1.61059 14 a - - < 1.38629 1.38629 1.38629 1.38629 0.07651 3.98796 2.89821 1.31188 0.31377 0.95759 0.48421 14 1.74939 0.78801 1.92223 1.49125 21 c - - < 1.38629 1.38629 1.38629 1.38629 0.13838 4.78913 2.11267 1.46634 0.26236 0.48197 0.96120 15 1.74047 0.76366 1.96321 1.52237 22 c - - - 1.38629 1.38629 1.38629 1.38629 0.14460 4.52372 2.08922 1.24726 0.33868 0.47518 0.97226 16 1.04875 1.55374 1.81008 1.29270 24 a - - - 1.38629 1.38629 1.38629 1.38629 0.02887 4.56087 4.01703 1.31400 0.31299 0.13579 2.06378 17 1.27613 0.60681 3.09204 2.03726 26 C - - - 1.38629 1.38629 1.38629 1.38629 0.02196 4.75358 4.33546 1.37821 0.29039 0.69954 0.68680 18 2.33654 0.76736 3.23272 0.91716 28 c - - - 1.38629 1.38629 1.38629 1.38629 0.01667 4.76285 4.82998 1.45833 0.26478 0.79135 0.60373 19 2.25904 1.00963 2.14810 0.88071 33 u - - < 1.38629 1.38629 1.38629 1.38629 0.01645 4.78164 4.83619 1.45974 0.26435 1.00881 0.45358 20 5.54695 4.56916 5.50428 0.01851 38 U - - < 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 21 4.78697 0.04004 4.67958 3.83380 39 C - - < 1.38629 1.38629 1.38629 1.38629 0.01674 4.83736 4.74801 1.46634 0.26236 1.09861 0.40547 22 6.08317 6.14295 6.29987 0.00629 40 U - - < 1.38629 1.38629 1.38629 1.38629 0.01907 4.51402 4.83662 1.49439 0.25410 1.12929 0.39047 23 5.52995 4.28785 5.60574 0.02161 47 U - - < 1.38629 1.38629 1.38629 1.38629 0.01599 4.83662 4.83662 1.46634 0.26236 1.12929 0.39047 24 2.12094 2.75268 0.30249 2.55946 48 G - - < 1.38629 1.38629 1.38629 1.38629 0.02224 4.83662 4.26470 1.46634 0.26236 1.12929 0.39047 25 1.27005 2.13728 2.41150 0.67035 49 U - - - 1.38629 1.38629 1.38629 1.38629 0.02071 4.38104 4.83048 0.99811 0.45978 0.93589 0.49797 26 3.31112 3.15785 3.73462 0.10856 51 U - - - 1.38629 1.38629 1.38629 1.38629 0.02696 3.98170 4.83459 1.33246 0.30629 0.98106 0.46987 27 1.05238 0.94098 2.80361 1.60914 58 c - - - 1.38629 1.38629 1.38629 1.38629 0.01698 4.72191 4.83662 1.32756 0.30805 1.12929 0.39047 28 1.73784 1.86842 1.40266 0.85852 60 u - - < 1.38629 1.38629 1.38629 1.38629 0.02410 4.14272 4.83662 0.81041 0.58821 1.12929 0.39047 29 0.15773 3.15891 2.71675 3.28726 62 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01756 4.65980 4.83662 1.25867 0.33412 1.12929 0.39047 30 1.25800 2.00360 1.50313 1.02584 64 u - - > 1.38629 1.38629 1.38629 1.38629 0.01690 4.78557 4.77874 1.49675 0.25342 1.03994 0.43615 31 2.73701 0.35079 2.58053 1.86195 71 C - - > 1.38629 1.38629 1.38629 1.38629 0.01599 4.83689 4.83689 1.46634 0.26236 1.06040 0.42513 32 0.02764 5.74177 3.98540 5.20940 72 A - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 33 0.00888 6.41642 5.58723 5.66567 73 A - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 34 4.03482 4.91102 0.03530 4.64251 74 G - - > 1.38629 1.38629 1.38629 1.38629 0.02099 4.63592 4.50310 1.27473 0.32782 1.09861 0.40547 35 0.02248 5.80687 4.26563 5.26347 77 A - - > 1.38629 1.38629 1.38629 1.38629 0.07294 2.79432 4.69034 0.24244 1.53577 1.22287 0.34869 36 1.25725 2.31171 0.70747 2.09084 79 g - - > 1.38629 1.38629 1.38629 1.38629 0.04280 3.51261 4.41614 0.49088 0.94697 0.93315 0.49974 37 1.53967 3.14272 0.43258 2.36924 82 G - - - 1.38629 1.38629 1.38629 1.38629 0.04844 3.27540 4.65861 0.39040 1.12945 0.78675 0.60756 38 2.20150 2.89439 0.36345 1.97502 85 G - - - 1.38629 1.38629 1.38629 1.38629 0.19607 2.02570 3.07595 0.11632 2.20897 1.04520 0.43328 39 1.69455 1.09937 1.67899 1.21512 87 c - - - 1.38629 1.38629 1.38629 1.38629 0.10128 2.59051 3.84735 0.35848 1.19978 0.29278 1.37116 40 1.68943 2.10984 0.65051 1.75828 90 G - - > 1.38629 1.38629 1.38629 1.38629 0.08524 2.68525 4.30475 0.22080 1.61887 0.57270 0.83011 41 1.80594 1.92045 1.26917 0.89631 92 u - - > 1.38629 1.38629 1.38629 1.38629 0.04473 3.33052 4.83194 0.39826 1.11318 0.78349 0.61029 42 6.00347 6.19858 5.88518 0.00731 94 U - - > 1.38629 1.38629 1.38629 1.38629 0.02094 4.35879 4.83736 0.97371 0.47430 1.09861 0.40547 43 0.09721 3.81114 3.21160 3.49914 96 A - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 44 5.19839 4.03400 5.14440 0.02949 97 U - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 45 5.90835 6.01466 5.73017 0.00844 98 U - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 46 2.67601 3.04710 0.19196 2.84163 99 G - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 47 2.93455 0.39482 2.64564 1.59909 100 C - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 48 5.41289 4.97408 5.35435 0.01623 101 U - - > 1.38629 1.38629 1.38629 1.38629 0.01598 4.83736 4.83736 1.46634 0.26236 1.09861 0.40547 49 2.80043 0.36459 2.67791 1.73711 102 C - - > 1.38629 1.38629 1.38629 1.38629 0.01601 4.83594 4.83594 1.46634 0.26236 1.09861 0.40547 50 4.26382 0.10536 4.26866 2.63203 103 C - - > 1.38629 1.38629 1.38629 1.38629 0.01606 4.83288 4.83288 1.46634 0.26236 1.09861 0.40547 51 2.09893 1.52787 1.91816 0.66643 104 U - - > 1.38629 1.38629 1.38629 1.38629 0.01615 4.82711 4.82711 1.46634 0.26236 1.09861 0.40547 52 3.32704 1.96321 3.42697 0.23419 105 U - - > 1.38629 1.38629 1.38629 1.38629 0.01638 4.81288 4.81288 1.46634 0.26236 1.09861 0.40547 53 1.84541 1.67185 1.98897 0.65912 106 U - - > 1.38629 1.38629 1.38629 1.38629 0.01676 4.79044 4.79044 1.46634 0.26236 1.09861 0.40547 54 1.07441 1.96022 2.40465 0.85009 107 u - - : 1.38629 1.38629 1.38629 1.38629 0.01817 4.75040 4.67204 1.46634 0.26236 1.09861 0.40547 55 1.74442 1.69753 2.62290 0.56295 108 U - - : 1.38629 1.38629 1.38629 1.38629 0.02104 4.70581 4.44173 1.46634 0.26236 1.12542 0.39233 56 2.77701 3.04944 3.57021 0.14822 109 U - - : 1.38629 1.38629 1.38629 1.38629 0.13647 4.56804 2.14393 1.46634 0.26236 1.21899 0.35031 57 2.18955 2.82544 3.13216 0.24191 110 U - - : 1.38629 1.38629 1.38629 1.38629 0.35190 1.21521 * 0.64719 0.74132 0.00000 * //