INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-psbA-2 ACC RF04343 DESC Plastid-psbA-2 3UTR RNA STATES 184 NODES 38 CLEN 60 W 75 ALPH RNA RF no CONS yes MAP yes DATE Wed Nov 5 16:06:03 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/psbA/psbA_NC_016433.2/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 121 EFFN 3.208893 CKSUM 3730750870 NULL 0.000 0.000 0.000 0.000 GA 55.80 TC 55.80 NC 55.60 EFP7GF -11.7468 0.71949 ECMLC 0.64887 -5.31129 3.91659 1600000 478174 0.002510 ECMGC 0.44053 -14.70113 0.69478 1600000 352865 0.001134 ECMLI 0.59799 -4.66852 4.72071 1600000 329319 0.003644 ECMGI 0.48168 -9.83702 3.20170 1600000 213611 0.001873 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 75 95 -7.280 -8.525 -0.538 -1.727 IL 1 1 2 1 4 1 1 77 96 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 2 77 96 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 90 - C - - MR 3 2 3 5 3 1 3 75 95 -8.318 -0.019 -6.635 -1.452 1.513 -2.272 -0.803 D 4 2 3 5 3 0 0 74 93 -8.331 -1.572 -0.598 IR 5 5 3 5 3 1 1 76 95 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 89 - U - - MR 6 5 3 8 3 1 2 74 94 -8.478 -0.017 -6.796 -0.820 -1.111 -1.573 1.398 D 7 5 3 8 3 0 0 73 92 -7.919 -0.882 -1.141 IR 8 8 3 8 3 1 1 75 94 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 88 - U - - MR 9 8 3 11 3 1 2 73 93 -8.661 -0.015 -6.979 -2.104 -1.995 -2.863 1.757 D 10 8 3 11 3 0 0 72 91 -7.119 -0.737 -1.349 IR 11 11 3 11 3 1 1 74 93 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 87 - U - - MR 12 11 3 14 5 1 1 72 92 -7.466 -0.441 -7.281 -2.010 -8.385 -1.293 -1.585 -2.277 1.610 D 13 11 3 14 5 0 0 71 91 -5.352 -0.707 -2.978 -4.409 -2.404 IR 14 14 3 14 5 1 1 73 92 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 3 86 c g - - MP 15 14 3 19 6 2 2 71 91 -9.094 -9.033 -0.021 -7.810 -8.089 -8.485 -2.045 -2.083 -2.210 1.243 -2.066 -3.036 1.571 -1.247 -2.257 1.218 -2.801 -0.459 1.463 -2.351 -0.114 0.928 ML 16 14 3 19 6 1 1 70 89 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 17 14 3 19 6 1 1 70 89 -8.426 -7.155 -1.955 -7.133 -0.514 -5.347 -0.202 -0.729 -1.038 1.029 D 18 14 3 19 6 0 0 68 87 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 19 19 5 19 6 1 1 71 91 -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 1 71 90 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 4 85 a u - - MP 21 20 6 25 6 2 2 69 89 -9.140 -9.080 -0.021 -7.856 -8.136 -8.531 0.510 -1.707 -1.973 1.504 -1.549 -2.813 1.485 -2.284 -2.038 1.240 -2.596 -0.405 1.346 -2.107 -0.070 -1.195 ML 22 20 6 25 6 1 1 68 87 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 6 1 1 68 87 -8.211 -6.940 -1.943 -6.918 -0.532 -5.132 0.964 -0.815 -0.897 -0.083 D 24 20 6 25 6 0 0 66 85 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 25 25 5 25 6 1 1 69 89 -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 1 69 88 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 5 84 a u - - MP 27 26 6 31 6 2 2 67 87 -9.175 -9.114 -0.020 -7.890 -8.170 -8.565 -1.744 -1.522 -1.992 1.464 -1.977 -2.820 1.394 -2.323 -2.064 1.436 -2.615 -0.318 1.448 -1.734 -0.136 0.347 ML 28 26 6 31 6 1 1 66 85 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 29 26 6 31 6 1 1 66 86 -8.025 -6.754 -0.576 -6.732 -1.866 -4.945 -0.023 -0.612 -0.933 0.878 D 30 26 6 31 6 0 0 64 83 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 67 87 -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 1 67 86 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 6 83 A U - - MP 33 32 6 37 6 2 2 65 85 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.531 -2.424 -4.453 3.669 -5.489 -6.354 -1.197 -4.526 -4.424 0.320 -5.016 -0.844 -1.442 -5.322 -3.090 -3.325 ML 34 32 6 37 6 1 1 64 83 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 6 1 1 64 83 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 36 32 6 37 6 0 0 61 81 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 65 85 -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 1 65 84 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 7 82 A U - - MP 39 38 6 43 6 2 2 63 83 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.353 -2.455 -4.332 3.600 -5.314 -6.135 -1.006 -4.430 -4.255 0.675 -4.843 -0.678 -1.240 -5.110 -2.904 -3.176 ML 40 38 6 43 6 1 1 62 81 -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 1 62 81 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 42 38 6 43 6 0 0 59 79 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 63 83 -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 1 63 82 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 8 81 G C - - MP 45 44 6 49 6 2 2 61 81 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -5.554 -3.491 -5.779 -0.369 -6.363 -4.996 -1.525 -6.044 -4.818 3.784 -5.106 -1.233 -1.893 -4.988 -3.615 -4.644 ML 46 44 6 49 6 1 1 60 79 -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 60 79 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 48 44 6 49 6 0 0 57 77 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 61 81 -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 1 61 80 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 9 80 G C - - MP 51 50 6 55 6 2 2 59 79 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -5.290 -2.606 -5.438 -0.166 -6.240 -4.913 -1.370 -5.832 -4.726 3.746 -5.016 -1.094 -1.670 -4.784 -3.441 -4.334 ML 52 50 6 55 6 1 1 58 77 -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 58 77 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 54 50 6 55 6 0 0 55 75 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 1 59 79 -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 1 59 78 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 10 79 A U - - MP 57 56 6 61 6 2 2 57 77 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.549 -2.551 -4.470 3.674 -5.519 -6.401 -1.214 -4.536 -4.436 0.300 -5.029 -0.845 -1.463 -5.360 -3.112 -3.336 ML 58 56 6 61 6 1 1 56 75 -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 56 75 -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 53 73 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 6 1 1 57 77 -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 1 57 76 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 11 78 G C - - MP 63 62 6 67 6 2 2 55 75 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.604 -2.190 -4.610 0.529 -5.500 -4.723 -0.718 -5.093 -4.412 3.570 -4.728 -0.311 -0.990 -4.307 -2.736 -3.530 ML 64 62 6 67 6 1 1 54 73 -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 54 73 -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 51 71 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 55 75 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 68 68 6 68 5 1 1 55 74 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 12 77 C G - - MP 69 68 6 73 6 2 2 53 73 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.083 -4.022 -2.481 -0.089 -3.096 -4.671 3.429 -3.787 -4.044 -0.081 -4.452 -2.004 0.641 -4.271 -0.474 -2.938 ML 70 68 6 73 6 1 1 52 71 -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 52 71 -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 49 69 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 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 74 74 6 74 5 1 1 53 72 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 13 76 A U - - MP 75 74 6 79 6 2 2 51 71 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.597 -3.450 -4.523 3.677 -5.311 -6.480 -0.956 -4.509 -4.420 0.203 -5.006 -0.819 -1.366 -5.506 -2.892 -3.337 ML 76 74 6 79 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 77 74 6 79 6 1 1 50 69 -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 47 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 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 80 80 6 80 5 1 1 51 70 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 14 75 A U - - MP 81 80 6 85 6 2 2 49 69 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -4.597 -3.450 -4.523 3.677 -5.311 -6.480 -0.956 -4.509 -4.420 0.203 -5.006 -0.819 -1.366 -5.506 -2.892 -3.337 ML 82 80 6 85 6 1 1 48 67 -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 48 67 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 84 80 6 85 6 0 0 45 65 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 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 86 86 6 86 5 1 1 49 68 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 15 74 u a - - MP 87 86 6 91 6 2 2 47 67 -9.295 -9.234 -0.019 -8.011 -8.290 -8.685 -2.493 -2.856 -2.969 0.696 -2.182 -3.802 1.617 -3.013 -2.978 0.935 -3.521 -1.020 2.701 -3.119 -0.129 -1.720 ML 88 86 6 91 6 1 1 46 65 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 89 86 6 91 6 1 1 46 65 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 6 91 6 0 0 43 63 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 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 92 92 6 92 5 1 1 47 66 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 16 73 A U - - MP 93 92 6 97 6 2 2 45 65 -9.295 -6.602 -0.031 -8.011 -8.290 -8.685 -5.004 -4.345 -4.627 3.772 -5.227 -6.199 -1.147 -3.220 -5.044 -0.501 -5.579 -1.956 -1.501 -5.439 -3.013 -3.322 ML 94 92 6 97 6 1 1 44 63 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 6 1 1 44 63 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 96 92 6 97 6 0 0 41 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 6 1 1 45 65 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 98 98 6 98 5 1 1 45 64 -2.178 -0.542 -6.079 -4.247 -5.353 0.000 0.000 0.000 0.000 [ MATP 19 ] 17 70 a u - - MP 99 98 6 103 6 2 2 43 63 -9.295 -5.094 -0.066 -7.462 -7.373 -8.685 -2.335 -1.951 -1.537 2.816 -2.515 -3.337 0.946 -2.401 -2.587 1.087 -2.966 -0.685 0.699 -2.624 -0.663 -1.705 ML 100 98 6 103 6 1 1 42 61 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 101 98 6 103 6 1 1 42 61 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 102 98 6 103 6 0 0 39 59 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 103 103 5 103 6 1 1 43 62 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 104 104 6 104 5 1 1 43 62 -2.439 -0.450 -6.212 -4.380 -5.486 0.000 0.000 0.000 0.000 [ MATP 20 ] 18 67 c g - - MP 105 104 6 109 6 2 2 41 61 -9.288 -4.167 -0.123 -6.062 -7.213 -8.679 -1.199 -1.420 -0.048 1.463 -1.609 -1.863 1.619 -1.611 -1.812 0.937 -2.216 -0.449 1.325 -1.885 0.030 -0.939 ML 106 104 6 109 6 1 1 40 59 -6.289 -6.635 -1.255 -1.044 -6.485 -4.014 0.315 -0.232 -0.297 0.125 MR 107 104 6 109 6 1 1 40 59 -7.040 -5.769 -1.521 -5.748 -0.882 -3.961 0.374 -0.521 0.074 -0.067 D 108 104 6 109 6 0 0 37 57 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 109 109 5 109 6 1 1 41 60 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 110 110 6 110 5 1 1 41 60 -2.591 -0.432 -6.416 -4.020 -5.689 0.000 0.000 0.000 0.000 [ MATP 21 ] 19 63 C G - - MP 111 110 6 115 6 2 2 39 59 -9.268 -6.687 -0.031 -7.983 -8.263 -8.658 -3.497 -3.549 -3.027 -0.068 -2.614 -3.788 3.415 -3.238 -3.628 -0.004 -4.113 -1.767 0.556 -3.776 -0.721 -2.651 ML 112 110 6 115 6 1 1 38 57 -6.473 -6.819 -1.034 -1.228 -6.669 -4.198 0.120 0.171 -0.561 0.150 MR 113 110 6 115 6 1 1 38 57 -7.126 -5.855 -1.373 -5.833 -0.967 -4.047 0.283 -0.600 0.266 -0.118 D 114 110 6 115 6 0 0 36 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 115 115 5 115 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 116 116 6 116 5 1 1 39 58 -2.283 -0.514 -6.042 -4.210 -5.316 0.000 0.000 0.000 0.000 [ MATP 22 ] 20 60 c g - - MP 117 116 6 121 6 2 2 37 57 -9.295 -5.449 -0.050 -8.011 -8.290 -8.685 -1.895 -2.226 -1.934 1.007 -1.931 -3.105 1.955 -2.308 -2.300 0.905 -2.540 -0.686 1.526 -2.402 1.311 -1.426 ML 118 116 6 121 6 1 1 36 56 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 119 116 6 121 6 1 1 36 56 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 120 116 6 121 6 0 0 34 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 121 121 5 121 6 1 1 37 56 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 122 122 6 122 5 1 1 37 56 -1.954 -0.595 -6.285 -4.452 -5.558 0.000 0.000 0.000 0.000 [ MATP 23 ] 21 57 c g - - MP 123 122 6 127 4 2 2 35 54 -7.395 -5.162 -0.125 -4.356 -1.289 -2.102 -1.275 0.869 -1.389 -2.604 2.563 -2.407 -2.160 0.751 -2.725 -0.712 1.138 -2.243 -0.001 -1.337 ML 124 122 6 127 4 1 1 36 55 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 125 122 6 127 4 1 1 35 55 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 126 122 6 127 4 0 0 34 54 -4.568 -4.250 -2.265 -0.520 IL 127 127 5 127 4 1 1 37 56 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 128 128 6 128 3 1 1 36 55 -1.404 -0.840 -3.975 0.000 0.000 0.000 0.000 [ MATL 24 ] 22 - U - - - ML 129 128 6 131 3 1 1 32 51 -8.330 -0.016 -6.984 -1.483 -0.929 -2.230 1.538 D 130 128 6 131 3 0 0 31 50 -6.710 -1.989 -0.437 IL 131 131 3 131 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 23 - U - - - ML 132 131 3 134 5 1 1 31 50 -7.424 -0.031 -7.239 -7.451 -8.343 -1.417 -0.774 -2.167 1.495 D 133 131 3 134 5 0 0 30 49 -5.249 -0.620 -4.510 -2.885 -2.798 IL 134 134 3 134 5 1 1 31 50 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 24 53 U A - - MP 135 134 3 139 6 2 2 30 49 -8.250 -5.637 -0.048 -8.011 -8.290 -8.685 -4.728 -4.706 -4.512 -0.947 -3.310 -4.997 1.033 -4.072 -4.529 -0.764 -4.874 -2.710 3.488 -4.822 -0.082 -3.298 ML 136 134 3 139 6 1 1 28 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 137 134 3 139 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 138 134 3 139 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 139 139 5 139 6 1 1 30 49 -2.606 -2.869 -0.742 -4.525 -5.301 -4.961 0.000 0.000 0.000 0.000 IR 140 140 6 140 5 1 1 30 49 -1.929 -0.639 -6.265 -4.047 -5.538 0.000 0.000 0.000 0.000 [ MATP 27 ] 26 49 C G - - MP 141 140 6 145 6 2 2 28 47 -9.291 -7.577 -0.028 -8.007 -7.444 -8.682 -4.388 -4.388 -4.176 -0.588 -1.760 -4.663 3.425 -3.736 -4.198 -0.428 -4.531 -2.386 0.666 -4.491 0.325 -3.048 ML 142 140 6 145 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 143 140 6 145 6 1 1 26 45 -7.037 -5.766 -1.527 -5.744 -0.878 -3.958 0.377 -0.517 0.064 -0.064 D 144 140 6 145 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 145 145 5 145 6 1 1 28 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 146 146 6 146 5 1 1 27 46 -2.302 -0.516 -5.988 -4.155 -5.261 0.000 0.000 0.000 0.000 [ MATP 28 ] 27 46 U A - - MP 147 146 6 151 6 2 2 26 45 -7.510 -5.499 -0.055 -8.007 -8.287 -8.682 -4.995 -4.977 -5.076 -1.485 -4.509 -5.851 -0.361 -5.053 -4.260 -1.285 -5.599 -3.112 3.781 -4.404 -2.214 -3.724 ML 148 146 6 151 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 149 146 6 151 6 1 1 25 43 -7.035 -5.764 -1.673 -5.742 -0.793 -3.956 0.517 -0.489 -0.203 -0.019 D 150 146 6 151 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 151 151 5 151 6 1 1 26 45 -2.367 -2.962 -0.778 -4.617 -5.394 -5.054 0.000 0.000 0.000 0.000 IR 152 152 6 152 5 1 1 26 45 -1.784 -0.660 -6.340 -4.508 -5.614 0.000 0.000 0.000 0.000 [ MATP 29 ] 30 41 U A - - MP 153 152 6 157 6 2 2 24 43 -9.291 -9.230 -0.019 -8.007 -8.287 -8.682 -5.260 -5.099 -4.972 -1.336 -3.714 -5.434 0.623 -4.474 -4.970 -1.203 -5.290 -2.968 3.669 -5.358 -1.365 -3.653 ML 154 152 6 157 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 155 152 6 157 6 1 1 23 42 -7.035 -5.764 -1.673 -5.742 -0.793 -3.956 0.517 -0.489 -0.203 -0.019 D 156 152 6 157 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 157 157 5 157 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 158 158 6 158 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 31 40 G C - - MP 159 158 6 163 4 2 2 22 41 -7.387 -7.594 -0.039 -6.008 -3.350 -1.762 -3.339 1.010 -3.863 -2.815 0.341 -3.860 -2.362 3.177 -3.930 -0.183 0.102 -2.781 -1.494 -2.405 ML 160 158 6 163 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 161 158 6 163 4 1 1 22 41 -4.864 -3.893 -1.590 -0.821 0.295 -0.182 -0.331 0.133 D 162 158 6 163 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520 IL 163 163 5 163 4 1 1 24 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 164 164 6 164 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 32 - U - - - ML 165 164 6 167 3 1 1 19 38 -8.384 -0.015 -7.038 -0.464 -1.068 -1.205 1.241 D 166 164 6 167 3 0 0 18 37 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 33 - U - - - ML 168 167 3 170 3 1 1 18 36 -8.384 -0.015 -7.038 -1.350 -1.477 -1.964 1.581 D 169 167 3 170 3 0 0 17 36 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 34 - c - - - ML 171 170 3 173 3 1 1 16 35 -8.384 -0.015 -7.038 -0.486 0.948 -1.675 0.061 D 172 170 3 173 3 0 0 16 35 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 20 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 35 - U - - - ML 174 173 3 176 3 1 1 15 34 -6.951 -0.023 -7.038 -0.934 -1.289 -1.395 1.426 D 175 173 3 176 3 0 0 15 33 -6.174 -1.687 -0.566 IL 176 176 3 176 3 1 1 19 38 -1.426 -0.804 -4.187 0.000 0.000 0.000 0.000 [ MATL 35 ] 38 - A - - - ML 177 176 3 179 3 1 1 13 31 -8.384 -0.015 -7.038 1.629 -1.823 -1.764 -1.604 D 178 176 3 179 3 0 0 13 32 -6.174 -1.687 -0.566 IL 179 179 3 179 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 39 - U - - - ML 180 179 3 182 2 1 1 1 1 * 0.000 -0.590 -0.901 -1.350 1.268 D 181 179 3 182 2 0 0 0 0 * 0.000 IL 182 182 3 182 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 37 ] - - - - - - E 183 182 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-psbA-2 ACC RF04343 DESC Plastid-psbA-2 3UTR RNA LENG 60 MAXL 135 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Nov 5 16:06:03 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/psbA/psbA_NC_016433.2/CM NSEQ 121 EFFN 5.328461 CKSUM 3730750870 STATS LOCAL MSV -7.9598 0.71949 STATS LOCAL VITERBI -8.6289 0.71949 STATS LOCAL FORWARD -3.6782 0.71949 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.36706 1.62830 1.64904 1.03100 1.38629 1.38629 1.38629 1.38629 1.04928 1.09373 1.15567 0.51627 0.90818 0.00000 * 1 1.68152 1.50278 1.69354 0.89764 3 u - - < 1.38629 1.38629 1.38629 1.38629 0.03866 3.96525 3.96525 1.46634 0.26236 1.45912 0.26454 2 1.05182 1.58708 1.61160 1.39995 4 a - - < 1.38629 1.38629 1.38629 1.38629 0.03526 4.05567 4.05567 1.46634 0.26236 1.47183 0.26072 3 1.43400 1.66127 1.51699 1.04305 5 u - - < 1.38629 1.38629 1.38629 1.38629 0.03306 4.11893 4.11893 1.46634 0.26236 0.12507 2.14080 4 0.09114 4.34530 2.86013 4.08157 6 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 5 0.12522 4.16881 2.50289 3.89338 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 6 3.25657 4.18935 0.07228 4.13206 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 7 3.00664 4.07143 0.08913 3.97580 9 G - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 8 0.08918 4.37146 2.87752 4.10989 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 9 2.37651 3.47645 0.17360 3.33606 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 10 2.75033 0.26915 2.93441 2.12946 12 C - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 11 0.10189 4.06980 2.81326 3.92289 13 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 12 0.10183 4.07086 2.81354 3.92419 14 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 13 2.12566 1.62305 1.91241 0.62432 15 U - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 14 0.03857 4.55243 4.07352 4.57779 16 A - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 15 0.57166 2.02624 1.85854 1.91269 17 A - - < 1.38629 1.38629 1.38629 1.38629 0.03363 4.32421 3.92054 1.46634 0.26236 1.09861 0.40547 16 1.16225 1.36997 1.71268 1.37547 18 a - - < 1.38629 1.38629 1.38629 1.38629 0.04557 4.31761 3.46694 1.46634 0.26236 0.84832 0.55885 17 2.84403 0.25009 2.81025 2.27414 19 C - - < 1.38629 1.38629 1.38629 1.38629 0.02734 4.30629 4.30629 1.46634 0.26236 0.61749 0.77501 18 1.77876 1.29458 1.80805 0.93352 20 u - - < 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 19 1.66007 0.88802 1.82158 1.44124 21 c - - < 1.38629 1.38629 1.38629 1.38629 0.06959 4.32421 2.91907 1.46634 0.26236 1.09861 0.40547 20 2.86994 2.19016 3.39084 0.22600 22 U - - - 1.38629 1.38629 1.38629 1.38629 0.02800 4.28262 4.28262 1.46634 0.26236 1.48711 0.25622 21 2.81732 2.04794 3.34139 0.25380 23 U - - - 1.38629 1.38629 1.38629 1.38629 0.02786 4.28776 4.28776 1.46634 0.26236 0.43187 1.04780 22 3.89482 2.47664 3.73508 0.13724 24 U - - < 1.38629 1.38629 1.38629 1.38629 0.03726 4.06443 3.94228 1.17264 0.37041 1.09861 0.40547 23 3.40719 0.26510 3.22097 1.83371 26 C - - < 1.38629 1.38629 1.38629 1.38629 0.03311 4.31804 3.95070 1.46634 0.26236 0.86081 0.54960 24 4.85155 4.33997 4.72974 0.03013 27 U - - < 1.38629 1.38629 1.38629 1.38629 0.03635 3.79979 4.31832 1.12951 0.39037 1.23660 0.34301 25 4.25841 2.99568 4.15901 0.08313 30 U - - < 1.38629 1.38629 1.38629 1.38629 0.02701 4.31832 4.31832 1.46634 0.26236 1.23660 0.34301 26 1.98776 2.58102 0.35225 2.47457 31 G - - < 1.38629 1.38629 1.38629 1.38629 0.02701 4.31832 4.31832 1.46634 0.26236 0.86927 0.54345 27 1.84171 2.37378 2.37179 0.42310 32 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 28 2.71036 2.77630 3.07723 0.19221 33 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 29 1.86538 0.60851 2.87272 1.40872 34 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 30 2.33054 2.61965 2.54399 0.28585 35 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03272 3.96628 4.32421 1.21157 0.35344 1.09861 0.40547 31 0.18437 2.85439 2.92296 2.86454 38 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 32 1.95966 2.19251 2.50683 0.40657 39 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 33 2.61891 0.39363 2.48743 1.77554 40 C - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 34 0.09696 4.31191 2.81459 3.95975 41 A - - > 1.38629 1.38629 1.38629 1.38629 0.07669 2.80379 4.32421 1.00021 0.45855 1.09861 0.40547 35 0.03741 4.79325 4.04960 4.50957 46 A - - > 1.38629 1.38629 1.38629 1.38629 0.03538 3.83905 4.32421 1.14530 0.38291 1.09861 0.40547 36 2.33997 3.36885 0.19032 3.15722 49 G - - > 1.38629 1.38629 1.38629 1.38629 0.07178 2.88208 4.32421 0.91739 0.51009 1.09861 0.40547 37 0.19717 3.85834 2.03506 3.60559 53 A - - > 1.38629 1.38629 1.38629 1.38629 0.05197 3.28616 4.32421 0.89980 0.52197 1.09861 0.40547 38 1.57153 1.96342 0.76213 1.68620 57 g - - > 1.38629 1.38629 1.38629 1.38629 0.07876 2.77270 4.32421 0.84337 0.56257 1.09861 0.40547 39 1.51739 1.99575 0.78994 1.65582 60 g - - > 1.38629 1.38629 1.38629 1.38629 0.07291 3.45786 3.24894 0.90566 0.51798 1.09861 0.40547 40 2.51303 2.94815 0.22348 2.70595 63 G - - > 1.38629 1.38629 1.38629 1.38629 0.17371 1.95477 4.02494 0.27567 1.42321 0.52023 0.90235 41 1.54713 1.78112 1.06568 1.29389 67 g - - > 1.38629 1.38629 1.38629 1.38629 0.09536 2.55552 4.32004 0.43536 1.04138 0.92490 0.50513 42 2.13270 1.99554 1.77029 0.55293 70 U - - > 1.38629 1.38629 1.38629 1.38629 0.04764 3.40279 4.32421 0.97931 0.47092 1.09861 0.40547 43 4.86718 4.40256 4.64687 0.02998 73 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 44 0.71624 2.06550 1.42941 1.92958 74 a - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 45 4.11185 3.20813 3.87136 0.08082 75 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 46 4.10639 3.20703 3.86858 0.08103 76 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 47 2.48863 3.10240 0.21388 2.73965 77 G - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 48 3.53447 0.21281 3.29303 2.07642 78 C - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 49 4.22701 3.13509 4.13638 0.07696 79 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 50 4.03202 0.10397 3.88126 2.80699 80 C - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 51 4.08323 0.09445 3.96464 2.91329 81 C - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 52 3.83303 2.70799 3.81701 0.11688 82 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 53 3.79577 3.02016 3.85161 0.09707 83 U - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 54 1.49321 1.65039 1.54069 0.99657 84 u - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 55 1.01877 1.80932 1.53811 1.34550 85 a - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 56 1.59144 1.92062 1.61145 0.79794 86 u - - > 1.38629 1.38629 1.38629 1.38629 0.02685 4.32421 4.32421 1.46634 0.26236 1.09861 0.40547 57 2.59174 2.87351 3.42007 0.17925 87 U - - : 1.38629 1.38629 1.38629 1.38629 0.10221 4.32421 2.47796 1.46634 0.26236 1.09861 0.40547 58 3.47102 3.29984 4.01141 0.09001 88 U - - : 1.38629 1.38629 1.38629 1.38629 0.18704 4.25092 1.85572 1.46634 0.26236 2.12059 0.12779 59 2.24542 2.46568 2.79781 0.29005 89 U - - : 1.38629 1.38629 1.38629 1.38629 0.17666 4.09767 1.92880 1.46634 0.26236 2.90725 0.05617 60 2.98023 0.19215 3.56001 2.34764 90 C - - : 1.38629 1.38629 1.38629 1.38629 0.51313 0.91284 * 0.09418 2.40927 0.00000 * //