INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-psbJ-5 ACC RF04341 DESC Plastid-psbJ-5 3UTR RNA STATES 181 NODES 38 CLEN 59 W 98 ALPH RNA RF no CONS yes MAP yes DATE Thu Sep 25 17:09:40 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_044183.1/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 205 EFFN 4.563828 CKSUM 2742900762 NULL 0.000 0.000 0.000 0.000 GA 53.10 TC 53.10 NC 53.00 EFP7GF -10.4127 0.71982 ECMLC 0.63796 -4.83992 4.60833 1600000 497659 0.002411 ECMGC 0.48561 -14.82374 0.00761 1600000 536992 0.000745 ECMLI 0.61684 -3.72535 5.52789 1600000 361425 0.003320 ECMGI 0.48865 -10.55447 3.06853 1600000 311263 0.001285 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 98 144 -7.619 -8.864 -0.696 -1.414 IL 1 1 2 1 4 1 1 99 145 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 99 145 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 214 - C - - MR 3 2 3 5 5 1 1 98 144 -7.211 -0.164 -7.027 -3.478 -8.130 -2.070 1.702 -2.901 -1.418 D 4 2 3 5 5 0 0 96 142 -7.203 -1.005 -2.449 -2.709 -2.653 IR 5 5 3 5 5 1 1 98 144 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 2 ] 1 213 A U - - MP 6 5 3 10 6 2 2 97 143 -9.257 -9.196 -0.019 -7.973 -8.252 -8.647 -4.438 -3.322 -4.389 3.629 -5.080 -6.223 -0.735 -4.386 -4.278 0.376 -4.856 -0.708 -1.148 -5.287 -2.673 -3.201 ML 7 5 3 10 6 1 1 95 141 -6.988 -7.335 -1.250 -0.942 -7.184 -4.714 1.163 -1.053 -0.799 -0.508 MR 8 5 3 10 6 1 1 95 141 -8.016 -6.745 -0.766 -6.723 -1.488 -4.937 -0.643 -0.807 -1.313 1.254 D 9 5 3 10 6 0 0 92 139 -9.738 -8.437 -2.562 -1.841 -4.309 -1.009 IL 10 10 5 10 6 1 1 96 142 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 11 11 6 11 5 1 1 96 142 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 3 ] 2 212 A U - - MP 12 11 6 16 6 2 2 95 141 -9.392 -9.332 -0.017 -8.108 -8.388 -8.783 -4.618 -2.294 -4.568 3.666 -5.815 -6.565 -1.492 -4.664 -4.505 0.459 -5.105 -0.683 -1.663 -5.455 -3.372 -3.415 ML 13 11 6 16 6 1 1 93 139 -7.000 -7.346 -1.722 -0.648 -7.196 -4.725 1.171 -1.063 -0.808 -0.517 MR 14 11 6 16 6 1 1 93 139 -7.231 -5.960 -1.442 -5.938 -0.898 -4.152 0.057 -0.389 -0.538 0.592 D 15 11 6 16 6 0 0 89 135 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 16 16 5 16 6 1 1 94 140 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 17 17 6 17 5 1 1 94 140 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 3 211 c g - - MP 18 17 6 22 6 2 2 93 139 -9.413 -9.352 -0.017 -8.129 -8.409 -8.804 -3.404 -3.458 -3.441 0.154 0.646 -4.159 2.930 -2.054 -3.452 0.172 -3.932 -1.623 0.963 -3.644 0.384 -2.426 ML 19 17 6 22 6 1 1 91 137 -6.905 -7.251 -1.348 -0.877 -7.101 -4.631 0.185 0.141 -0.522 0.090 MR 20 17 6 22 6 1 1 91 137 -7.088 -5.817 -1.436 -5.795 -0.929 -4.009 0.525 -0.565 -0.074 -0.097 D 21 17 6 22 6 0 0 87 133 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 22 22 5 22 6 1 1 92 138 -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 92 138 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 5 ] 4 210 U A - - MP 24 23 6 28 6 2 2 91 137 -9.439 -9.378 -0.017 -8.155 -8.435 -8.830 -6.084 -6.083 -6.049 -2.437 -4.144 -6.691 -0.849 -5.804 -6.012 -2.281 -6.493 -4.159 3.867 -4.989 -2.552 -4.337 ML 25 23 6 28 6 1 1 89 135 -6.693 -7.039 -1.528 -0.784 -6.889 -4.418 -0.043 -0.166 -0.710 0.610 MR 26 23 6 28 6 1 1 89 135 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 27 23 6 28 6 0 0 85 131 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 28 28 5 28 6 1 1 90 136 -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 90 136 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 5 209 c g - - MP 30 29 6 34 6 2 2 89 135 -9.445 -9.384 -0.017 -8.161 -8.441 -8.836 -1.694 -1.873 -2.035 0.976 -0.134 -1.991 2.282 -1.910 -1.956 0.822 -2.662 -0.639 1.267 -2.177 0.066 -1.267 ML 31 29 6 34 6 1 1 87 133 -6.619 -6.965 -1.151 -1.079 -6.815 -4.344 0.011 0.167 -0.678 0.316 MR 32 29 6 34 6 1 1 87 133 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 6 34 6 0 0 83 129 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 1 88 134 -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 88 134 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 6 208 A U - - MP 36 35 6 40 6 2 2 87 133 -9.460 -9.399 -0.017 -8.176 -8.456 -8.851 -3.449 -2.305 -4.311 3.605 -5.057 -5.715 -1.014 -4.500 -4.457 0.400 -5.003 -0.451 -1.000 -4.856 -2.819 -3.335 ML 37 35 6 40 6 1 1 85 131 -6.404 -6.750 -1.367 -0.933 -6.600 -4.130 0.667 -0.590 -0.294 -0.102 MR 38 35 6 40 6 1 1 85 131 -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 81 127 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 86 132 -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 86 132 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 7 207 A U - - MP 42 41 6 46 6 2 2 85 131 -9.463 -9.402 -0.020 -8.178 -7.488 -8.853 -5.480 -4.630 -3.523 3.844 -5.868 -6.609 -1.965 -4.372 -5.596 -0.764 -6.123 -2.551 -2.207 -5.835 -3.736 -4.207 ML 43 41 6 46 6 1 1 83 129 -6.367 -6.713 -1.428 -0.896 -6.563 -4.093 0.619 -0.557 -0.258 -0.076 MR 44 41 6 46 6 1 1 83 129 -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 79 125 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 84 130 -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 84 130 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 8 206 c g - - MP 48 47 6 52 6 2 2 83 129 -9.459 -9.398 -0.017 -8.174 -8.454 -8.849 -2.467 -2.585 -2.624 0.673 -0.223 -2.819 2.642 -2.446 -2.655 0.801 -2.790 -0.959 1.320 -2.775 -0.041 -1.746 ML 49 47 6 52 6 1 1 81 127 -6.367 -6.713 -1.153 -1.122 -6.563 -4.093 0.218 -0.176 -0.417 0.266 MR 50 47 6 52 6 1 1 81 127 -7.045 -5.774 -1.513 -5.752 -0.886 -3.965 0.281 -0.150 -0.352 0.137 D 51 47 6 52 6 0 0 77 123 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 82 128 -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 82 128 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 9 205 G C - - MP 54 53 6 58 6 2 2 81 127 -9.470 -7.069 -0.025 -8.186 -8.465 -8.860 -4.135 -2.360 -4.030 1.126 -4.976 -4.535 -0.194 -4.615 -3.343 3.352 -4.547 -0.054 -0.345 -3.881 -2.189 -2.984 ML 55 53 6 58 6 1 1 79 125 -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 79 125 -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 75 121 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 80 126 -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 80 126 -2.473 -0.471 -5.984 -4.152 -5.258 0.000 0.000 0.000 0.000 [ MATP 11 ] 10 203 G C - - MP 60 59 6 64 6 2 2 79 125 -9.470 -8.305 -0.019 -8.186 -8.465 -8.860 -5.205 -2.564 -5.231 -0.123 -6.110 -3.074 -1.205 -5.818 -4.832 3.708 -5.070 -0.772 -1.490 -4.606 -3.256 -4.207 ML 61 59 6 64 6 1 1 77 123 -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 77 123 -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 73 119 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 6 1 1 78 124 -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 78 124 -2.427 -0.489 -5.938 -4.106 -5.212 0.000 0.000 0.000 0.000 [ MATP 12 ] 11 201 G C - - MP 66 65 6 70 6 2 2 77 123 -9.470 -7.542 -0.022 -8.186 -8.465 -8.860 -4.433 -1.761 -4.357 0.529 -5.269 -4.638 -0.258 -4.937 -3.197 3.518 -4.711 -0.531 -0.748 -4.102 -2.480 -3.316 ML 67 65 6 70 6 1 1 75 121 -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 75 121 -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 71 117 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 6 1 1 76 122 -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 76 122 -2.451 -0.479 -5.962 -4.130 -5.236 0.000 0.000 0.000 0.000 [ MATP 13 ] 12 199 a u - - MP 72 71 6 76 6 2 2 75 121 -6.165 -6.856 -0.084 -5.167 -8.070 -8.860 -2.291 -1.512 -2.439 2.704 -2.499 -3.285 0.878 -2.079 -2.224 1.301 -2.833 -0.360 0.697 -2.574 -0.656 -1.435 ML 73 71 6 76 6 1 1 73 119 -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 73 119 -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 69 115 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 6 1 1 75 121 -1.631 -3.391 -0.999 -4.588 -5.823 -5.483 0.000 0.000 0.000 0.000 IR 77 77 6 77 5 1 1 74 120 -2.022 -0.590 -6.121 -4.288 -5.394 0.000 0.000 0.000 0.000 [ MATP 14 ] 17 195 C G - - MP 78 77 6 82 6 2 2 73 119 -5.755 -7.991 -0.050 -8.147 -7.340 -8.821 -3.827 -3.801 -3.801 -0.047 -1.087 -4.479 3.109 -3.524 -3.785 0.102 -4.238 -1.783 1.199 -4.026 0.603 -2.179 ML 79 77 6 82 6 1 1 71 117 -6.775 -7.122 -1.758 -0.653 -6.971 -4.501 -0.121 0.556 -0.828 0.066 MR 80 77 6 82 6 1 1 71 117 -7.007 -5.736 -1.644 -5.714 -0.814 -3.927 0.399 -0.468 -0.044 -0.016 D 81 77 6 82 6 0 0 67 113 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 6 1 1 73 119 -1.207 -3.721 -1.200 -5.376 -6.152 -5.812 0.000 0.000 0.000 0.000 IR 83 83 6 83 5 1 1 72 118 -2.434 -0.486 -5.945 -4.113 -5.219 0.000 0.000 0.000 0.000 [ MATP 15 ] 22 193 C G - - MP 84 83 6 88 6 2 2 71 117 -6.581 -8.415 -0.110 -6.076 -4.581 -8.263 -5.563 -5.594 -5.179 -1.751 -1.652 -5.519 3.749 -4.707 -5.279 -1.607 -5.445 -3.603 -0.252 -5.608 -1.212 -4.103 ML 85 83 6 88 6 1 1 69 115 -6.753 -7.099 -1.813 -0.631 -6.949 -4.478 -0.104 0.532 -0.809 0.075 MR 86 83 6 88 6 1 1 68 115 -7.072 -5.801 -1.710 -5.779 -0.766 -3.993 0.340 -0.552 0.153 -0.089 D 87 83 6 88 6 0 0 65 111 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 88 88 5 88 6 1 1 71 117 -1.533 -3.369 -1.040 -5.025 -5.801 -5.461 0.000 0.000 0.000 0.000 IR 89 89 6 89 5 1 1 70 116 -2.424 -0.490 -5.935 -4.102 -5.208 0.000 0.000 0.000 0.000 [ MATP 16 ] 27 191 u a - - MP 90 89 6 94 6 2 2 69 115 -4.226 -7.810 -0.114 -8.068 -6.363 -8.743 -2.689 -2.777 -2.819 0.673 -0.682 -3.634 1.702 -2.888 -2.839 0.645 -2.776 -1.061 2.540 -2.980 0.408 -1.888 ML 91 89 6 94 6 1 1 67 113 -5.354 -7.278 -0.968 -1.282 -7.128 -4.657 -0.227 -0.410 -0.884 0.888 MR 92 89 6 94 6 1 1 66 112 -7.685 -6.414 -2.265 -6.392 -0.469 -4.606 0.695 -0.859 0.009 -0.280 D 93 89 6 94 6 0 0 63 109 -9.080 -7.779 -3.576 -4.258 -4.275 -0.312 IL 94 94 5 94 6 1 1 71 117 -0.766 -4.432 -1.595 -5.798 -7.095 -6.756 0.000 0.000 0.000 0.000 IR 95 95 6 95 5 1 1 68 114 -2.370 -0.497 -5.990 -4.157 -5.263 0.000 0.000 0.000 0.000 [ MATP 17 ] 33 188 u a - - MP 96 95 6 100 6 2 2 66 113 -5.185 -7.812 -0.081 -7.102 -6.285 -8.769 -2.101 -2.256 -2.275 0.861 -1.740 -3.121 1.580 -2.266 -2.321 0.815 -2.884 -0.746 2.014 -2.161 1.115 -0.319 ML 97 95 6 100 6 1 1 65 111 -6.498 -6.844 -1.270 -0.993 -6.694 -4.223 0.083 -0.382 -0.509 0.556 MR 98 95 6 100 6 1 1 64 110 -7.780 -6.509 -2.112 -6.488 -0.507 -4.701 -0.021 -0.485 -0.260 0.551 D 99 95 6 100 6 0 0 61 107 -9.080 -7.779 -3.576 -4.258 -4.275 -0.312 IL 100 100 5 100 6 1 1 67 113 -1.036 -3.997 -1.310 -5.652 -6.429 -6.089 0.000 0.000 0.000 0.000 IR 101 101 6 101 5 1 1 66 112 -2.112 -0.570 -6.035 -4.202 -5.308 0.000 0.000 0.000 0.000 [ MATP 18 ] 39 183 c g - - MP 102 101 6 106 6 2 2 64 111 -6.238 -9.314 -0.035 -8.091 -8.371 -8.766 -0.954 -2.033 -1.791 1.299 -1.203 -2.891 2.094 -2.334 -2.097 1.034 -2.563 -0.611 1.383 -2.183 0.140 -1.264 ML 103 101 6 106 6 1 1 62 109 -6.459 -6.806 -1.216 -1.046 -6.655 -4.185 0.392 -0.161 -0.443 0.081 MR 104 101 6 106 6 1 1 63 109 -7.830 -6.559 -0.836 -6.537 -1.408 -4.750 0.055 -1.001 0.747 -0.354 D 105 101 6 106 6 0 0 59 105 -9.080 -7.779 -3.246 -4.258 -4.275 -0.351 IL 106 106 5 106 6 1 1 64 110 -1.414 -3.479 -1.093 -5.134 -5.911 -5.571 0.000 0.000 0.000 0.000 IR 107 107 6 107 5 1 1 63 110 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 44 182 C G - - MP 108 107 6 112 6 2 2 62 109 -7.625 -6.533 -0.039 -7.848 -7.759 -8.844 -3.729 -3.668 -3.318 0.225 -1.554 -4.529 3.207 -3.566 -3.738 0.269 -4.226 -1.396 0.995 -3.960 -0.089 -2.635 ML 109 107 6 112 6 1 1 60 107 -6.337 -6.683 -1.191 -1.091 -6.533 -4.062 0.256 -0.094 -0.390 0.144 MR 110 107 6 112 6 1 1 60 107 -7.141 -5.870 -1.350 -5.848 -0.982 -4.062 0.515 -0.600 -0.019 -0.114 D 111 107 6 112 6 0 0 57 103 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 112 112 5 112 6 1 1 62 108 -1.915 -3.099 -0.910 -4.754 -5.530 -5.191 0.000 0.000 0.000 0.000 IR 113 113 6 113 5 1 1 62 108 -2.168 -0.542 -6.102 -4.270 -5.375 0.000 0.000 0.000 0.000 [ MATP 20 ] 50 177 C G - - MP 114 113 6 118 6 2 2 60 107 -7.840 -7.164 -0.029 -8.182 -8.462 -8.857 -2.969 -3.061 -3.084 0.367 -0.806 -3.028 3.027 -1.253 -3.108 0.353 -3.633 -1.350 1.069 -3.255 -0.345 -2.154 ML 115 113 6 118 6 1 1 58 105 -6.271 -6.617 -1.280 -1.026 -6.467 -3.996 0.339 -0.296 -0.254 0.113 MR 116 113 6 118 6 1 1 58 105 -7.024 -5.753 -1.552 -5.731 -0.865 -3.945 0.389 -0.500 0.025 -0.050 D 117 113 6 118 6 0 0 55 101 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 118 118 5 118 6 1 1 60 106 -1.793 -3.132 -0.962 -4.788 -5.564 -5.224 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 59 106 -2.468 -0.473 -5.979 -4.147 -5.253 0.000 0.000 0.000 0.000 [ MATP 21 ] 57 175 C G - - MP 120 119 6 124 6 2 2 58 105 -8.475 -8.322 -0.026 -8.186 -7.289 -8.860 -3.699 -3.756 -2.798 -0.277 -1.445 -4.536 3.428 -3.782 -3.808 -0.196 -3.601 -1.953 0.525 -3.972 -0.510 -2.815 ML 121 119 6 124 6 1 1 57 103 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 122 119 6 124 6 1 1 56 103 -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 53 100 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 58 104 -2.040 -3.010 -0.886 -4.666 -5.442 -5.102 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 58 104 -2.153 -0.559 -6.008 -4.176 -5.282 0.000 0.000 0.000 0.000 [ MATP 22 ] 65 169 c g - - MP 126 125 6 130 6 2 2 56 103 -7.416 -5.096 -0.064 -8.180 -8.460 -8.855 -4.994 -5.110 -4.599 -1.355 2.433 -4.925 2.844 -4.024 -4.656 -1.253 -4.900 -3.263 0.653 -4.997 -0.877 -3.493 ML 127 125 6 130 6 1 1 55 101 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 128 125 6 130 6 1 1 55 101 -7.062 -5.791 -1.482 -5.769 -0.903 -3.983 0.351 -0.543 0.129 -0.083 D 129 125 6 130 6 0 0 52 99 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 56 102 -1.870 -3.133 -0.921 -4.788 -5.564 -5.225 0.000 0.000 0.000 0.000 IR 131 131 6 131 5 1 1 56 102 -1.244 -0.944 -6.745 -4.913 -6.018 0.000 0.000 0.000 0.000 [ MATP 23 ] 70 163 U A - - MP 132 131 6 136 6 2 2 54 100 -9.470 -5.061 -0.060 -7.807 -8.465 -8.860 -3.715 -3.757 -3.776 -0.216 -1.626 -4.526 1.211 -3.683 -2.658 -0.115 -4.280 -1.909 3.282 -3.964 -0.295 -2.711 ML 133 131 6 136 6 1 1 54 100 -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 53 99 -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 51 98 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 6 1 1 54 100 -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 54 101 -1.196 -0.979 -6.790 -4.957 -6.063 0.000 0.000 0.000 0.000 [ MATP 24 ] 71 158 c g - - MP 138 137 6 142 4 2 2 52 98 -5.442 -3.061 -0.243 -6.372 -2.556 -2.675 -2.064 0.593 -0.634 -3.539 2.757 -2.298 -2.738 0.597 -2.879 -1.044 1.157 -2.862 0.377 -1.824 ML 139 137 6 142 4 1 1 53 100 -3.777 -3.959 -0.499 -2.689 0.333 -0.280 -0.265 0.116 MR 140 137 6 142 4 1 1 52 98 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 141 137 6 142 4 0 0 51 98 -4.568 -4.250 -2.265 -0.520 IL 142 142 5 142 4 1 1 59 106 -0.570 -3.715 -2.080 -6.200 0.000 0.000 0.000 0.000 IR 143 143 6 143 3 1 1 53 95 -0.629 -1.579 -5.736 0.000 0.000 0.000 0.000 [ MATL 25 ] 83 - G - - - ML 144 143 6 146 3 1 1 43 80 -8.725 -0.012 -7.379 -0.375 -1.690 1.303 -1.148 D 145 143 6 146 3 0 0 41 78 -6.174 -1.687 -0.566 IL 146 146 3 146 3 1 1 44 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 26 ] 84 - A - - - ML 147 146 3 149 3 1 1 42 79 -6.636 -0.023 -7.379 1.776 -2.502 -2.565 -2.120 D 148 146 3 149 3 0 0 40 77 -6.174 -1.687 -0.566 IL 149 149 3 149 3 1 1 43 80 -1.289 -0.889 -4.307 0.000 0.000 0.000 0.000 [ MATL 27 ] 89 - A - - - ML 150 149 3 152 3 1 1 41 78 -6.790 -0.025 -6.984 1.624 -1.490 -1.894 -1.768 D 151 149 3 152 3 0 0 39 76 -6.174 -1.687 -0.566 IL 152 152 3 152 3 1 1 42 79 -1.359 -0.843 -4.251 0.000 0.000 0.000 0.000 [ MATL 28 ] 93 - U - - - ML 153 152 3 155 3 1 1 40 77 -4.759 -0.063 -7.377 -1.680 -1.846 -2.445 1.690 D 154 152 3 155 3 0 0 38 75 -6.216 -1.598 -0.608 IL 155 155 3 155 3 1 1 42 79 -0.927 -1.188 -4.837 0.000 0.000 0.000 0.000 [ MATL 29 ] 103 - c - - - ML 156 155 3 158 3 1 1 39 76 -8.725 -0.012 -7.379 -0.695 0.663 -1.653 0.567 D 157 155 3 158 3 0 0 37 74 -6.174 -1.687 -0.566 IL 158 158 3 158 3 1 1 40 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 104 - A - - - ML 159 158 3 161 3 1 1 38 75 -8.725 -0.012 -7.379 1.704 -1.713 -2.343 -2.063 D 160 158 3 161 3 0 0 36 73 -6.174 -1.687 -0.566 IL 161 161 3 161 3 1 1 39 76 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 105 - G - - - ML 162 161 3 164 3 1 1 37 74 -4.339 -0.082 -7.379 -0.700 -2.343 1.501 -1.490 D 163 161 3 164 3 0 0 34 71 -6.174 -1.687 -0.566 IL 164 164 3 164 3 1 1 38 75 -1.051 -1.054 -4.801 0.000 0.000 0.000 0.000 [ MATL 32 ] 111 - A - - - ML 165 164 3 167 3 1 1 36 73 -4.288 -0.085 -7.379 1.721 -2.172 -1.948 -2.167 D 166 164 3 167 3 0 0 33 70 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 38 75 -0.850 -1.270 -5.030 0.000 0.000 0.000 0.000 [ MATL 33 ] 118 - C - - - ML 168 167 3 170 3 1 1 34 71 -3.209 -0.175 -7.379 -1.466 1.538 -2.400 -0.876 D 169 167 3 170 3 0 0 29 66 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 37 75 -0.718 -1.431 -5.560 0.000 0.000 0.000 0.000 [ MATL 34 ] 124 - A - - - ML 171 170 3 173 3 1 1 29 62 -3.830 -0.115 -7.379 1.840 -2.831 -2.842 -2.828 D 172 170 3 173 3 0 0 26 59 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 32 65 -0.857 -1.252 -5.147 0.000 0.000 0.000 0.000 [ MATL 35 ] 135 - A - - - ML 174 173 3 176 3 1 1 27 60 -4.027 -0.101 -7.379 1.841 -3.297 -2.395 -3.001 D 175 173 3 176 3 0 0 23 56 -6.174 -1.687 -0.566 IL 176 176 3 176 3 1 1 31 64 -0.799 -1.332 -5.165 0.000 0.000 0.000 0.000 [ MATL 36 ] 146 - A - - - ML 177 176 3 179 2 1 1 1 1 * 0.000 1.750 -2.495 -1.922 -2.362 D 178 176 3 179 2 0 0 0 0 * 0.000 IL 179 179 3 179 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 37 ] - - - - - - E 180 179 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-psbJ-5 ACC RF04341 DESC Plastid-psbJ-5 3UTR RNA LENG 59 MAXL 179 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Sep 25 17:09:40 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_044183.1/CM NSEQ 205 EFFN 8.498917 CKSUM 2742900762 STATS LOCAL MSV -7.6941 0.71982 STATS LOCAL VITERBI -8.7281 0.71982 STATS LOCAL FORWARD -3.4801 0.71982 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.22737 1.40039 1.43346 1.50528 1.38629 1.38629 1.38629 1.38629 0.02769 4.29369 4.29369 1.46634 0.26236 0.00000 * 1 0.12117 3.77783 2.77576 3.54238 1 A - - < 1.38629 1.38629 1.38629 1.38629 0.02769 4.29369 4.29369 1.46634 0.26236 1.09861 0.40547 2 0.11758 4.19158 2.59949 3.84007 2 A - - < 1.38629 1.38629 1.38629 1.38629 0.02284 4.48383 4.48383 1.46634 0.26236 1.09861 0.40547 3 2.85246 0.33209 2.89557 1.77427 3 C - - < 1.38629 1.38629 1.38629 1.38629 0.02249 4.49889 4.49889 1.46634 0.26236 1.09861 0.40547 4 4.62806 4.17715 4.94962 0.03273 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 5 1.85365 0.77203 1.88729 1.47063 5 c - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 6 0.11933 4.32039 2.57765 3.76189 6 A - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 7 0.02653 5.12926 4.29561 5.01613 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.02775 4.50850 4.11320 1.46634 0.26236 1.09861 0.40547 8 2.26250 0.60709 1.99992 1.53420 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.02240 4.50315 4.50315 1.46634 0.26236 0.85312 0.55527 9 1.91010 3.01087 0.30130 2.76732 9 G - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 10 3.09803 3.72510 0.09144 4.01005 10 G - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 11 2.41868 3.12984 0.18760 3.26248 11 G - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 12 0.72086 1.98912 1.53156 1.82851 12 a - - < 1.38629 1.38629 1.38629 1.38629 0.04968 3.33286 4.36047 1.17128 0.37102 1.09861 0.40547 13 3.02590 0.40631 2.86995 1.47543 17 C - - < 1.38629 1.38629 1.38629 1.38629 0.06305 3.12806 4.05692 1.40020 0.28309 1.15043 0.38053 14 4.11418 0.09493 4.15474 2.83812 22 C - - < 1.38629 1.38629 1.38629 1.38629 0.12393 3.55945 2.42922 1.40915 0.28018 1.31576 0.31234 15 2.29597 1.46705 2.21610 0.58036 27 U - - < 1.38629 1.38629 1.38629 1.38629 0.16050 2.13489 3.50560 1.40719 0.28081 2.21867 0.11513 16 2.01891 1.62765 1.96417 0.63386 33 U - - < 1.38629 1.38629 1.38629 1.38629 0.10305 2.72478 3.43093 1.39320 0.28539 1.83026 0.17480 17 1.46993 1.08055 1.72747 1.37471 39 c - - < 1.38629 1.38629 1.38629 1.38629 0.05016 3.30798 4.39525 1.40559 0.28133 0.30572 1.33406 18 2.57102 0.41209 2.44813 1.74399 44 C - - < 1.38629 1.38629 1.38629 1.38629 0.03359 3.99665 4.22324 1.46119 0.26391 0.61561 0.77721 19 2.69279 0.34564 2.61761 1.88673 50 C - - < 1.38629 1.38629 1.38629 1.38629 0.02832 4.08231 4.50508 1.63160 0.21768 0.92677 0.50390 20 2.87695 0.29171 2.80436 1.99390 57 C - - < 1.38629 1.38629 1.38629 1.38629 0.03232 4.28511 4.01554 1.63283 0.21738 1.09861 0.40547 21 4.09900 0.13975 4.01952 2.34469 65 C - - < 1.38629 1.38629 1.38629 1.38629 0.03145 3.91876 4.50146 1.42161 0.27618 0.79824 0.59806 22 3.27537 1.94342 2.91248 0.26835 70 U - - < 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 23 2.31106 0.54864 2.24635 1.52637 71 C - - < 1.38629 1.38629 1.38629 1.38629 0.04161 3.51538 4.50850 2.22577 0.11427 1.09861 0.40547 24 1.77241 2.81244 0.37755 2.47126 83 G - - _ 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 25 0.10332 3.43480 3.69520 3.19195 84 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03071 3.95158 4.50850 1.42279 0.27581 1.09861 0.40547 26 0.18559 2.51884 3.07968 3.14993 89 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03167 4.00975 4.33989 1.29245 0.32103 1.09861 0.40547 27 2.93651 3.12383 3.49009 0.13643 93 U - - _ 1.38629 1.38629 1.38629 1.38629 0.06076 3.03826 4.50648 1.51022 0.24957 0.98942 0.46488 28 2.10320 0.80954 2.87301 0.97725 103 c - - _ 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 29 0.13761 2.69987 3.57387 3.40208 104 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02228 4.50850 4.50850 1.46634 0.26236 1.09861 0.40547 30 2.00619 3.41704 0.27113 2.65677 105 G - - _ 1.38629 1.38629 1.38629 1.38629 0.07498 2.79324 4.50850 1.18425 0.36525 1.09861 0.40547 31 0.13303 3.12599 3.03821 3.41888 111 A - - _ 1.38629 1.38629 1.38629 1.38629 0.07703 2.76261 4.50850 1.48547 0.25670 1.09861 0.40547 32 2.73167 0.22329 3.42293 2.27898 118 C - - _ 1.38629 1.38629 1.38629 1.38629 0.14487 2.08865 4.50850 1.39528 0.28471 1.09861 0.40547 33 0.06416 3.70342 3.97151 3.98147 124 A - - _ 1.38629 1.38629 1.38629 1.38629 0.09931 2.48262 4.50850 1.33899 0.30396 1.09861 0.40547 34 0.06442 4.31017 3.39540 4.17156 135 A - - _ 1.38629 1.38629 1.38629 1.38629 0.08877 2.60464 4.50850 1.48994 0.25539 1.09861 0.40547 35 0.11803 3.44372 2.96956 3.57354 146 A - - _ 1.38629 1.38629 1.38629 1.38629 0.15337 2.04685 4.33945 1.53012 0.24400 1.09861 0.40547 36 1.71670 2.44811 0.48201 2.15121 158 G - - > 1.38629 1.38629 1.38629 1.38629 0.08150 2.69959 4.50647 1.34860 0.30057 0.98914 0.46505 37 0.29330 3.25299 1.78580 3.03896 163 A - - > 1.38629 1.38629 1.38629 1.38629 0.07961 2.72557 4.50850 1.31313 0.31331 1.09861 0.40547 38 0.73603 4.10464 0.72830 3.82755 169 g - - > 1.38629 1.38629 1.38629 1.38629 0.02561 4.24937 4.50850 1.51589 0.24796 1.09861 0.40547 39 2.11351 3.03022 0.25931 2.82519 175 G - - > 1.38629 1.38629 1.38629 1.38629 0.03512 3.82534 4.36602 0.81789 0.58225 1.09861 0.40547 40 1.82252 2.68966 0.42256 2.16185 177 G - - > 1.38629 1.38629 1.38629 1.38629 0.04852 3.53390 4.00806 0.93930 0.49577 1.00591 0.45525 41 1.95349 2.67216 0.36677 2.34187 182 G - - > 1.38629 1.38629 1.38629 1.38629 0.03578 4.50136 3.72734 1.46634 0.26236 1.29382 0.32051 42 1.45678 1.90392 0.92864 1.50084 183 g - - > 1.38629 1.38629 1.38629 1.38629 0.03917 4.09354 3.82894 1.43139 0.27309 1.09695 0.40630 43 1.13856 2.08109 1.08034 1.53505 188 g - - > 1.38629 1.38629 1.38629 1.38629 0.08444 3.88803 2.80532 0.97669 0.47249 1.63724 0.21631 44 0.66808 2.41259 1.28802 2.10449 191 A - - > 1.38629 1.38629 1.38629 1.38629 0.02701 4.21421 4.43418 1.21312 0.35278 1.10706 0.40127 45 2.85768 4.36384 0.09039 4.11712 193 G - - > 1.38629 1.38629 1.38629 1.38629 0.03122 4.10778 4.24821 1.08469 0.41250 1.99632 0.14599 46 1.87215 3.05880 0.30504 2.77784 195 G - - > 1.38629 1.38629 1.38629 1.38629 0.03880 3.63236 4.45654 1.17596 0.36893 0.30553 1.33459 47 2.05116 1.69035 1.84070 0.63818 199 U - - > 1.38629 1.38629 1.38629 1.38629 0.03015 3.98012 4.50850 0.93334 0.49962 1.09861 0.40547 48 3.31826 0.20948 2.98619 2.27983 201 C - - > 1.38629 1.38629 1.38629 1.38629 0.02569 4.24438 4.50850 1.16832 0.37235 1.09861 0.40547 49 4.14249 0.10431 3.94539 2.75163 203 C - - > 1.38629 1.38629 1.38629 1.38629 0.03438 3.78167 4.50850 0.78785 0.60664 1.09861 0.40547 50 2.91378 0.36997 2.81723 1.63370 205 C - - > 1.38629 1.38629 1.38629 1.38629 0.02250 4.49871 4.49871 1.46634 0.26236 1.09861 0.40547 51 1.47723 2.12664 0.64996 2.03695 206 G - - > 1.38629 1.38629 1.38629 1.38629 0.02250 4.49871 4.49871 1.46634 0.26236 1.09861 0.40547 52 5.18932 4.55402 4.85861 0.02415 207 U - - > 1.38629 1.38629 1.38629 1.38629 0.02257 4.49542 4.49542 1.46634 0.26236 1.09861 0.40547 53 3.73177 3.03626 4.14130 0.09197 208 U - - > 1.38629 1.38629 1.38629 1.38629 0.02306 4.47439 4.47439 1.46634 0.26236 1.09861 0.40547 54 1.41393 1.95637 0.83774 1.69959 209 g - - > 1.38629 1.38629 1.38629 1.38629 0.02325 4.46622 4.46622 1.46634 0.26236 1.09861 0.40547 55 0.02819 5.12017 4.32642 4.75568 210 A - - > 1.38629 1.38629 1.38629 1.38629 0.02388 4.43995 4.43995 1.46634 0.26236 1.09861 0.40547 56 1.49014 3.10691 0.42191 2.60197 211 G - - > 1.38629 1.38629 1.38629 1.38629 0.02420 4.42669 4.42669 1.46634 0.26236 1.09861 0.40547 57 3.85900 2.77146 4.00217 0.10751 212 U - - > 1.38629 1.38629 1.38629 1.38629 0.02572 4.36641 4.36641 1.46634 0.26236 1.09861 0.40547 58 3.56463 3.02689 3.65551 0.10828 213 U - - > 1.38629 1.38629 1.38629 1.38629 0.03594 4.03685 4.03685 1.46634 0.26236 1.09861 0.40547 59 3.72359 0.08600 4.25934 3.12062 214 C - - : 1.38629 1.38629 1.38629 1.38629 0.01813 4.01904 * 1.46634 0.26236 0.00000 * //