INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-ccsA-ndhD-1 ACC RF04346 DESC Plastid-ccsA-ndhD-1 3UTR RNA STATES 175 NODES 40 CLEN 57 W 118 ALPH RNA RF no CONS yes MAP yes DATE Thu Nov 13 15:37:34 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_041480.1/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 488 EFFN 7.479797 CKSUM 739686501 NULL 0.000 0.000 0.000 0.000 GA 48.50 TC 48.50 NC 48.40 EFP7GF -12.8621 0.71936 ECMLC 0.62887 -5.56263 3.69207 1600000 404358 0.002968 ECMGC 0.49282 -13.11876 0.65207 1600000 354355 0.001129 ECMLI 0.62578 -4.43576 4.50136 1600000 322127 0.003725 ECMGI 0.50772 -9.96719 2.89187 1600000 273830 0.001461 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 118 203 -8.313 -8.520 -0.755 -1.317 IL 1 1 2 1 4 1 1 120 205 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 119 205 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 4 - A - - - ML 3 2 3 5 3 1 1 118 203 -8.571 -0.013 -7.225 1.174 -1.439 -0.168 -1.044 D 4 2 3 5 3 0 0 114 199 -9.452 -2.378 -0.311 IL 5 5 3 5 3 1 1 118 204 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 5 - A - - - ML 6 5 3 8 3 1 1 117 202 -8.722 -0.012 -7.376 1.906 -3.861 -3.362 -3.549 D 7 5 3 8 3 0 0 113 198 -9.200 -4.095 -0.090 IL 8 8 3 8 3 1 1 117 203 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 6 - A - - - ML 9 8 3 11 3 1 1 116 201 -8.737 -0.012 -7.391 1.109 -1.765 0.143 -1.171 D 10 8 3 11 3 0 0 113 198 -9.170 -3.719 -0.117 IL 11 11 3 11 3 1 1 116 202 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 7 - C - - - ML 12 11 3 14 3 1 1 115 200 -8.764 -0.012 -7.418 -1.241 1.271 -2.195 -0.081 D 13 11 3 14 3 0 0 112 198 -9.116 -3.953 -0.099 IL 14 14 3 14 3 1 1 116 201 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 8 - c - - - ML 15 14 3 17 3 1 1 114 199 -8.781 -0.012 -7.435 -0.305 0.944 -1.452 -0.149 D 16 14 3 17 3 0 0 112 198 -9.080 -2.501 -0.284 IL 17 17 3 17 3 1 1 115 200 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 9 - G - - - ML 18 17 3 20 3 1 1 113 198 -9.214 -0.691 -1.400 0.099 -1.734 1.078 -0.952 D 19 17 3 20 3 0 0 112 197 -7.737 -0.808 -1.237 IL 20 20 3 20 3 1 1 114 199 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 131 - A - - MR 21 20 3 23 3 1 1 112 198 -8.889 -0.013 -7.206 1.757 -2.484 -2.152 -2.204 D 22 20 3 23 3 0 0 111 196 -9.506 -0.414 -2.012 IR 23 23 3 23 3 1 1 113 198 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 130 - A - - MR 24 23 3 26 3 1 1 111 197 -9.484 -0.009 -7.802 1.910 -3.610 -3.591 -3.698 D 25 23 3 26 3 0 0 109 195 -7.711 -1.923 -0.451 IR 26 26 3 26 3 1 1 112 197 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 129 - A - - MR 27 26 3 29 5 1 1 110 196 -8.195 -0.186 -8.010 -3.163 -9.114 1.880 -3.027 -3.360 -3.345 D 28 26 3 29 5 0 0 109 194 -6.083 -0.935 -1.779 -4.905 -2.865 IR 29 29 3 29 5 1 1 111 196 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 10 128 g c - - MP 30 29 3 34 6 2 2 110 195 -9.648 -9.587 -0.014 -8.363 -8.643 -9.038 -1.975 -1.128 -2.157 0.958 -2.198 -1.313 1.026 -2.523 -1.359 2.147 -2.494 -0.312 1.079 0.221 -0.363 -1.211 ML 31 29 3 34 6 1 1 107 193 -6.783 -7.129 -1.568 -0.750 -6.979 -4.508 -0.019 -0.915 0.766 -0.355 MR 32 29 3 34 6 1 1 108 193 -8.172 -6.901 -1.041 -6.879 -1.107 -5.093 0.543 -0.080 -0.827 0.047 D 33 29 3 34 6 0 0 103 188 -9.135 -7.834 -3.419 -3.565 -4.330 -0.384 IL 34 34 5 34 6 1 1 109 194 -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 1 109 194 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 11 127 u a - - MP 36 35 6 40 6 2 2 108 193 -9.720 -9.659 -0.014 -8.436 -8.715 -9.110 -1.852 -2.349 -2.359 0.707 1.419 -3.208 1.415 -2.317 -1.856 0.639 -2.849 -0.892 2.011 -2.358 -0.038 -1.563 ML 37 35 6 40 6 1 1 106 191 -6.726 -7.072 -0.809 -1.480 -6.922 -4.451 -0.078 -0.285 -0.730 0.704 MR 38 35 6 40 6 1 1 105 191 -7.565 -6.294 -2.007 -6.272 -0.566 -4.486 1.102 -0.977 -0.724 -0.434 D 39 35 6 40 6 0 0 101 186 -9.066 -7.764 -3.373 -4.243 -4.261 -0.336 IL 40 40 5 40 6 1 1 107 192 -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 1 107 192 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 12 126 G C - - MP 42 41 6 46 6 2 2 106 191 -9.752 -9.691 -0.013 -8.468 -8.747 -9.142 -3.254 -1.521 -3.182 0.899 -4.861 -3.615 -0.077 -4.513 -4.260 3.304 -4.532 0.199 -0.337 -2.541 -2.053 -2.835 ML 43 41 6 46 6 1 1 103 189 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 104 189 -7.519 -6.248 -0.910 -6.226 -1.360 -4.439 -0.176 0.632 -0.888 0.035 D 45 41 6 46 6 0 0 99 184 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 105 190 -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 1 105 190 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 13 125 A U - - MP 48 47 6 52 6 2 2 104 189 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -5.438 -4.155 -5.345 3.776 -7.050 -8.111 -1.349 -5.351 -5.224 -0.670 -5.860 -0.256 -2.753 -6.672 -4.485 -4.136 ML 49 47 6 52 6 1 1 101 187 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 6 1 1 101 187 -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 97 182 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 103 188 -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 1 103 188 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 14 124 G C - - MP 54 53 6 58 6 2 2 102 187 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -5.283 -2.556 -5.269 0.359 -6.350 -5.209 -1.387 -5.830 -5.030 3.693 -5.303 -1.123 -1.219 -4.849 -3.433 -4.194 ML 55 53 6 58 6 1 1 99 185 -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 99 185 -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 95 180 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 101 186 -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 1 101 186 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 15 123 A U - - MP 60 59 6 64 6 2 2 100 185 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -6.083 -4.775 -5.547 3.901 -7.980 -9.104 -3.545 -5.489 -5.849 -1.398 -6.497 -1.680 -3.633 -7.479 -5.403 -4.569 ML 61 59 6 64 6 1 1 97 183 -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 97 183 -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 93 178 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 6 1 1 99 184 -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 99 184 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 16 122 A U - - MP 66 65 6 70 6 2 2 98 183 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -6.837 -4.276 -5.626 3.923 -8.458 -9.253 -4.210 -5.539 -6.667 -2.126 -7.285 -2.596 -4.279 -7.974 -6.031 -2.366 ML 67 65 6 70 6 1 1 96 181 -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 95 181 -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 91 176 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 6 1 1 97 182 -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 97 182 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 17 121 C G - - MP 72 71 6 76 6 2 2 96 181 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -6.952 -7.087 -6.233 -3.232 -1.661 -6.352 3.877 -5.751 -6.495 -3.128 -6.366 -5.217 -1.263 -6.879 -2.256 -5.291 ML 73 71 6 76 6 1 1 94 179 -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 93 179 -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 89 174 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 6 1 1 95 180 -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 1 95 180 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 18 120 C G - - MP 78 77 6 82 6 2 2 94 179 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -6.805 -6.825 -2.380 -2.986 -3.651 -6.504 3.884 -6.018 -6.558 -2.842 -6.434 -4.821 -1.271 -6.876 -2.701 -5.385 ML 79 77 6 82 6 1 1 92 177 -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 91 177 -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 87 172 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 6 1 1 93 178 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 83 83 6 83 5 1 1 93 178 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 19 119 a u - - MP 84 83 6 88 6 2 2 92 177 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -1.333 -1.501 -1.793 2.102 -1.668 -2.615 1.409 -1.869 -2.078 0.730 -2.651 -0.509 1.518 -2.152 -0.190 -0.889 ML 85 83 6 88 6 1 1 90 175 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 86 83 6 88 6 1 1 89 175 -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 85 170 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 88 88 5 88 6 1 1 91 176 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 89 89 6 89 5 1 1 91 176 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 20 118 U A - - MP 90 89 6 94 6 2 2 90 175 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -2.801 -2.951 -2.666 0.197 -2.315 -3.820 0.937 -3.191 -1.438 0.190 -3.402 -1.418 3.141 -2.845 -0.069 -2.110 ML 91 89 6 94 6 1 1 88 173 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 92 89 6 94 6 1 1 87 173 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 93 89 6 94 6 0 0 83 168 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 94 94 5 94 6 1 1 89 174 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 95 95 6 95 5 1 1 89 174 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 21 117 u a - - MP 96 95 6 100 6 2 2 88 173 -9.178 -9.726 -0.014 -8.503 -8.782 -9.177 -2.453 -2.406 -2.617 0.871 -2.492 -3.456 1.157 -2.878 -1.816 1.590 -3.231 -0.886 2.472 -0.913 -0.535 -1.789 ML 97 95 6 100 6 1 1 86 171 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 98 95 6 100 6 1 1 85 171 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 99 95 6 100 6 0 0 80 166 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 100 100 5 100 6 1 1 87 172 -2.354 -2.815 -0.826 -4.563 -5.339 -5.000 0.000 0.000 0.000 0.000 IR 101 101 6 101 5 1 1 87 172 -2.285 -0.525 -5.960 -4.128 -5.234 0.000 0.000 0.000 0.000 [ MATP 22 ] 27 111 U A - - MP 102 101 6 106 6 2 2 86 171 -9.787 -6.861 -0.024 -8.503 -8.782 -9.177 -4.327 -4.328 -4.318 -0.636 -0.548 -5.004 0.985 -4.081 -3.054 -0.317 -4.769 -2.365 3.370 -4.536 -0.305 -3.191 ML 103 101 6 106 6 1 1 84 169 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 104 101 6 106 6 1 1 83 169 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 105 101 6 106 6 0 0 78 164 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 106 106 5 106 6 1 1 85 171 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 107 107 6 107 5 1 1 86 171 -1.092 -1.092 -6.653 -4.820 -5.926 0.000 0.000 0.000 0.000 [ MATP 23 ] 28 98 G C - - MP 108 107 6 112 6 2 2 84 169 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -3.800 -0.362 -3.707 1.156 -4.503 -2.004 0.033 -4.072 -3.233 3.184 -3.622 -0.304 -0.255 -3.282 -1.914 -2.489 ML 109 107 6 112 6 1 1 81 167 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 110 107 6 112 6 1 1 81 166 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 111 107 6 112 6 0 0 76 161 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 112 112 5 112 6 1 1 83 168 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 113 113 6 113 5 1 1 83 168 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 24 ] 29 97 A U - - MP 114 113 6 118 6 2 2 82 167 -7.554 -9.726 -0.019 -8.503 -8.782 -9.177 -6.085 -4.777 -5.547 3.902 -7.980 -9.104 -3.545 -5.489 -5.851 -1.400 -6.498 -1.688 -3.634 -7.481 -5.403 -4.571 ML 115 113 6 118 6 1 1 79 165 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 116 113 6 118 6 1 1 79 164 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 117 113 6 118 6 0 0 73 159 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 118 118 5 118 6 1 1 82 167 -1.198 -3.514 -1.279 -5.169 -5.945 -5.605 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 81 166 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 25 ] 39 96 A U - - MP 120 119 6 124 6 2 2 80 165 -9.787 -9.726 -0.013 -8.503 -8.782 -9.177 -3.866 -3.861 -5.418 3.866 -7.426 -8.122 -2.577 -5.407 -5.989 -1.276 -6.589 -1.190 -3.303 -6.996 -5.016 -4.589 ML 121 119 6 124 6 1 1 77 162 -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 76 162 -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 70 156 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 79 164 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 125 125 6 125 5 1 1 79 164 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 40 95 U A - - MP 126 125 6 130 6 2 2 78 163 -9.787 -6.919 -0.023 -8.503 -8.782 -9.177 -9.660 -9.561 -9.436 -5.970 -8.087 -9.813 -3.995 -8.968 -8.979 -5.822 -9.755 -7.684 3.983 -7.964 -4.791 -4.937 ML 127 125 6 130 6 1 1 74 159 -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 73 158 -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 66 152 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 77 162 -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 78 163 -1.073 -1.110 -6.665 -4.832 -5.938 0.000 0.000 0.000 0.000 [ MATP 27 ] 41 84 C G - - MP 132 131 6 136 6 2 2 76 161 -4.118 -4.855 -0.150 -8.503 -8.782 -9.177 -7.258 -7.329 -3.096 -3.729 -5.397 -4.331 3.935 -6.819 -7.180 -3.620 -6.787 -5.500 -2.536 -7.421 -3.191 -6.092 ML 133 131 6 136 6 1 1 68 154 -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 66 151 -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 58 144 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 136 136 5 136 6 1 1 87 173 -0.311 -5.991 -2.586 -7.647 -8.423 -8.083 0.000 0.000 0.000 0.000 IR 137 137 6 137 5 1 1 62 120 -0.460 -2.010 -7.969 -6.136 -7.242 0.000 0.000 0.000 0.000 [ MATP 28 ] 52 73 a u - - MP 138 137 6 142 4 2 2 38 73 -8.313 -8.520 -0.376 -2.162 -1.409 -1.775 -2.112 2.920 -1.558 -3.197 0.798 -2.615 -2.363 0.440 -2.883 -0.750 0.682 -2.172 -0.460 -1.534 ML 139 137 6 142 4 1 1 37 73 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 140 137 6 142 4 1 1 36 72 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 141 137 6 142 4 0 0 35 70 -4.568 -4.250 -2.265 -0.520 IL 142 142 5 142 4 1 1 38 74 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 143 143 6 143 3 1 1 38 73 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 29 ] 53 - A - - - ML 144 143 6 146 3 1 1 36 71 -8.927 -0.011 -7.581 1.109 -0.082 -1.537 -0.854 D 145 143 6 146 3 0 0 31 66 -8.701 -4.214 -0.084 IL 146 146 3 146 3 1 1 37 72 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 54 - g - - - ML 147 146 3 149 3 1 1 35 70 -8.927 -0.065 -4.570 -0.513 -1.368 0.769 0.272 D 148 146 3 149 3 0 0 30 65 -8.701 -4.214 -0.084 IL 149 149 3 149 3 1 1 36 71 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 55 - u - - - ML 150 149 3 152 3 1 1 34 70 -8.872 -0.036 -5.483 0.242 -0.706 -1.315 0.850 D 151 149 3 152 3 0 0 29 64 -8.858 -4.371 -0.075 IL 152 152 3 152 3 1 1 35 70 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 56 - a - - - ML 153 152 3 155 3 1 1 33 69 -8.848 -0.019 -6.487 0.975 -0.199 -1.385 -0.358 D 154 152 3 155 3 0 0 27 62 -8.923 -4.436 -0.071 IL 155 155 3 155 3 1 1 34 69 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 57 - a - - - ML 156 155 3 158 3 1 1 32 68 -3.888 -0.110 -7.494 0.788 -1.602 0.513 -0.951 D 157 155 3 158 3 0 0 24 60 -8.943 -4.149 -0.087 IL 158 158 3 158 3 1 1 36 72 -0.751 -1.394 -5.308 0.000 0.000 0.000 0.000 [ MATL 34 ] 68 - U - - - ML 159 158 3 161 3 1 1 17 35 -8.846 -0.011 -7.500 -1.026 -0.116 -1.723 1.191 D 160 158 3 161 3 0 0 15 34 -8.928 -4.340 -0.076 IL 161 161 3 161 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 35 ] 69 - g - - - ML 162 161 3 164 3 1 1 16 34 -8.848 -0.011 -7.502 -0.180 -1.067 0.529 0.259 D 163 161 3 164 3 0 0 14 33 -8.923 -2.405 -0.306 IL 164 164 3 164 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 36 ] 70 - u - - - ML 165 164 3 167 3 1 1 14 33 -8.927 -0.011 -7.581 0.275 -0.939 -0.850 0.777 D 166 164 3 167 3 0 0 13 31 -8.701 -4.214 -0.084 IL 167 167 3 167 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 37 ] 71 - A - - - ML 168 167 3 170 3 1 1 12 31 -8.927 -0.011 -7.581 1.028 -0.180 -1.239 -0.611 D 169 167 3 170 3 0 0 12 30 -8.701 -4.214 -0.084 IL 170 170 3 170 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 72 - g - - - ML 171 170 3 173 2 1 1 1 1 * 0.000 -0.507 -1.435 0.856 0.158 D 172 170 3 173 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 39 ] - - - - - - E 174 173 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-ccsA-ndhD-1 ACC RF04346 DESC Plastid-ccsA-ndhD-1 3UTR RNA LENG 57 MAXL 189 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Nov 13 15:37:34 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_041480.1/CM NSEQ 488 EFFN 16.199402 CKSUM 739686501 STATS LOCAL MSV -7.7604 0.71936 STATS LOCAL VITERBI -8.1819 0.71936 STATS LOCAL FORWARD -3.9454 0.71936 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.07651 1.62911 1.58244 1.35620 1.38629 1.38629 1.38629 1.38629 0.43490 1.13849 3.43063 1.10152 0.40401 0.00000 * 1 0.45110 2.73518 1.47881 2.65524 4 A - - : 1.38629 1.38629 1.38629 1.38629 0.02142 4.54711 4.54711 1.46634 0.26236 1.09861 0.40547 2 0.02431 5.03993 4.65071 4.83009 5 A - - : 1.38629 1.38629 1.38629 1.38629 0.01902 4.66501 4.66501 1.46634 0.26236 1.09861 0.40547 3 0.51400 3.16407 1.21652 2.75847 6 A - - : 1.38629 1.38629 1.38629 1.38629 0.01880 4.67665 4.67665 1.46634 0.26236 1.09861 0.40547 4 2.66079 0.38543 3.41941 1.52686 7 C - - : 1.38629 1.38629 1.38629 1.38629 0.01841 4.69705 4.69705 1.46634 0.26236 1.09861 0.40547 5 1.71295 0.58204 2.68060 1.64824 8 C - - : 1.38629 1.38629 1.38629 1.38629 0.01818 4.70967 4.70967 1.46634 0.26236 1.09861 0.40547 6 1.36036 3.03051 0.50933 2.36192 9 G - - : 1.38629 1.38629 1.38629 1.38629 0.01888 4.77579 4.57812 1.46634 0.26236 1.09861 0.40547 7 1.91779 2.03348 0.78003 1.33258 10 g - - < 1.38629 1.38629 1.38629 1.38629 0.01431 4.94729 4.94729 1.46634 0.26236 0.97127 0.47578 8 2.26550 0.89917 2.15464 0.98519 11 c - - < 1.38629 1.38629 1.38629 1.38629 0.01315 5.03095 5.03095 1.46634 0.26236 1.09861 0.40547 9 2.09397 2.99938 0.26969 2.75872 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.01308 5.03621 5.03621 1.46634 0.26236 1.09861 0.40547 10 0.12031 3.64891 2.56012 4.60108 13 A - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 11 2.57753 4.26600 0.12300 3.65975 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 12 0.02893 5.53410 3.94655 5.25139 15 A - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 13 0.03745 5.63936 4.13892 4.05900 16 A - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 14 5.04733 0.04885 5.01462 3.36366 17 C - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 15 3.30018 0.09465 4.80745 3.09532 18 C - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 16 0.91688 1.63742 1.97761 1.31917 19 a - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 17 2.55556 2.05235 2.12166 0.39440 20 U - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 18 2.21728 2.26766 1.39127 0.61845 21 U - - < 1.38629 1.38629 1.38629 1.38629 0.01358 4.92774 5.07667 1.49830 0.25297 1.09861 0.40547 19 4.14193 2.02235 3.32114 0.20377 27 U - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 20 1.66128 2.69248 0.37830 2.85830 28 G - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 21 0.02811 5.58515 3.96334 5.30559 29 A - - < 1.38629 1.38629 1.38629 1.38629 0.01977 4.31766 5.07667 1.99976 0.14545 1.09861 0.40547 22 0.06651 4.57105 3.04712 5.03579 39 A - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 23 6.36284 6.60164 6.68454 0.00434 40 U - - < 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 24 3.21780 0.08771 4.94191 3.30264 41 C - - < 1.38629 1.38629 1.38629 1.38629 0.11467 2.28180 5.07667 2.16518 0.12186 1.09861 0.40547 25 0.61041 1.93077 1.99728 1.73652 52 A - - < 1.38629 1.38629 1.38629 1.38629 0.26921 5.07668 1.47066 1.46634 0.26236 1.09861 0.40547 26 0.50340 1.36163 2.90911 2.46790 53 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01621 4.82367 4.82367 1.46634 0.26236 3.65891 0.02610 27 2.02028 2.74724 0.70170 1.17917 54 g - - _ 1.38629 1.38629 1.38629 1.38629 0.05781 4.82367 3.03368 1.46634 0.26236 3.65891 0.02610 28 1.19105 2.01750 2.57722 0.71923 55 u - - _ 1.38629 1.38629 1.38629 1.38629 0.03579 4.78275 3.61997 1.46634 0.26236 3.77983 0.02309 29 0.60494 1.47650 2.71777 1.83614 56 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02438 4.76417 4.16324 1.46634 0.26236 3.82880 0.02198 30 0.77377 2.93169 0.91688 2.45741 57 a - - _ 1.38629 1.38629 1.38629 1.38629 0.09421 2.50941 4.75711 1.48290 0.25745 3.41105 0.03356 31 2.53024 1.44136 2.96371 0.45867 68 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01725 4.76179 4.76179 1.46634 0.26236 3.58946 0.02800 32 1.64362 2.37336 0.89117 1.19278 69 g - - _ 1.38629 1.38629 1.38629 1.38629 0.01721 4.76417 4.76417 1.46634 0.26236 1.72610 0.19599 33 1.17342 2.26112 2.07369 0.77493 70 u - - _ 1.38629 1.38629 1.38629 1.38629 0.01621 4.82367 4.82367 1.46634 0.26236 3.65891 0.02610 34 0.56945 1.44821 2.51910 2.13168 71 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01621 4.82367 4.82367 1.46634 0.26236 3.65891 0.02610 35 2.00678 2.81920 0.64248 1.27318 72 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01621 4.82367 4.82367 1.46634 0.26236 0.05290 2.96576 36 1.79567 2.11651 1.76887 0.61063 73 U - - > 1.38629 1.38629 1.38629 1.38629 0.07140 2.76987 5.07667 2.25296 0.11103 1.09861 0.40547 37 3.95689 3.95951 0.04747 4.80735 84 G - - > 1.38629 1.38629 1.38629 1.38629 0.02477 4.00494 5.07667 2.15768 0.12284 1.09861 0.40547 38 0.00693 6.76501 5.89547 5.80926 95 A - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 39 4.51834 3.93793 4.47636 0.04267 96 U - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 40 5.49192 4.57833 5.41448 0.01902 97 U - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 41 3.10597 0.32048 2.80028 1.78008 98 C - - > 1.38629 1.38629 1.38629 1.38629 0.02587 3.94802 5.07667 2.07475 0.13420 1.09861 0.40547 42 0.18013 3.64026 2.13249 3.90931 111 A - - > 1.38629 1.38629 1.38629 1.38629 0.01358 4.92774 5.07667 1.49830 0.25297 1.09861 0.40547 43 0.71487 1.34718 2.08526 2.06754 117 a - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 44 0.45325 2.57233 1.61358 2.42012 118 A - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 45 1.44672 2.08966 1.52774 0.85825 119 u - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 46 3.14209 4.93376 0.06150 4.68294 120 G - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 47 2.93242 5.11792 0.06948 4.84481 121 G - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 48 5.46195 4.45957 5.43092 0.02040 122 U - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 49 5.27856 4.52288 5.27599 0.02130 123 U - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 50 3.71991 0.13408 4.04953 2.47912 124 C - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 51 4.49783 3.64289 3.53361 0.06882 125 U - - > 1.38629 1.38629 1.38629 1.38629 0.01256 5.07667 5.07667 1.46634 0.26236 1.09861 0.40547 52 3.02524 0.31603 2.81018 1.81877 126 C - - > 1.38629 1.38629 1.38629 1.38629 0.01297 5.04438 5.04438 1.46634 0.26236 1.09861 0.40547 53 0.52279 2.39522 1.62506 2.12793 127 A - - > 1.38629 1.38629 1.38629 1.38629 0.01308 5.03652 5.03652 1.46634 0.26236 1.09861 0.40547 54 1.72711 0.66058 2.03748 1.74129 128 C - - > 1.38629 1.38629 1.38629 1.38629 0.01345 5.00881 5.00881 1.46634 0.26236 1.09861 0.40547 55 0.04754 3.76195 4.48417 4.43133 129 A - - : 1.38629 1.38629 1.38629 1.38629 0.01371 4.98943 4.98943 1.46634 0.26236 1.09861 0.40547 56 0.03194 4.32885 4.67854 4.71531 130 A - - : 1.38629 1.38629 1.38629 1.38629 0.02204 4.51889 4.51889 1.46634 0.26236 1.09861 0.40547 57 0.09885 3.53369 3.35894 3.50137 131 A - - : 1.38629 1.38629 1.38629 1.38629 0.16495 1.88343 * 0.96782 0.47789 0.00000 * //