INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-atpF ACC RF04355 DESC Plastid-atpF group II-D1 intron STATES 163 NODES 48 CLEN 53 W 67 ALPH RNA RF no CONS yes MAP yes DATE Sat Nov 15 13:49:16 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/atpF/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 49 EFFN 6.014343 CKSUM 3583117081 NULL 0.000 0.000 0.000 0.000 GA 52.50 TC 52.50 NC 52.40 EFP7GF -13.7822 0.71923 ECMLC 0.49877 -6.05882 6.06354 1600000 507046 0.002367 ECMGC 0.40091 -13.48041 1.85683 1600000 187286 0.002136 ECMLI 0.51796 -3.65198 7.28334 1600000 345977 0.003468 ECMGI 0.44921 -9.55267 3.41231 1600000 135323 0.002956 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 67 86 -8.059 -8.266 -0.024 -6.680 IL 1 1 2 1 4 1 14 72 91 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 13 71 90 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - u - - - ML 3 2 3 5 3 1 14 67 86 -9.019 -0.010 -7.673 0.191 -0.863 0.037 0.359 D 4 2 3 5 3 0 7 66 85 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 13 69 89 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - a - - - ML 6 5 3 8 3 1 13 66 85 -9.019 -0.010 -7.673 0.900 -1.402 0.105 -0.557 D 7 5 3 8 3 0 7 65 84 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 12 68 88 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - a - - - ML 9 8 3 11 3 1 13 65 84 -9.019 -0.010 -7.673 0.547 -0.909 -0.562 0.411 D 10 8 3 11 3 0 6 64 83 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 11 67 87 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - a - - - ML 12 11 3 14 3 1 12 64 83 -9.019 -0.010 -7.673 0.889 -0.945 -1.206 0.257 D 13 11 3 14 3 0 5 63 82 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 10 66 86 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - a - - - ML 15 14 3 17 3 1 11 63 82 -9.019 -0.010 -7.673 0.695 -1.352 -1.266 0.654 D 16 14 3 17 3 0 4 62 81 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 9 65 84 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 10 62 80 -9.019 -0.010 -7.673 -0.297 -1.324 -2.044 1.347 D 19 17 3 20 3 0 3 61 80 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 8 64 83 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - U - - - ML 21 20 3 23 3 1 9 61 79 -9.019 -0.010 -7.673 -2.324 -2.245 -2.570 1.774 D 22 20 3 23 3 0 3 60 79 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 8 63 82 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - U - - - ML 24 23 3 26 3 1 8 59 78 -9.019 -0.010 -7.673 -1.478 -2.178 -2.931 1.718 D 25 23 3 26 3 0 2 59 78 -6.174 -1.687 -0.566 IL 26 26 3 26 3 1 7 62 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 9 - U - - - ML 27 26 3 29 3 1 8 58 77 -9.019 -0.010 -7.673 -1.507 -1.520 -0.896 1.466 D 28 26 3 29 3 0 1 57 76 -6.174 -1.687 -0.566 IL 29 29 3 29 3 1 6 61 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 10 - U - - - ML 30 29 3 32 3 1 7 57 76 -9.360 -0.009 -7.677 -0.380 -1.135 -2.030 1.340 D 31 29 3 32 3 0 1 56 75 -5.620 -0.734 -1.403 IL 32 32 3 32 3 1 5 58 77 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 54 - U - - MR 33 32 3 35 3 1 6 56 75 -9.360 -0.009 -7.677 -1.351 -1.623 -2.679 1.645 D 34 32 3 35 3 0 0 55 73 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 4 57 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 53 - U - - MR 36 35 3 38 3 1 6 55 74 -9.360 -0.009 -7.677 -0.981 -1.525 -2.480 1.569 D 37 35 3 38 3 0 0 54 72 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 3 56 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 52 - u - - MR 39 38 3 41 3 1 5 54 73 -9.360 -0.009 -7.677 -0.385 -0.135 -0.953 0.853 D 40 38 3 41 3 0 0 53 71 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 2 55 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 51 - c - - MR 42 41 3 44 3 1 4 53 72 -9.360 -0.009 -7.677 0.180 0.411 -1.052 0.078 D 43 41 3 44 3 0 0 52 70 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 2 54 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 50 - C - - MR 45 44 3 47 3 1 4 52 71 -9.360 -0.009 -7.677 -1.141 1.169 -2.403 0.149 D 46 44 3 47 3 0 0 51 69 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 1 53 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 49 - c - - MR 48 47 3 50 3 1 3 51 70 -9.360 -0.009 -7.677 0.273 0.630 -1.417 -0.202 D 49 47 3 50 3 0 0 50 68 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 1 52 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 48 - A - - MR 51 50 3 53 3 1 3 50 69 -9.360 -0.009 -7.677 1.548 -1.506 -1.567 -1.369 D 52 50 3 53 3 0 0 49 67 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 1 51 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 47 - A - - MR 54 53 3 56 3 1 2 49 68 -9.360 -0.009 -7.677 1.516 -2.366 -0.653 -1.689 D 55 53 3 56 3 0 0 48 66 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 1 50 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 46 - G - - MR 57 56 3 59 3 1 2 48 67 -9.360 -0.009 -7.677 -1.193 -2.163 1.351 -0.343 D 58 56 3 59 3 0 0 47 65 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 1 49 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 45 - U - - MR 60 59 3 62 3 1 2 47 66 -9.360 -0.009 -7.677 -1.726 -2.252 -3.045 1.751 D 61 59 3 62 3 0 0 46 64 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 1 48 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 44 - U - - MR 63 62 3 65 3 1 1 46 65 -9.360 -0.009 -7.677 -1.726 -2.252 -3.045 1.751 D 64 62 3 65 3 0 0 45 64 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 1 47 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 43 - U - - MR 66 65 3 68 3 1 1 45 64 -9.360 -0.084 -4.180 -1.335 -1.151 -2.162 1.551 D 67 65 3 68 3 0 0 44 63 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 1 46 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 42 - A - - MR 69 68 3 71 3 1 1 44 63 -9.285 -0.010 -7.603 1.870 -3.616 -2.600 -3.361 D 70 68 3 71 3 0 0 44 63 -1.622 -1.637 -1.500 IR 71 71 3 71 3 1 1 45 64 -2.224 -0.433 -4.462 0.000 0.000 0.000 0.000 [ MATR 24 ] - 40 - g - - MR 72 71 3 74 3 1 1 43 62 -9.360 -0.009 -7.677 -0.308 -1.285 0.772 0.104 D 73 71 3 74 3 0 0 42 60 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 1 44 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 39 - U - - MR 75 74 3 77 3 1 1 42 61 -9.360 -0.009 -7.677 -1.654 -1.816 -2.367 1.680 D 76 74 3 77 3 0 0 41 59 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 38 - A - - MR 78 77 3 80 3 1 1 41 60 -9.360 -0.009 -7.677 1.836 -2.547 -3.001 -2.898 D 79 77 3 80 3 0 0 40 58 -6.390 -1.568 -0.620 IR 80 80 3 80 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 37 - A - - MR 81 80 3 83 3 1 1 40 59 -9.360 -0.009 -7.677 1.935 -4.377 -3.850 -4.092 D 82 80 3 83 3 0 0 39 57 -6.390 -1.568 -0.620 IR 83 83 3 83 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 36 - A - - MR 84 83 3 86 3 1 1 39 58 -9.360 -0.009 -7.677 1.797 -2.516 -2.368 -2.670 D 85 83 3 86 3 0 0 38 56 -6.390 -1.568 -0.620 IR 86 86 3 86 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 29 ] - 35 - A - - MR 87 86 3 89 3 1 1 38 57 -9.360 -0.009 -7.677 1.688 -1.856 -1.840 -2.163 D 88 86 3 89 3 0 0 37 56 -6.390 -1.568 -0.620 IR 89 89 3 89 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 30 ] - 34 - U - - MR 90 89 3 92 5 1 1 37 56 -8.050 -0.020 -7.865 -8.077 -8.969 -1.881 -1.994 -1.332 1.623 D 91 89 3 92 5 0 0 36 55 -5.352 -0.707 -2.978 -4.409 -2.404 IR 92 92 3 92 5 1 1 38 56 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 31 ] 11 33 U A - - MP 93 92 3 97 6 2 2 36 55 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -5.939 -5.998 -5.501 -2.167 -4.031 -5.810 0.305 -4.881 -5.537 -2.056 -5.780 -4.049 3.692 -5.907 0.053 -4.171 ML 94 92 3 97 6 1 1 35 54 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 95 92 3 97 6 1 1 35 53 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 96 92 3 97 6 0 0 32 51 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 6 1 1 36 55 -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 36 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 32 ] 12 32 C G - - MP 99 98 6 103 6 2 2 34 53 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -5.857 -5.973 -5.302 -2.100 -3.744 -5.530 3.757 -4.653 -5.393 -1.989 -5.537 -4.069 0.085 -5.781 -0.820 -4.188 ML 100 98 6 103 6 1 1 33 52 -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 33 51 -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 30 49 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 103 103 5 103 6 1 1 34 53 -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 34 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 33 ] 13 31 G C - - MP 105 104 6 109 6 2 2 32 51 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -6.030 -3.847 -6.306 -0.301 -7.317 -5.370 -2.257 -6.670 -5.227 3.812 -5.506 -1.071 -2.533 -5.388 -4.377 -5.169 ML 106 104 6 109 6 1 1 31 50 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 107 104 6 109 6 1 1 31 49 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 108 104 6 109 6 0 0 28 47 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 109 109 5 109 6 1 1 32 51 -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 32 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 34 ] 14 30 A U - - MP 111 110 6 115 6 2 2 30 49 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -5.395 -4.093 -5.231 3.815 -7.276 -8.315 -2.806 -5.228 -5.173 -0.658 -5.821 -0.494 -2.879 -6.720 -4.675 -4.060 ML 112 110 6 115 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 113 110 6 115 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 114 110 6 115 6 0 0 27 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 115 115 5 115 6 1 1 30 49 -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 30 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 35 ] 15 29 U G - - MP 117 116 6 121 6 2 2 28 47 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -5.340 -5.411 -4.926 -1.597 -3.485 -5.249 1.286 -4.327 -4.976 -0.618 -5.217 -3.485 1.361 -5.331 3.251 -3.796 ML 118 116 6 121 6 1 1 27 46 -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 27 46 -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 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 121 121 5 121 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 122 122 6 122 5 1 1 28 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 36 ] 16 28 A U - - MP 123 122 6 127 6 2 2 26 45 -9.636 -9.575 -0.015 -8.352 -8.632 -9.027 -5.767 -4.496 -5.355 3.876 -6.985 -8.306 -2.594 -5.281 -5.526 -1.084 -6.147 -1.781 -2.949 -7.039 -4.504 -4.309 ML 124 122 6 127 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 125 122 6 127 6 1 1 26 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 126 122 6 127 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 127 127 5 127 6 1 1 26 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 128 128 6 128 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 37 ] 17 27 U A - - MP 129 128 6 133 4 2 2 24 43 -8.059 -8.266 -0.024 -6.680 -6.027 -6.087 -5.584 -2.256 -4.110 -5.890 0.225 -4.961 -5.619 -2.146 -5.862 -4.140 3.716 -5.990 -0.101 -4.222 ML 130 128 6 133 4 1 1 26 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 131 128 6 133 4 1 1 25 44 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 132 128 6 133 4 0 0 24 43 -4.568 -4.250 -2.265 -0.520 IL 133 133 5 133 4 1 1 27 46 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 134 134 6 134 3 1 1 26 45 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 38 ] 18 - A - - - ML 135 134 6 137 3 1 1 21 40 -9.019 -0.010 -7.673 1.935 -4.377 -3.850 -4.092 D 136 134 6 137 3 0 0 21 40 -6.174 -1.687 -0.566 IL 137 137 3 137 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 39 ] 19 - G - - - ML 138 137 3 140 3 1 1 20 39 -9.019 -0.010 -7.673 -3.503 -4.941 1.936 -4.244 D 139 137 3 140 3 0 0 20 39 -6.174 -1.687 -0.566 IL 140 140 3 140 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 40 ] 20 - A - - - ML 141 140 3 143 3 1 1 19 38 -9.019 -0.010 -7.673 1.935 -4.377 -3.850 -4.092 D 142 140 3 143 3 0 0 19 38 -6.174 -1.687 -0.566 IL 143 143 3 143 3 1 1 23 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 41 ] 21 - A - - - ML 144 143 3 146 3 1 1 18 37 -9.019 -0.010 -7.673 1.841 -3.473 -2.181 -3.222 D 145 143 3 146 3 0 0 18 36 -6.174 -1.687 -0.566 IL 146 146 3 146 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 42 ] 22 - C - - - ML 147 146 3 149 3 1 1 17 35 -9.019 -0.010 -7.673 -3.600 1.874 -4.328 -2.305 D 148 146 3 149 3 0 0 17 35 -6.174 -1.687 -0.566 IL 149 149 3 149 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 43 ] 23 - A - - - ML 150 149 3 152 3 1 1 15 34 -9.019 -0.010 -7.673 1.831 -3.421 -2.074 -3.166 D 151 149 3 152 3 0 0 16 34 -6.174 -1.687 -0.566 IL 152 152 3 152 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 44 ] 24 - C - - - ML 153 152 3 155 3 1 1 14 32 -9.019 -0.010 -7.673 -4.033 1.920 -4.715 -3.110 D 154 152 3 155 3 0 0 15 33 -6.174 -1.687 -0.566 IL 155 155 3 155 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 45 ] 25 - U - - - ML 156 155 3 158 3 1 1 12 31 -9.019 -0.010 -7.673 -3.417 -3.118 -4.203 1.902 D 157 155 3 158 3 0 0 13 32 -6.174 -1.687 -0.566 IL 158 158 3 158 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 26 - C - - - ML 159 158 3 161 2 1 1 1 1 * 0.000 -3.545 1.867 -4.283 -2.208 D 160 158 3 161 2 0 0 0 0 * 0.000 IL 161 161 3 161 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 47 ] - - - - - - E 162 161 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-atpF ACC RF04355 DESC Plastid-atpF group II-D1 intron LENG 53 MAXL 123 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Nov 15 13:49:16 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/atpF/CM NSEQ 49 EFFN 6.923523 CKSUM 3583117081 STATS LOCAL MSV -7.3225 0.71923 STATS LOCAL VITERBI -7.9711 0.71923 STATS LOCAL FORWARD -4.3075 0.71923 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.08864 1.80292 1.90443 1.05096 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 0.00000 * 1 1.25680 2.01150 1.34868 1.13300 1 u - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 2 0.74611 2.41208 1.30164 1.80742 2 a - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 3 0.99778 2.04821 1.78290 1.09606 3 a - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 4 0.75235 2.07487 2.26288 1.20692 4 a - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 5 0.88845 2.39374 2.31066 0.92074 5 a - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 6 1.60741 2.37315 2.90669 0.42809 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 7 3.11911 3.05047 3.23369 0.14035 7 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 8 2.46209 3.01136 3.54934 0.17820 8 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 9 2.55779 2.52234 2.01392 0.34420 9 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 10 1.66778 2.22606 2.89320 0.43389 10 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 11 4.14098 2.58573 3.99601 0.11613 11 U - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 12 4.04525 0.14916 3.90395 2.29358 12 C - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 13 2.91299 4.23832 0.08858 4.13333 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 14 0.10973 4.56343 2.53831 4.23366 14 A - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 15 3.76007 1.89171 3.07298 0.24895 15 U - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 16 0.06999 4.47424 3.15393 4.30383 16 A - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 17 4.17107 2.64549 4.04271 0.10977 17 U - - < 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 18 0.03760 4.59884 4.22597 4.40385 18 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 19 3.96853 4.98238 0.03780 4.47999 19 G - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 20 0.03760 4.59884 4.22597 4.40385 20 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 21 0.09956 3.93265 2.95152 3.77594 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 22 4.04270 0.07691 4.52099 3.08785 22 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 23 0.10617 3.89569 2.87205 3.73731 23 A - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 24 4.35268 0.04670 4.79690 3.70911 24 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 25 3.92916 3.70333 4.47721 0.05728 25 U - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 26 4.00475 0.08176 4.49095 3.01454 26 C - - _ 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 27 0.17430 4.19790 2.07834 3.92242 27 A - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 28 4.50594 3.56833 4.28233 0.05452 28 U - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 29 1.79282 3.16090 0.27246 3.51922 29 G - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 30 4.41550 3.25438 4.34539 0.06578 30 U - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 31 4.29770 0.11513 4.09482 2.54475 31 C - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 32 2.66333 4.05750 0.11552 3.81257 32 G - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 33 0.18901 4.16607 1.99195 3.89819 33 A - - > 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 34 2.83144 2.88778 2.32419 0.23888 34 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 35 0.20054 2.70991 2.72133 3.00817 35 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 36 0.12890 3.18649 3.10535 3.35789 36 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 37 0.03760 4.59884 4.22597 4.40385 37 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 38 0.10215 3.20571 3.60019 3.53168 38 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 39 2.61426 2.73243 3.10640 0.20217 39 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 40 1.62951 2.33025 0.82343 1.31758 40 g - - : 1.38629 1.38629 1.38629 1.38629 0.03519 4.70660 3.66756 1.46634 0.26236 1.09861 0.40547 41 0.07938 4.03798 3.27079 3.87748 42 A - - : 1.38629 1.38629 1.38629 1.38629 0.01855 4.68996 4.68996 1.46634 0.26236 0.53508 0.88097 42 2.38475 2.22825 2.96796 0.28933 43 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 43 2.64481 3.06038 3.62392 0.15615 44 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 44 2.64481 3.06038 3.62392 0.15615 45 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 45 2.29874 2.99780 0.42437 1.63202 46 G - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 46 0.31673 3.14517 1.84412 2.65574 47 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 47 0.29270 2.47063 2.53014 2.41268 48 A - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 48 1.19545 0.92304 2.42072 1.55465 49 c - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 49 2.23988 0.55096 3.16485 1.29130 50 C - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 50 1.26292 1.08104 2.14227 1.34499 51 c - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 51 1.67738 1.47611 2.06116 0.78240 52 u - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 52 2.10695 2.51683 3.22846 0.27700 53 U - - : 1.38629 1.38629 1.38629 1.38629 0.01824 4.70660 4.70660 1.46634 0.26236 1.09861 0.40547 53 2.37904 2.58407 3.36762 0.22637 54 U - - : 1.38629 1.38629 1.38629 1.38629 0.02611 3.65848 * 0.60116 0.79446 0.00000 * //