INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-ndhA-ndhB-1 ACC RF04356 DESC Plastid-ndhA-ndhB-1 group II-D5 intron STATES 151 NODES 36 CLEN 49 W 63 ALPH RNA RF no CONS yes MAP yes DATE Sat Nov 15 18:36:44 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_041414.1/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 432 EFFN 4.400024 CKSUM 2699854558 NULL 0.000 0.000 0.000 0.000 GA 61.00 TC 61.00 NC 60.90 EFP7GF -12.4220 0.71944 ECMLC 0.68750 -5.81611 3.44068 1600000 696720 0.001722 ECMGC 0.48943 -15.97056 -2.20112 1600000 337945 0.001184 ECMLI 0.69637 -3.94316 4.37497 1600000 393383 0.003050 ECMGI 0.54402 -11.84412 -0.00903 1600000 250181 0.001599 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 63 82 -7.715 -7.922 -0.385 -2.151 IL 1 1 2 1 4 1 4 68 87 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 4 66 86 -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 4 63 82 -8.360 -0.016 -7.014 -2.239 -2.108 -3.001 1.779 D 4 2 3 5 3 0 0 62 81 -8.213 -0.397 -2.074 IL 5 5 3 5 3 1 2 65 85 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - U - - - ML 6 5 3 8 3 1 4 62 81 -8.659 -0.013 -7.313 -2.799 -2.581 -3.575 1.850 D 7 5 3 8 3 0 0 61 80 -6.553 -1.589 -0.606 IL 8 8 3 8 3 1 2 64 83 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - C - - - ML 9 8 3 11 3 1 3 61 79 -8.671 -0.013 -7.325 -1.835 1.615 -2.702 -0.992 D 10 8 3 11 3 0 0 60 79 -6.411 -1.591 -0.607 IL 11 11 3 11 3 1 1 63 82 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 3 60 78 -8.679 -0.013 -7.333 -0.955 -2.306 1.590 -1.877 D 13 11 3 14 3 0 0 59 78 -6.309 -1.426 -0.701 IL 14 14 3 14 3 1 1 62 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - C - - - ML 15 14 3 17 3 1 2 58 77 -8.688 -0.012 -7.342 -1.812 1.537 -2.787 -0.582 D 16 14 3 17 3 0 0 58 76 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 61 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - G - - - ML 18 17 3 20 3 1 2 57 76 -8.688 -0.012 -7.342 -1.149 -2.945 1.685 -2.297 D 19 17 3 20 3 0 0 56 75 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 60 79 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - A - - - ML 21 20 3 23 3 1 1 56 75 -9.041 -0.040 -5.306 1.837 -3.033 -2.581 -2.854 D 22 20 3 23 3 0 0 55 74 -5.620 -0.734 -1.403 IL 23 23 3 23 3 1 1 57 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 66 - A - - MR 24 23 3 26 3 1 1 55 74 -9.013 -0.012 -7.331 1.898 -3.745 -3.254 -3.424 D 25 23 3 26 3 0 0 54 72 -6.720 -1.109 -0.924 IR 26 26 3 26 3 1 1 56 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 65 - U - - MR 27 26 3 29 3 1 1 54 73 -9.040 -0.012 -7.357 -1.962 -1.834 -2.510 1.717 D 28 26 3 29 3 0 0 53 71 -6.407 -1.585 -0.611 IR 29 29 3 29 3 1 1 55 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 64 - G - - MR 30 29 3 32 3 1 1 53 72 -9.040 -0.012 -7.357 -0.210 -1.989 1.312 -1.319 D 31 29 3 32 3 0 0 52 70 -6.407 -1.585 -0.611 IR 32 32 3 32 3 1 1 54 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 63 - A - - MR 33 32 3 35 3 1 1 52 71 -9.040 -0.012 -7.357 1.869 -3.479 -2.756 -3.182 D 34 32 3 35 3 0 0 51 69 -6.407 -1.535 -0.637 IR 35 35 3 35 3 1 1 53 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 62 - u - - MR 36 35 3 38 3 1 1 51 70 -9.041 -0.012 -7.358 -0.294 -0.259 -0.931 0.867 D 37 35 3 38 3 0 0 50 68 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 52 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 61 - G - - MR 39 38 3 41 5 1 1 50 69 -7.743 -0.025 -7.558 -7.770 -8.662 -2.986 -4.373 1.907 -3.726 D 40 38 3 41 5 0 0 49 68 -5.352 -0.707 -2.978 -4.409 -2.404 IR 41 41 3 41 5 1 1 51 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 8 60 G U - - MP 42 41 3 46 6 2 2 49 68 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.427 -3.038 -4.666 0.614 -6.206 -6.719 -1.661 -4.655 -4.184 0.414 -4.743 3.571 -1.857 -5.671 -3.578 -2.348 ML 43 41 3 46 6 1 1 48 66 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 3 46 6 1 1 48 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 3 46 6 0 0 45 64 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 49 68 -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 49 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 9 59 G C - - MP 48 47 6 52 6 2 2 47 66 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.463 -2.558 -4.381 0.497 -5.335 -4.616 -0.502 -4.985 -4.447 3.491 -4.718 0.280 -0.775 -2.974 -2.513 -3.344 ML 49 47 6 52 6 1 1 46 64 -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 46 64 -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 43 62 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 47 66 -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 47 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 10 58 A U - - MP 54 53 6 58 6 2 2 45 64 -9.044 -9.389 -0.017 -8.166 -8.445 -8.840 -5.181 -3.952 -4.978 3.802 -6.167 -7.430 -1.782 -4.929 -4.961 -0.444 -5.568 -1.270 -2.173 -6.304 -3.709 -3.832 ML 55 53 6 58 6 1 1 44 62 -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 44 62 -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 41 60 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 58 58 5 58 6 1 1 45 64 -2.270 -2.923 -0.827 -4.579 -5.355 -5.015 0.000 0.000 0.000 0.000 IR 59 59 6 59 5 1 1 45 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 21 57 G U - - MP 60 59 6 64 6 2 2 43 62 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.472 -3.104 -4.684 0.479 -6.262 -6.932 -1.727 -4.691 -4.229 0.848 -4.818 3.547 -1.901 -5.739 -3.634 -3.288 ML 61 59 6 64 6 1 1 42 60 -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 42 60 -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 39 58 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 64 64 5 64 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 65 65 6 65 5 1 1 43 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 22 56 C G - - MP 66 65 6 70 6 2 2 41 60 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.527 -4.500 -4.489 -0.776 -1.686 -5.144 3.610 -2.773 -4.517 -0.627 -4.903 -2.147 0.153 -4.744 -1.346 -3.424 ML 67 65 6 70 6 1 1 40 58 -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 40 58 -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 37 56 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 70 70 5 70 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 71 71 6 71 5 1 1 41 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 23 55 c g - - MP 72 71 6 76 6 2 2 39 58 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -2.032 -2.359 -2.389 0.813 -1.423 -3.052 2.117 -2.598 -2.215 0.779 -2.991 -0.804 1.891 -2.412 0.763 -1.352 ML 73 71 6 76 6 1 1 38 56 -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 38 56 -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 35 54 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 76 76 5 76 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 77 77 6 77 5 1 1 39 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 24 54 G C - - MP 78 77 6 82 6 2 2 37 56 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.294 -2.718 -4.208 0.693 -5.072 -3.118 -0.337 -4.818 -4.339 3.495 -3.645 -0.535 -0.609 -3.361 -2.324 -3.197 ML 79 77 6 82 6 1 1 36 54 -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 36 54 -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 33 52 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 82 82 5 82 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 83 83 6 83 5 1 1 37 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 25 53 G C - - MP 84 83 6 88 6 2 2 35 54 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -3.549 -2.194 -3.465 1.106 -4.163 -3.524 0.319 -4.036 -3.794 3.118 -4.128 -0.089 0.540 -1.843 -1.599 -2.421 ML 85 83 6 88 6 1 1 34 52 -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 34 52 -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 31 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 88 88 5 88 6 1 1 35 54 -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 35 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 22 ] 26 52 A U - - MP 90 89 6 94 6 2 2 33 52 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -5.027 -3.107 -4.883 3.770 -6.515 -7.378 -2.114 -4.919 -4.857 -0.089 -5.482 -0.896 -2.250 -6.086 -4.001 -3.738 ML 91 89 6 94 6 1 1 32 51 -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 32 50 -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 30 48 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 94 94 5 94 6 1 1 33 52 -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 33 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 27 51 U G - - MP 96 95 6 100 4 2 2 31 50 -7.582 -8.827 -0.049 -5.281 -4.983 -5.066 -4.582 -1.351 -3.181 -4.907 1.193 -4.016 -4.643 -1.236 -3.058 -3.209 0.885 -4.990 3.372 -3.488 ML 97 95 6 100 4 1 1 31 49 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 98 95 6 100 4 1 1 30 49 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 99 95 6 100 4 0 0 28 47 -12.737 -14.007 -2.036 -0.404 IL 100 100 5 100 4 1 1 31 49 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 101 101 6 101 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 50 - U - - MR 102 101 6 104 3 1 1 29 48 -9.041 -0.012 -7.358 -1.177 0.029 -1.950 1.188 D 103 101 6 104 3 0 0 28 46 -6.390 -1.568 -0.620 IR 104 104 3 104 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 49 - A - - MR 105 104 3 107 5 1 1 28 47 -7.390 -0.027 -7.558 -7.770 -8.662 1.830 -3.210 -2.306 -2.905 D 106 104 3 107 5 0 0 27 46 -5.352 -0.707 -2.978 -4.409 -2.404 IR 107 107 3 107 5 1 1 29 47 -2.316 -0.517 -5.952 -4.120 -5.226 0.000 0.000 0.000 0.000 [ MATP 26 ] 28 44 G C - - MP 108 107 3 112 6 2 2 27 46 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -6.112 -3.772 -6.494 -0.783 -7.109 -5.198 -2.138 -6.727 -5.119 3.846 -5.383 -1.553 -2.500 -5.332 -4.276 -5.353 ML 109 107 3 112 6 1 1 26 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 110 107 3 112 6 1 1 26 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 111 107 3 112 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 112 112 5 112 6 1 1 27 46 -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 27 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 29 43 A U - - MP 114 113 6 118 6 2 2 25 44 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -5.247 -2.859 -4.988 3.813 -6.608 -7.544 -2.237 -4.994 -5.073 -0.447 -5.693 -1.362 -2.428 -6.303 -4.126 -3.905 ML 115 113 6 118 6 1 1 24 42 -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 24 42 -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 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 118 118 5 118 6 1 1 25 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 119 119 6 119 5 1 1 25 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 28 ] 30 42 G C - - MP 120 119 6 124 6 2 2 23 42 -9.450 -7.977 -0.020 -8.166 -8.445 -8.840 -3.848 -2.041 -3.754 0.999 -4.575 -4.317 0.038 -4.341 -2.578 3.266 -3.535 0.236 -0.153 -3.631 -1.912 -2.747 ML 121 119 6 124 6 1 1 22 41 -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 22 41 -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 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 124 124 5 124 6 1 1 23 42 -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 23 41 -2.435 -0.485 -5.946 -4.114 -5.220 0.000 0.000 0.000 0.000 [ MATP 29 ] 31 40 A U - - MP 126 125 6 130 6 2 2 21 40 -9.450 -9.389 -0.017 -8.166 -8.445 -8.840 -4.062 -2.546 -3.342 3.544 -4.462 -5.132 -0.640 -3.429 -4.217 0.539 -4.740 -0.429 -0.852 -4.360 -2.364 -3.119 ML 127 125 6 130 6 1 1 21 40 -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 21 40 -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 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 130 130 5 130 6 1 1 21 40 -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 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 32 39 a u - - MP 132 131 6 136 4 2 2 19 38 -7.715 -7.922 -0.031 -6.336 -1.488 1.135 -1.565 1.386 -1.830 -1.972 1.255 -2.280 -1.995 1.137 -2.551 -0.461 1.271 -1.919 -0.157 -1.173 ML 133 131 6 136 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 134 131 6 136 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 135 131 6 136 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 136 136 5 136 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 137 137 6 137 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 33 - G - - - ML 138 137 6 140 3 1 1 16 34 -7.660 -0.016 -7.342 -1.599 -2.913 1.712 -1.941 D 139 137 6 140 3 0 0 16 34 -6.174 -1.687 -0.566 IL 140 140 3 140 3 1 1 20 38 -1.444 -0.794 -4.163 0.000 0.000 0.000 0.000 [ MATL 32 ] 36 - A - - - ML 141 140 3 143 3 1 1 14 33 -8.688 -0.012 -7.342 1.902 -3.798 -3.304 -3.482 D 142 140 3 143 3 0 0 15 33 -6.174 -1.687 -0.566 IL 143 143 3 143 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 37 - A - - - ML 144 143 3 146 3 1 1 13 31 -8.688 -0.012 -7.342 1.902 -3.798 -3.304 -3.482 D 145 143 3 146 3 0 0 13 32 -6.174 -1.687 -0.566 IL 146 146 3 146 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 38 - A - - - ML 147 146 3 149 2 1 1 1 1 * 0.000 1.867 -3.464 -2.731 -3.168 D 148 146 3 149 2 0 0 0 0 * 0.000 IL 149 149 3 149 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 35 ] - - - - - - E 150 149 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-ndhA-ndhB-1 ACC RF04356 DESC Plastid-ndhA-ndhB-1 group II-D5 intron LENG 49 MAXL 121 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Nov 15 18:36:44 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_041414.1/CM NSEQ 432 EFFN 6.291870 CKSUM 2699854558 STATS LOCAL MSV -7.3491 0.71944 STATS LOCAL VITERBI -7.7813 0.71944 STATS LOCAL FORWARD -3.9178 0.71944 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.29203 1.69060 1.28133 1.33480 1.38629 1.38629 1.38629 1.38629 0.27099 4.42526 1.48985 1.46634 0.26236 0.00000 * 1 3.38165 3.22293 3.92041 0.09834 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.03091 4.18518 4.18518 1.46634 0.26236 0.19675 1.72260 2 3.77534 3.56605 4.32082 0.06666 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.02475 4.40445 4.40445 1.46634 0.26236 1.02337 0.44532 3 2.94055 0.20635 3.54237 2.25695 3 C - - : 1.38629 1.38629 1.38629 1.38629 0.02454 4.41293 4.41293 1.46634 0.26236 1.01248 0.45148 4 2.15455 3.12850 0.24316 2.88033 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.02440 4.41851 4.41851 1.46634 0.26236 0.82439 0.57714 5 2.91906 0.26223 3.64022 1.89420 5 C - - : 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 6 2.29461 3.69737 0.18111 3.21716 6 G - - : 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 7 0.08229 3.76240 3.44407 3.73677 7 A - - : 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 8 2.44993 4.14144 0.13965 3.57073 8 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 9 2.43939 3.22842 0.19570 2.97776 9 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 10 0.07950 4.34358 3.03255 4.18380 10 A - - < 1.38629 1.38629 1.38629 1.38629 0.02517 4.35203 4.42526 1.60347 0.22464 1.09861 0.40547 11 2.55989 4.14103 0.12229 3.82189 21 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 12 3.45415 0.16170 3.15547 2.58930 22 C - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 13 1.95394 1.15098 1.87873 0.94373 23 u - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 14 2.26036 2.96272 0.23770 2.89008 24 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 15 1.92043 2.56386 0.44439 2.00074 25 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 16 0.09201 4.57793 2.75718 4.25775 26 A - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 17 3.86443 2.12359 3.51313 0.18679 27 U - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 18 3.41775 4.39756 0.05966 4.35679 28 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 19 0.06758 4.67882 3.12838 4.40047 29 A - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 20 1.96992 2.77144 0.32611 2.57392 30 G - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 21 0.17063 3.56636 2.32843 3.46872 31 A - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 22 0.96557 1.68205 1.65614 1.41729 32 a - - < 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 23 2.68725 3.67310 0.16293 2.86681 33 G - - _ 1.38629 1.38629 1.38629 1.38629 0.02695 4.22573 4.42526 1.27287 0.32854 1.09861 0.40547 24 0.04248 4.47768 4.10985 4.28156 36 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 25 0.04248 4.47768 4.10985 4.28156 37 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 26 0.06326 4.18535 3.57033 4.02081 38 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 27 1.59981 1.10972 1.49629 1.40873 39 c - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 28 3.69356 2.72510 3.39898 0.13220 40 U - - > 1.38629 1.38629 1.38629 1.38629 0.02922 4.08510 4.42526 1.09518 0.40719 1.09861 0.40547 29 2.69594 0.42642 2.54426 1.60370 42 C - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 30 4.62320 3.39605 4.50244 0.05594 43 U - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 31 4.52563 0.07146 4.30693 3.10868 44 C - - > 1.38629 1.38629 1.38629 1.38629 0.02575 4.30898 4.42526 1.45314 0.26636 1.09861 0.40547 32 0.08539 3.97811 3.19233 3.81449 49 A - - - 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 33 2.44752 1.34484 2.98959 0.50650 50 U - - - 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 34 2.20414 3.89018 0.17141 3.62170 51 G - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 35 4.43148 3.13779 4.36530 0.07041 52 U - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 36 2.30521 0.48194 2.40238 1.64934 53 C - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 37 3.18882 0.26741 2.83943 2.00276 54 C - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 38 1.22745 2.04684 0.89695 1.77190 55 g - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 39 2.56929 3.42002 0.17374 2.99212 56 G - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 40 3.99548 2.30567 3.90754 0.14871 57 U - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 41 4.40146 3.44484 4.15457 0.06173 58 U - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 42 3.34446 0.27359 3.04934 1.85349 59 C - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 43 4.02254 2.65622 3.91898 0.11427 60 U - - > 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 44 3.86421 4.86614 0.04212 4.37709 61 G - - : 1.38629 1.38629 1.38629 1.38629 0.02423 4.42526 4.42526 1.46634 0.26236 1.09861 0.40547 45 1.64064 1.56921 2.06949 0.75144 62 u - - : 1.38629 1.38629 1.38629 1.38629 0.02522 4.42526 4.34782 1.46634 0.26236 1.09861 0.40547 46 0.06214 4.19781 3.59371 4.03279 63 A - - : 1.38629 1.38629 1.38629 1.38629 0.02426 4.42429 4.42429 1.46634 0.26236 1.12510 0.39248 47 1.58394 2.96732 0.41560 2.48353 64 G - - : 1.38629 1.38629 1.38629 1.38629 0.02426 4.42429 4.42429 1.46634 0.26236 1.12510 0.39248 48 3.04827 2.89546 3.36018 0.14785 65 U - - : 1.38629 1.38629 1.38629 1.38629 0.04499 4.42429 3.44174 1.46634 0.26236 1.12510 0.39248 49 0.04409 4.44095 4.07476 4.24404 66 A - - : 1.38629 1.38629 1.38629 1.38629 0.16470 1.88484 * 0.15575 1.93637 0.00000 * //