INFERNAL1/a [1.1.4 | Dec 2020] NAME Plastid-ndhJ ACC RF04350 DESC Plastid-ndhJ 3UTR RNA STATES 175 NODES 53 CLEN 57 W 72 ALPH RNA RF no CONS yes MAP yes DATE Thu Nov 13 20:24:35 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/extended/3UTR-ndhJ/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 50 EFFN 5.227661 CKSUM 125694808 NULL 0.000 0.000 0.000 0.000 GA 43.00 TC 43.10 NC 42.90 EFP7GF -12.9736 0.71911 ECMLC 0.58857 -9.23142 1.57582 1600000 694486 0.001728 ECMGC 0.39563 -19.65703 -5.15426 1600000 124136 0.003222 ECMLI 0.52347 -8.39040 2.50292 1600000 359464 0.003338 ECMGI 0.40525 -16.51193 -3.03214 1600000 94293 0.004242 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 72 92 -7.902 -8.109 -0.027 -6.523 IL 1 1 2 1 4 1 22 76 96 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 21 75 95 -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 22 72 92 -8.867 -0.011 -7.521 -0.350 -0.018 -1.698 0.941 D 4 2 3 5 3 0 15 71 91 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 20 74 94 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - c - - - ML 6 5 3 8 3 1 21 71 91 -8.867 -0.011 -7.521 -0.062 0.526 -0.511 -0.151 D 7 5 3 8 3 0 15 70 90 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 20 73 93 -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 20 70 90 -8.867 -0.011 -7.521 1.077 -0.039 -1.707 -0.711 D 10 8 3 11 3 0 14 69 88 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 19 72 92 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - U - - - ML 12 11 3 14 3 1 19 69 89 -8.867 -0.011 -7.521 -0.805 -0.493 -2.021 1.305 D 13 11 3 14 3 0 13 68 87 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 18 71 91 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - G - - - ML 15 14 3 17 3 1 19 68 88 -8.867 -0.011 -7.521 -1.544 -2.414 1.495 -0.619 D 16 14 3 17 3 0 12 67 86 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 17 70 90 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - A - - - ML 18 17 3 20 3 1 18 67 86 -8.867 -0.011 -7.521 1.453 -1.287 -1.930 -0.763 D 19 17 3 20 3 0 12 66 85 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 16 69 89 -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 17 66 85 -8.867 -0.011 -7.521 1.518 -1.926 -0.927 -1.523 D 22 20 3 23 3 0 11 65 84 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 16 68 88 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - C - - - ML 24 23 3 26 3 1 16 65 84 -8.867 -0.011 -7.521 -1.951 1.399 -2.882 -0.045 D 25 23 3 26 3 0 10 64 83 -6.174 -1.687 -0.566 IL 26 26 3 26 3 1 15 67 87 -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 15 64 83 -8.867 -0.011 -7.521 -2.272 -1.358 -3.021 1.713 D 28 26 3 29 3 0 9 63 82 -6.174 -1.687 -0.566 IL 29 29 3 29 3 1 14 66 86 -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 15 63 82 -8.867 -0.011 -7.521 0.244 -1.450 -1.759 1.108 D 31 29 3 32 3 0 8 62 81 -6.174 -1.687 -0.566 IL 32 32 3 32 3 1 13 65 85 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 11 - U - - - ML 33 32 3 35 3 1 14 62 81 -8.867 -0.011 -7.521 -3.164 -2.896 -3.946 1.883 D 34 32 3 35 3 0 7 61 80 -6.174 -1.687 -0.566 IL 35 35 3 35 3 1 12 64 84 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 12 - G - - - ML 36 35 3 38 3 1 13 61 80 -8.867 -0.011 -7.521 -3.275 -4.689 1.925 -4.017 D 37 35 3 38 3 0 6 60 79 -6.174 -1.687 -0.566 IL 38 38 3 38 3 1 12 63 83 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - U - - - ML 39 38 3 41 3 1 12 60 79 -8.867 -0.011 -7.521 -2.090 -2.053 -2.317 1.733 D 40 38 3 41 3 0 5 59 78 -6.174 -1.687 -0.566 IL 41 41 3 41 3 1 11 62 82 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 14 - A - - - ML 42 41 3 44 3 1 11 59 78 -8.867 -0.011 -7.521 1.922 -4.118 -3.605 -3.823 D 43 41 3 44 3 0 5 58 77 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 10 61 81 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 15 - C - - - ML 45 44 3 47 3 1 10 58 77 -8.867 -0.011 -7.521 -2.486 1.659 -3.382 -0.819 D 46 44 3 47 3 0 4 56 76 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 9 60 80 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 16 - C - - - ML 48 47 3 50 3 1 9 57 76 -8.867 -0.011 -7.521 -2.408 1.632 -3.312 -0.709 D 49 47 3 50 3 0 3 55 75 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 8 59 78 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 17 - G - - - ML 51 50 3 53 3 1 9 56 75 -8.867 -0.011 -7.521 -3.275 -4.689 1.925 -4.017 D 52 50 3 53 3 0 2 54 74 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 7 58 77 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 18 - C - - - ML 54 53 3 56 3 1 8 55 74 -9.213 -0.010 -7.531 -2.781 1.745 -3.636 -1.241 D 55 53 3 56 3 0 2 53 73 -5.620 -0.734 -1.403 IL 56 56 3 56 3 1 6 55 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 59 - G - - MR 57 56 3 59 3 1 7 54 73 -9.213 -0.010 -7.531 -0.387 -0.910 1.002 -0.513 D 58 56 3 59 3 0 0 52 71 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 5 54 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 58 - A - - MR 60 59 3 62 3 1 6 53 72 -9.213 -0.010 -7.531 1.572 -2.271 -1.025 -1.609 D 61 59 3 62 3 0 0 51 70 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 4 53 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 57 - G - - MR 63 62 3 65 3 1 6 52 71 -9.213 -0.010 -7.531 -0.474 -1.669 1.301 -0.994 D 64 62 3 65 3 0 0 50 69 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 3 52 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 56 - G - - MR 66 65 3 68 3 1 5 51 70 -9.213 -0.010 -7.531 -0.725 -2.359 1.494 -1.380 D 67 65 3 68 3 0 0 49 68 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 3 51 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 55 - A - - MR 69 68 3 71 3 1 4 50 69 -9.213 -0.010 -7.531 1.626 -2.096 -1.207 -2.022 D 70 68 3 71 3 0 0 48 67 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 2 50 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 54 - U - - MR 72 71 3 74 3 1 4 49 68 -9.213 -0.010 -7.531 -0.629 -1.235 -0.893 1.257 D 73 71 3 74 3 0 0 47 66 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 2 49 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 53 - g - - MR 75 74 3 77 3 1 3 48 67 -9.213 -0.010 -7.531 0.768 -2.430 0.884 -1.909 D 76 74 3 77 3 0 0 46 65 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 1 48 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 52 - c - - MR 78 77 3 80 3 1 3 47 66 -9.213 -0.010 -7.531 -0.549 0.744 -1.320 0.312 D 79 77 3 80 3 0 0 45 64 -6.390 -1.568 -0.620 IR 80 80 3 80 3 1 1 47 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 51 - A - - MR 81 80 3 83 3 1 2 46 65 -9.213 -0.010 -7.531 1.442 -2.528 -0.192 -2.093 D 82 80 3 83 3 0 0 44 63 -6.390 -1.568 -0.620 IR 83 83 3 83 3 1 1 46 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 50 - C - - MR 84 83 3 86 3 1 2 45 64 -9.213 -0.010 -7.531 -0.161 1.282 -2.359 -1.064 D 85 83 3 86 3 0 0 43 62 -6.390 -1.568 -0.620 IR 86 86 3 86 3 1 1 45 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 29 ] - 49 - U - - MR 87 86 3 89 3 1 1 44 63 -9.213 -0.043 -5.160 -1.970 -1.652 -2.362 1.692 D 88 86 3 89 3 0 0 42 61 -6.390 -1.568 -0.620 IR 89 89 3 89 3 1 1 44 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 30 ] - 48 - G - - MR 90 89 3 92 3 1 1 43 62 -9.180 -0.011 -7.498 -2.243 -4.035 1.863 -3.453 D 91 89 3 92 3 0 0 41 60 -6.813 -0.983 -1.043 IR 92 92 3 92 3 1 1 43 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 31 ] - 47 - A - - MR 93 92 3 95 3 1 1 42 61 -9.213 -0.010 -7.531 1.721 -2.276 -1.783 -2.277 D 94 92 3 95 3 0 0 40 59 -6.390 -1.568 -0.620 IR 95 95 3 95 3 1 1 42 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 32 ] - 46 - A - - MR 96 95 3 98 3 1 1 41 60 -9.213 -0.010 -7.531 1.858 -3.486 -2.492 -3.217 D 97 95 3 98 3 0 0 39 58 -6.390 -1.568 -0.620 IR 98 98 3 98 3 1 1 41 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 33 ] - 45 - A - - MR 99 98 3 101 3 1 1 40 59 -9.213 -0.010 -7.531 1.922 -4.118 -3.605 -3.823 D 100 98 3 101 3 0 0 38 57 -6.390 -1.568 -0.620 IR 101 101 3 101 3 1 1 40 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 34 ] - 44 - G - - MR 102 101 3 104 3 1 1 39 58 -9.213 -0.010 -7.531 -2.529 -3.669 1.831 -2.394 D 103 101 3 104 3 0 0 37 56 -6.390 -1.568 -0.620 IR 104 104 3 104 3 1 1 39 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 35 ] - 43 - A - - MR 105 104 3 107 3 1 1 38 57 -9.213 -0.010 -7.531 1.469 -2.057 -0.495 -1.830 D 106 104 3 107 3 0 0 36 55 -6.390 -1.568 -0.620 IR 107 107 3 107 3 1 1 38 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 36 ] - 42 - u - - MR 108 107 3 110 3 1 1 37 56 -9.213 -0.010 -7.531 -1.250 0.469 -1.874 0.943 D 109 107 3 110 3 0 0 35 54 -6.390 -1.568 -0.620 IR 110 110 3 110 3 1 1 37 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 37 ] - 41 - C - - MR 111 110 3 113 3 1 1 36 55 -9.213 -0.010 -7.531 -1.053 1.470 -2.620 -0.776 D 112 110 3 113 3 0 0 34 53 -6.390 -1.568 -0.620 IR 113 113 3 113 3 1 1 36 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 38 ] - 40 - U - - MR 114 113 3 116 5 1 1 35 54 -7.908 -0.022 -7.724 -7.936 -8.827 -1.514 -0.802 -2.456 1.533 D 115 113 3 116 5 0 0 33 53 -5.352 -0.707 -2.978 -4.409 -2.404 IR 116 116 3 116 5 1 1 35 54 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 39 ] 19 39 G C - - MP 117 116 3 121 6 2 2 34 53 -9.548 -9.488 -0.016 -8.264 -8.544 -8.939 -4.741 -3.275 -4.808 0.264 -6.097 -5.634 -1.331 -5.103 -4.555 3.059 -5.014 2.378 -1.544 -4.990 -3.316 -3.586 ML 118 116 3 121 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 119 116 3 121 6 1 1 33 52 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 120 116 3 121 6 0 0 31 51 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 121 121 5 121 6 1 1 33 53 -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 33 52 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 40 ] 20 38 C G - - MP 123 122 6 127 4 2 2 32 51 -7.902 -8.109 -0.027 -6.523 -5.338 -5.396 -4.892 -1.501 -3.404 -5.198 3.620 -4.263 -4.940 -1.363 -5.164 -3.411 0.524 -5.309 0.015 -3.738 ML 124 122 6 127 4 1 1 32 52 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 125 122 6 127 4 1 1 32 51 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 126 122 6 127 4 0 0 31 50 -4.568 -4.250 -2.265 -0.520 IL 127 127 5 127 4 1 1 34 53 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 128 128 6 128 3 1 1 33 52 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 41 ] 21 - A - - - ML 129 128 6 131 3 1 1 29 48 -9.213 -0.010 -7.531 1.593 -1.542 -1.818 -1.488 D 130 128 6 131 3 0 0 28 47 -5.620 -0.734 -1.403 IL 131 131 3 131 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 42 ] - 37 - G - - MR 132 131 3 134 5 1 1 28 47 -7.908 -0.022 -7.724 -7.936 -8.827 -2.847 -4.091 1.880 -3.028 D 133 131 3 134 5 0 0 27 46 -5.352 -0.707 -2.978 -4.409 -2.404 IR 134 134 3 134 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 22 36 C G - - MP 135 134 3 139 6 2 2 27 46 -9.548 -9.488 -0.016 -8.264 -8.544 -8.939 -5.998 -6.112 -5.410 -2.258 -3.849 -5.614 3.807 -4.795 -5.535 -2.152 -5.623 -4.216 -0.509 -5.925 -0.917 -4.333 ML 136 134 3 139 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 137 134 3 139 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 138 134 3 139 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 139 139 5 139 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 140 140 6 140 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 44 ] 23 35 A U - - MP 141 140 6 145 6 2 2 25 44 -9.548 -9.488 -0.016 -8.264 -8.544 -8.939 -4.825 -3.555 -4.871 3.674 -6.505 -7.359 -2.036 -4.934 -4.636 0.458 -5.269 -0.063 -2.138 -5.960 -3.924 -3.597 ML 142 140 6 145 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 143 140 6 145 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 144 140 6 145 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 145 145 5 145 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 146 146 6 146 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 24 34 U A - - MP 147 146 6 151 6 2 2 23 42 -9.548 -9.488 -0.016 -8.264 -8.544 -8.939 -6.220 -6.258 -5.799 -2.439 -4.346 -6.119 -0.015 -5.191 -5.820 -2.320 -6.082 -4.296 3.790 -6.185 -0.970 -4.303 ML 148 146 6 151 6 1 1 23 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 149 146 6 151 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 150 146 6 151 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 151 151 5 151 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 152 152 6 152 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 46 ] 25 33 C G - - MP 153 152 6 157 4 2 2 21 40 -5.859 -8.109 -0.047 -6.523 -5.543 -5.637 -5.033 -1.768 -3.504 -5.293 3.691 -4.388 -5.104 -1.650 -5.286 -3.709 -0.079 -5.486 0.096 -3.903 ML 154 152 6 157 4 1 1 22 41 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 155 152 6 157 4 1 1 21 40 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 156 152 6 157 4 0 0 20 39 -4.568 -4.250 -2.265 -0.520 IL 157 157 5 157 4 1 1 23 42 -1.535 -2.657 -1.095 -5.143 0.000 0.000 0.000 0.000 IR 158 158 6 158 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 28 - A - - - ML 159 158 6 161 3 1 1 17 35 -8.867 -0.011 -7.521 1.526 -2.101 -0.690 -1.903 D 160 158 6 161 3 0 0 17 35 -6.174 -1.687 -0.566 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 48 ] 29 - C - - - ML 162 161 3 164 3 1 1 16 34 -8.867 -0.011 -7.521 -1.285 1.261 -2.420 0.008 D 163 161 3 164 3 0 0 16 34 -6.174 -1.687 -0.566 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 49 ] 30 - U - - - ML 165 164 3 167 3 1 1 14 33 -8.867 -0.011 -7.521 -1.655 -1.717 -2.327 1.669 D 166 164 3 167 3 0 0 15 33 -6.174 -1.687 -0.566 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 50 ] 31 - U - - - ML 168 167 3 170 3 1 1 12 31 -8.867 -0.011 -7.521 -3.164 -2.896 -3.946 1.883 D 169 167 3 170 3 0 0 13 32 -6.174 -1.687 -0.566 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 51 ] 32 - A - - - ML 171 170 3 173 2 1 1 1 1 * 0.000 1.922 -4.118 -3.605 -3.823 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 52 ] - - - - - - E 174 173 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME Plastid-ndhJ ACC RF04350 DESC Plastid-ndhJ 3UTR RNA LENG 57 MAXL 129 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Nov 13 20:24:35 2025 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED NSEQ 50 EFFN 5.844116 CKSUM 125694808 STATS LOCAL MSV -7.7079 0.71911 STATS LOCAL VITERBI -8.1343 0.71911 STATS LOCAL FORWARD -3.9502 0.71911 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.24263 1.56116 1.40676 1.36043 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 0.00000 * 1 1.64611 1.39207 2.62048 0.72181 1 u - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 2 1.44060 1.00101 1.74222 1.51151 2 c - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 3 0.62045 1.40253 2.64265 1.92997 3 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 4 1.98182 1.73879 2.86387 0.46299 4 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 5 2.55389 3.16555 0.32945 1.82813 5 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 6 0.35926 2.31201 2.80608 1.94979 6 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 7 0.31764 2.78032 2.04639 2.51435 7 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 8 2.84123 0.39768 3.49639 1.42936 8 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 9 3.06868 2.36294 3.58689 0.18430 9 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 10 1.21483 2.46391 2.67957 0.59866 10 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 11 3.71870 3.51597 4.26326 0.07049 11 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 12 3.78229 4.77547 0.04586 4.29611 12 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 13 2.93533 2.89617 3.04544 0.16951 13 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 14 0.04672 4.38368 4.02015 4.18511 14 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 15 3.22753 0.22035 3.84879 1.98920 15 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 16 3.17132 0.23885 3.80015 1.90954 16 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 17 3.78229 4.77547 0.04586 4.29611 17 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 18 3.43930 0.16312 4.02628 2.29675 18 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 19 2.52103 3.64525 0.14917 3.43940 19 G - - < 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 20 3.64871 0.23738 3.47196 1.86932 20 C - - < 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 21 0.26569 2.48522 2.70925 2.48376 21 A - - - 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 22 4.12731 0.11701 3.99058 2.57958 22 C - - < 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 23 0.20023 4.09814 1.95092 3.78505 23 A - - < 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 24 4.29266 2.83427 4.16283 0.09211 24 U - - < 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 25 3.80294 0.19254 3.65104 2.06459 25 C - - < 1.38629 1.38629 1.38629 1.38629 0.03455 3.74932 4.56377 1.01288 0.45125 1.09861 0.40547 26 0.31254 2.91189 1.87070 2.81299 28 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 27 2.33604 0.49132 3.15259 1.39139 29 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 28 2.60842 2.64593 3.06844 0.21206 30 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 29 3.71870 3.51597 4.26326 0.07049 31 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 30 0.04672 4.38368 4.02015 4.18511 32 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 31 2.75449 3.80237 0.12142 3.56204 33 G - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 32 0.12317 4.32718 2.46405 4.04040 34 A - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 33 3.98102 2.45135 3.87763 0.13415 35 U - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 34 3.06431 4.15105 0.08616 3.90632 36 G - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 35 3.47474 4.34311 0.07548 3.54968 37 G - - - 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 36 2.35234 3.63078 0.16813 3.40784 38 G - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 37 3.67033 0.63772 3.45399 0.88088 39 C - - > 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 38 2.51117 1.96327 3.18412 0.30515 40 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 39 2.15366 0.34591 3.30052 1.96969 41 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 40 2.32874 1.04348 2.74848 0.72087 42 u - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 41 0.35117 2.88362 1.73086 2.76350 43 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 42 3.24837 4.04359 0.10753 3.08836 44 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 43 0.04672 4.38368 4.02015 4.18511 45 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 44 0.08900 3.91723 3.17904 3.74528 46 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 45 0.18081 3.01499 2.66534 3.06225 47 A - - : 1.38629 1.38629 1.38629 1.38629 0.04637 4.56377 3.35566 1.46634 0.26236 1.09861 0.40547 46 3.00985 4.30228 0.08684 3.89505 48 G - - : 1.38629 1.38629 1.38629 1.38629 0.02160 4.53900 4.53900 1.46634 0.26236 0.46846 0.98341 47 2.84878 2.59081 3.08723 0.19663 49 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 48 1.50916 0.46900 3.13405 2.20965 50 C - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 49 0.37146 3.25766 1.51121 2.97301 51 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 50 1.79777 0.84812 2.33246 1.17423 52 c - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 51 0.84158 3.18683 0.75706 2.83663 53 g - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 52 1.85501 2.29207 2.01576 0.49549 54 U - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 53 0.24443 2.89497 2.24516 2.88895 55 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 54 1.91738 3.09484 0.33476 2.38357 56 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 55 1.74322 2.59004 0.46241 2.11808 57 G - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 56 0.28093 3.04404 2.11321 2.57137 58 A - - : 1.38629 1.38629 1.38629 1.38629 0.02107 4.56377 4.56377 1.46634 0.26236 1.09861 0.40547 57 1.68345 2.03336 0.66659 1.77247 59 G - - : 1.38629 1.38629 1.38629 1.38629 0.01059 4.55329 * 1.46634 0.26236 0.00000 * //