INFERNAL1/a [1.1.5 | Sep 2023] NAME GP_knot2 ACC RF01092 DESC Gag/pol translational readthrough site STATES 187 NODES 56 CLEN 61 W 77 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 12 14:13:10 2024 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/rescan/families/RF01092/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 2 EFFN 1.644531 CKSUM 3477186422 NULL 0.000 0.000 0.000 0.000 GA 80.00 TC 98.50 NC 59.60 EFP7GF -6.7069 0.72408 ECMLC 0.55793 -9.51148 1.80055 1600000 660935 0.001816 ECMGC 0.41069 -19.98339 -5.88665 1600000 130728 0.003060 ECMLI 0.56983 -6.75610 3.29197 1600000 367971 0.003261 ECMGI 0.44773 -14.54532 -2.53004 1600000 86779 0.004609 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 77 96 -6.826 -7.033 -0.058 -5.447 IL 1 1 2 1 4 1 21 81 101 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 20 80 100 -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 20 77 96 -7.852 -0.022 -6.506 -1.281 -1.314 -2.003 1.554 D 4 2 3 5 3 0 15 75 95 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 19 79 99 -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 19 76 95 -7.852 -0.022 -6.506 1.665 -2.146 -1.800 -1.667 D 7 5 3 8 3 0 14 74 94 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 19 78 98 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - G - - - ML 9 8 3 11 3 1 19 75 94 -7.852 -0.022 -6.506 -1.340 -2.520 1.662 -1.906 D 10 8 3 11 3 0 13 73 93 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 18 77 96 -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 18 74 93 -7.852 -0.022 -6.506 -1.340 -2.520 1.662 -1.906 D 13 11 3 14 3 0 12 72 92 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 17 76 95 -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 17 72 92 -7.852 -0.022 -6.506 -1.340 -2.520 1.662 -1.906 D 16 14 3 17 3 0 12 71 91 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 16 74 94 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - C - - - ML 18 17 3 20 3 1 16 71 91 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 19 17 3 20 3 0 11 70 90 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 15 73 93 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - C - - - ML 21 20 3 23 3 1 15 70 90 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 22 20 3 23 3 0 11 69 89 -6.174 -1.687 -0.566 IL 23 23 3 23 3 1 15 72 92 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 8 - G - - - ML 24 23 3 26 3 1 15 69 89 -7.852 -0.022 -6.506 -1.340 -2.520 1.662 -1.906 D 25 23 3 26 3 0 10 68 87 -6.174 -1.687 -0.566 IL 26 26 3 26 3 1 14 71 91 -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 14 68 88 -7.852 -0.022 -6.506 -1.281 -1.314 -2.003 1.554 D 28 26 3 29 3 0 9 67 86 -6.174 -1.687 -0.566 IL 29 29 3 29 3 1 13 70 90 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 10 ] 10 - C - - - ML 30 29 3 32 3 1 13 67 86 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 31 29 3 32 3 0 8 66 85 -6.174 -1.687 -0.566 IL 32 32 3 32 3 1 12 69 89 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 11 - A - - - ML 33 32 3 35 3 1 12 66 85 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 34 32 3 35 3 0 8 65 84 -5.620 -0.734 -1.403 IL 35 35 3 35 3 1 11 67 86 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 61 - C - - MR 36 35 3 38 3 1 11 65 84 -8.250 -0.020 -6.567 -1.471 1.543 -2.285 -0.941 D 37 35 3 38 3 0 6 63 83 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 10 66 85 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 60 - G - - MR 39 38 3 41 3 1 11 64 83 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 40 38 3 41 3 0 5 62 82 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 10 65 84 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 59 - G - - MR 42 41 3 44 3 1 10 63 82 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 43 41 3 44 3 0 4 61 81 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 9 64 83 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 58 - G - - MR 45 44 3 47 3 1 9 62 81 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 46 44 3 47 3 0 4 60 80 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 8 63 82 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 57 - G - - MR 48 47 3 50 3 1 9 61 80 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 49 47 3 50 3 0 3 59 79 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 7 62 81 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 56 - G - - MR 51 50 3 53 3 1 8 60 79 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 52 50 3 53 3 0 2 58 78 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 7 61 80 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 55 - G - - MR 54 53 3 56 3 1 7 59 78 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 55 53 3 56 3 0 2 57 77 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 6 60 79 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 54 - A - - MR 57 56 3 59 3 1 7 58 77 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 58 56 3 59 3 0 1 56 76 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 5 59 78 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 53 - U - - MR 60 59 3 62 3 1 6 57 76 -8.250 -0.020 -6.567 -1.281 -1.314 -2.003 1.554 D 61 59 3 62 3 0 1 55 75 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 5 58 77 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 52 - G - - MR 63 62 3 65 3 1 5 56 75 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 64 62 3 65 3 0 0 54 74 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 4 57 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 51 - G - - MR 66 65 3 68 3 1 5 55 74 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 67 65 3 68 3 0 0 53 73 -6.390 -1.568 -0.620 IR 68 68 3 68 3 1 3 56 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 23 ] - 50 - A - - MR 69 68 3 71 3 1 4 54 73 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 70 68 3 71 3 0 0 52 72 -6.390 -1.568 -0.620 IR 71 71 3 71 3 1 3 55 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 24 ] - 49 - A - - MR 72 71 3 74 3 1 4 53 72 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 73 71 3 74 3 0 0 51 71 -6.390 -1.568 -0.620 IR 74 74 3 74 3 1 2 54 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 25 ] - 48 - U - - MR 75 74 3 77 3 1 3 52 71 -8.250 -0.020 -6.567 -1.281 -1.314 -2.003 1.554 D 76 74 3 77 3 0 0 50 70 -6.390 -1.568 -0.620 IR 77 77 3 77 3 1 2 53 72 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 26 ] - 47 - U - - MR 78 77 3 80 3 1 3 51 70 -8.250 -0.020 -6.567 -1.281 -1.314 -2.003 1.554 D 79 77 3 80 3 0 0 49 69 -6.390 -1.568 -0.620 IR 80 80 3 80 3 1 1 52 71 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 27 ] - 46 - G - - MR 81 80 3 83 3 1 2 50 69 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 82 80 3 83 3 0 0 48 68 -6.390 -1.568 -0.620 IR 83 83 3 83 3 1 1 51 70 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 28 ] - 45 - A - - MR 84 83 3 86 3 1 2 49 68 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 85 83 3 86 3 0 0 47 67 -6.390 -1.568 -0.620 IR 86 86 3 86 3 1 1 50 69 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 29 ] - 44 - A - - MR 87 86 3 89 3 1 2 48 67 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 88 86 3 89 3 0 0 46 66 -6.390 -1.568 -0.620 IR 89 89 3 89 3 1 1 49 68 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 30 ] - 43 - A - - MR 90 89 3 92 3 1 1 47 66 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 91 89 3 92 3 0 0 45 65 -6.390 -1.568 -0.620 IR 92 92 3 92 3 1 1 48 67 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 31 ] - 42 - A - - MR 93 92 3 95 3 1 1 46 65 -8.250 -0.020 -6.567 1.665 -2.146 -1.800 -1.667 D 94 92 3 95 3 0 0 44 64 -6.390 -1.568 -0.620 IR 95 95 3 95 3 1 1 47 66 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 32 ] - 41 - U - - MR 96 95 3 98 3 1 1 45 64 -8.250 -0.020 -6.567 -1.281 -1.314 -2.003 1.554 D 97 95 3 98 3 0 0 43 63 -6.390 -1.568 -0.620 IR 98 98 3 98 3 1 1 46 65 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 33 ] - 40 - C - - MR 99 98 3 101 3 1 1 44 63 -8.250 -0.020 -6.567 -1.471 1.543 -2.285 -0.941 D 100 98 3 101 3 0 0 42 62 -6.390 -1.568 -0.620 IR 101 101 3 101 3 1 1 45 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 34 ] - 39 - G - - MR 102 101 3 104 3 1 1 43 62 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 103 101 3 104 3 0 0 41 61 -6.390 -1.568 -0.620 IR 104 104 3 104 3 1 1 44 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 35 ] - 38 - G - - MR 105 104 3 107 3 1 1 42 61 -8.250 -0.020 -6.567 -1.340 -2.520 1.662 -1.906 D 106 104 3 107 3 0 0 40 60 -6.390 -1.568 -0.620 IR 107 107 3 107 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 36 ] - 37 - A - - MR 108 107 3 110 5 1 1 41 60 -6.996 -0.042 -6.811 -7.023 -7.915 1.665 -2.146 -1.800 -1.667 D 109 107 3 110 5 0 0 40 59 -5.352 -0.707 -2.978 -4.409 -2.404 IR 110 110 3 110 5 1 1 41 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 37 ] 12 36 G C - - MP 111 110 3 115 6 2 2 40 59 -9.062 -9.001 -0.022 -7.778 -8.058 -8.453 -4.525 -2.991 -4.607 0.342 -4.927 -4.607 -0.345 -4.832 -4.183 3.582 -4.536 -0.683 -0.737 -4.325 -2.371 -3.487 ML 112 110 3 115 6 1 1 38 58 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 113 110 3 115 6 1 1 38 58 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 114 110 3 115 6 0 0 36 55 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 115 115 5 115 6 1 1 40 59 -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 39 59 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 38 ] 13 35 G C - - MP 117 116 6 121 6 2 2 38 57 -9.062 -9.001 -0.022 -7.778 -8.058 -8.453 -4.525 -2.991 -4.607 0.342 -4.927 -4.607 -0.345 -4.832 -4.183 3.582 -4.536 -0.683 -0.737 -4.325 -2.371 -3.487 ML 118 116 6 121 6 1 1 36 56 -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 36 56 -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 34 53 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 121 121 5 121 6 1 1 38 57 -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 37 57 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 39 ] 14 34 G C - - MP 123 122 6 127 6 2 2 36 55 -9.062 -9.001 -0.022 -7.778 -8.058 -8.453 -4.525 -2.991 -4.607 0.342 -4.927 -4.607 -0.345 -4.832 -4.183 3.582 -4.536 -0.683 -0.737 -4.325 -2.371 -3.487 ML 124 122 6 127 6 1 1 34 54 -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 34 54 -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 32 51 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 127 127 5 127 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 128 128 6 128 5 1 1 35 55 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 40 ] 15 33 U A - - MP 129 128 6 133 6 2 2 34 53 -9.062 -9.001 -0.022 -7.778 -8.058 -8.453 -3.960 -3.777 -3.823 -0.090 -2.816 -4.408 1.506 -3.495 -3.831 0.201 -4.215 -1.683 3.206 -4.120 -0.498 -2.677 ML 130 128 6 133 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 131 128 6 133 6 1 1 32 52 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 132 128 6 133 6 0 0 30 50 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 133 133 5 133 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 134 134 6 134 5 1 1 33 53 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 41 ] 16 32 U A - - MP 135 134 6 139 6 2 2 32 51 -9.062 -9.001 -0.022 -7.778 -8.058 -8.453 -3.960 -3.777 -3.823 -0.090 -2.816 -4.408 1.506 -3.495 -3.831 0.201 -4.215 -1.683 3.206 -4.120 -0.498 -2.677 ML 136 134 6 139 6 1 1 31 51 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 137 134 6 139 6 1 1 31 50 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 138 134 6 139 6 0 0 29 49 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 139 139 5 139 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 140 140 6 140 5 1 1 31 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 17 31 C G - - MP 141 140 6 145 4 2 2 30 49 -6.826 -7.033 -0.058 -5.447 -4.325 -4.209 -4.052 -0.463 -2.821 -4.492 3.475 -3.608 -4.094 -0.188 -4.378 -2.154 0.715 -4.408 -0.523 -2.942 ML 142 140 6 145 4 1 1 30 50 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 143 140 6 145 4 1 1 30 49 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 144 140 6 145 4 0 0 29 48 -4.568 -4.250 -2.265 -0.520 IL 145 145 5 145 4 1 1 32 51 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 146 146 6 146 3 1 1 31 50 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 43 ] 18 - U - - - ML 147 146 6 149 3 1 1 27 46 -8.250 -0.020 -6.567 -1.281 -1.314 -2.003 1.554 D 148 146 6 149 3 0 0 26 45 -5.620 -0.734 -1.403 IL 149 149 3 149 3 1 1 28 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 44 ] - 30 - U - - MR 150 149 3 152 5 1 1 26 45 -6.996 -0.042 -6.811 -7.023 -7.915 -1.281 -1.314 -2.003 1.554 D 151 149 3 152 5 0 0 25 44 -5.352 -0.707 -2.978 -4.409 -2.404 IR 152 152 3 152 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 19 29 C G - - MP 153 152 3 157 4 2 2 25 44 -6.826 -7.033 -0.058 -5.447 -4.325 -4.209 -4.052 -0.463 -2.821 -4.492 3.475 -3.608 -4.094 -0.188 -4.378 -2.154 0.715 -4.408 -0.523 -2.942 ML 154 152 3 157 4 1 1 26 45 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 155 152 3 157 4 1 1 25 45 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 156 152 3 157 4 0 0 24 44 -4.568 -4.250 -2.265 -0.520 IL 157 157 5 157 4 1 1 27 46 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 158 158 6 158 3 1 1 26 45 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 20 - C - - - ML 159 158 6 161 3 1 1 22 41 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 160 158 6 161 3 0 0 21 40 -6.174 -1.687 -0.566 IL 161 161 3 161 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 21 - C - - - ML 162 161 3 164 3 1 1 21 40 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 163 161 3 164 3 0 0 20 39 -6.174 -1.687 -0.566 IL 164 164 3 164 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 48 ] 22 - G - - - ML 165 164 3 167 3 1 1 20 39 -7.852 -0.022 -6.506 -1.340 -2.520 1.662 -1.906 D 166 164 3 167 3 0 0 19 38 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 49 ] 23 - C - - - ML 168 167 3 170 3 1 1 19 38 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 169 167 3 170 3 0 0 18 37 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 50 ] 24 - C - - - ML 171 170 3 173 3 1 1 18 36 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 172 170 3 173 3 0 0 17 36 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 51 ] 25 - C - - - ML 174 173 3 176 3 1 1 16 35 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 175 173 3 176 3 0 0 16 34 -6.174 -1.687 -0.566 IL 176 176 3 176 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 52 ] 26 - U - - - ML 177 176 3 179 3 1 1 15 33 -7.852 -0.022 -6.506 -1.281 -1.314 -2.003 1.554 D 178 176 3 179 3 0 0 15 33 -6.174 -1.687 -0.566 IL 179 179 3 179 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 53 ] 27 - C - - - ML 180 179 3 182 3 1 1 13 32 -7.852 -0.022 -6.506 -1.471 1.543 -2.285 -0.941 D 181 179 3 182 3 0 0 13 32 -6.174 -1.687 -0.566 IL 182 182 3 182 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 54 ] 28 - C - - - ML 183 182 3 185 2 1 1 1 1 * 0.000 -1.471 1.543 -2.285 -0.941 D 184 182 3 185 2 0 0 0 0 * 0.000 IL 185 185 3 185 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 55 ] - - - - - - E 186 185 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME GP_knot2 ACC RF01092 DESC Gag/pol translational readthrough site LENG 61 MAXL 148 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 12 14:13:10 2024 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/rescan/families/RF01092/CM NSEQ 2 EFFN 1.503906 CKSUM 3477186422 STATS LOCAL MSV -8.0319 0.72408 STATS LOCAL VITERBI -9.0739 0.72408 STATS LOCAL FORWARD -2.8600 0.72408 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.47630 1.38426 1.17456 1.55091 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.20137 2.23766 2.69729 0.33512 1 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 0.25424 2.79246 2.56124 2.45321 2 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.22773 3.03072 0.26138 2.60427 3 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.22773 3.03072 0.26138 2.60427 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.22773 3.03072 0.26138 2.60427 5 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.31079 0.35147 2.86977 1.96288 6 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.31079 0.35147 2.86977 1.96288 7 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.22773 3.03072 0.26138 2.60427 8 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.20137 2.23766 2.69729 0.33512 9 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.31079 0.35147 2.86977 1.96288 10 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 0.25424 2.79246 2.56124 2.45321 11 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 2.29986 2.76291 0.26113 2.71153 12 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.30248 2.76532 0.26028 2.71509 13 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.30347 2.76623 0.25996 2.71645 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.52328 1.58607 2.21363 0.50125 15 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.52319 1.58607 2.21360 0.50127 16 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 2.76004 0.37792 2.47266 1.78939 17 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.20137 2.23766 2.69729 0.33512 18 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 2.75498 0.37881 2.47068 1.78865 19 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.31079 0.35147 2.86977 1.96288 20 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.31079 0.35147 2.86977 1.96288 21 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 2.22773 3.03072 0.26138 2.60427 22 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.31079 0.35147 2.86977 1.96288 23 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 2.31079 0.35147 2.86977 1.96288 24 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.31079 0.35147 2.86977 1.96288 25 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 26 2.20137 2.23766 2.69729 0.33512 26 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 27 2.31079 0.35147 2.86977 1.96288 27 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 28 2.31079 0.35147 2.86977 1.96288 28 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 29 2.06454 2.64087 0.32658 2.52030 29 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 30 2.20137 2.23766 2.69729 0.33512 30 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 31 2.06212 2.63822 0.32767 2.51666 31 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 32 0.57163 2.38882 1.42249 2.27746 32 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 33 0.57153 2.38908 1.42246 2.27785 33 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 34 2.93986 0.30268 2.59665 2.01165 34 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 35 2.94156 0.30243 2.59729 2.01199 35 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 36 2.94350 0.30215 2.59803 2.01236 36 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 37 0.25424 2.79246 2.56124 2.45321 37 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 38 2.22773 3.03072 0.26138 2.60427 38 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 39 2.22773 3.03072 0.26138 2.60427 39 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 40 2.31079 0.35147 2.86977 1.96288 40 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 41 2.20137 2.23766 2.69729 0.33512 41 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 42 0.25424 2.79246 2.56124 2.45321 42 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 43 0.25424 2.79246 2.56124 2.45321 43 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 44 0.25424 2.79246 2.56124 2.45321 44 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 45 0.25424 2.79246 2.56124 2.45321 45 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 46 2.22773 3.03072 0.26138 2.60427 46 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 47 2.20137 2.23766 2.69729 0.33512 47 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 48 2.20137 2.23766 2.69729 0.33512 48 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 49 0.25424 2.79246 2.56124 2.45321 49 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 50 0.25424 2.79246 2.56124 2.45321 50 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 51 2.22773 3.03072 0.26138 2.60427 51 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 52 2.22773 3.03072 0.26138 2.60427 52 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 53 2.20137 2.23766 2.69729 0.33512 53 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 54 0.25424 2.79246 2.56124 2.45321 54 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 55 2.22773 3.03072 0.26138 2.60427 55 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 56 2.22773 3.03072 0.26138 2.60427 56 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 57 2.22773 3.03072 0.26138 2.60427 57 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 58 2.22773 3.03072 0.26138 2.60427 58 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 59 2.22773 3.03072 0.26138 2.60427 59 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 60 2.22773 3.03072 0.26138 2.60427 60 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 61 2.31079 0.35147 2.86977 1.96288 61 C - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //