INFERNAL1/a [1.1.4 | Dec 2020] NAME PK-PYVV ACC RF01078 DESC 3'-terminal pseudoknot in PYVV STATES 178 NODES 50 CLEN 58 W 73 ALPH RNA RF no CONS yes MAP yes DATE Thu Jun 6 12:05:06 2019 COM [1] /nfs/production/xfam/rfam/rfam_rh7/software/bin/cmbuild -F CM SEED COM [2] /nfs/production/xfam/rfam/rfam_rh7/software/bin/cmcalibrate --cpu 8 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 3 EFFN 2.311523 CKSUM 1850675342 NULL 0.000 0.000 0.000 0.000 GA 65.00 TC 74.60 NC 37.40 EFP7GF -8.6731 0.72156 ECMLC 0.55599 -9.51218 1.50531 1600000 548923 0.002186 ECMGC 0.40920 -17.22438 -2.28495 1600000 180719 0.002213 ECMLI 0.52333 -8.23124 2.68581 1600000 363420 0.003302 ECMGI 0.42996 -12.91851 0.21915 1600000 113559 0.003522 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 73 92 -7.097 -7.304 -0.048 -5.718 IL 1 1 2 1 4 1 15 77 96 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 15 76 95 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - c - - - ML 3 2 3 5 3 1 14 73 92 -8.485 -0.273 -2.561 0.305 0.671 -1.316 -0.376 D 4 2 3 5 3 0 12 71 91 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 15 74 93 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 58 - G - - MR 6 5 3 8 3 1 15 72 91 -8.232 -0.020 -6.550 -1.300 -2.473 1.650 -1.858 D 7 5 3 8 3 0 10 70 89 -7.690 -2.868 -0.221 IR 8 8 3 8 3 1 14 73 92 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 57 - C - - MR 9 8 3 11 3 1 14 71 90 -8.232 -0.020 -6.550 -1.427 1.527 -2.238 -0.906 D 10 8 3 11 3 0 10 69 89 -7.690 -0.452 -1.920 IR 11 11 3 11 3 1 13 72 91 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 56 - G - - MR 12 11 3 14 3 1 13 70 89 -8.485 -0.017 -6.802 -1.874 -3.138 1.782 -2.526 D 13 11 3 14 3 0 7 68 87 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 12 71 90 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 55 - G - - MR 15 14 3 17 3 1 12 69 88 -8.485 -0.017 -6.802 -1.874 -3.138 1.782 -2.526 D 16 14 3 17 3 0 6 67 86 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 11 70 89 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 54 - A - - MR 18 17 3 20 3 1 11 68 87 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 19 17 3 20 3 0 5 66 85 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 10 68 88 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 53 - U - - MR 21 20 3 23 3 1 10 67 86 -8.485 -0.017 -6.802 -1.746 -1.697 -2.492 1.685 D 22 20 3 23 3 0 4 65 84 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 9 67 87 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 52 - A - - MR 24 23 3 26 3 1 10 66 85 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 25 23 3 26 3 0 4 64 83 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 8 66 86 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 51 - A - - MR 27 26 3 29 3 1 9 65 84 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 28 26 3 29 3 0 3 63 82 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 8 65 85 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 50 - A - - MR 30 29 3 32 3 1 8 64 83 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 31 29 3 32 3 0 2 62 81 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 7 64 84 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 49 - U - - MR 33 32 3 35 3 1 7 63 82 -8.485 -0.017 -6.802 -1.746 -1.697 -2.492 1.685 D 34 32 3 35 3 0 1 61 80 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 6 63 83 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 48 - A - - MR 36 35 3 38 3 1 7 62 81 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 37 35 3 38 3 0 1 60 79 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 5 62 82 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 47 - A - - MR 39 38 3 41 3 1 6 61 80 -8.485 -0.017 -6.802 1.018 -1.519 0.151 -0.955 D 40 38 3 41 3 0 0 59 78 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 5 61 81 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 46 - A - - MR 42 41 3 44 3 1 5 60 79 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 43 41 3 44 3 0 0 58 77 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 4 60 80 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 45 - U - - MR 45 44 3 47 3 1 5 59 78 -8.485 -0.017 -6.802 -1.746 -1.697 -2.492 1.685 D 46 44 3 47 3 0 0 57 76 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 3 59 79 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 44 - g - - MR 48 47 3 50 3 1 4 58 77 -8.485 -0.017 -6.802 0.388 -1.628 0.912 -1.041 D 49 47 3 50 3 0 0 56 75 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 3 58 78 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 43 - A - - MR 51 50 3 53 3 1 4 57 76 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 52 50 3 53 3 0 0 55 74 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 2 57 77 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 42 - U - - MR 54 53 3 56 3 1 3 56 75 -8.485 -0.017 -6.802 -1.746 -1.697 -2.492 1.685 D 55 53 3 56 3 0 0 54 73 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 2 56 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 41 - A - - MR 57 56 3 59 3 1 3 55 74 -8.485 -0.017 -6.802 1.773 -2.653 -2.257 -2.223 D 58 56 3 59 3 0 0 53 72 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 1 55 75 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 40 - u - - MR 60 59 3 62 3 1 2 54 73 -8.485 -0.017 -6.802 0.240 -0.912 -1.212 0.892 D 61 59 3 62 3 0 0 52 71 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 1 54 74 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 39 - a - - MR 63 62 3 65 3 1 2 53 72 -8.485 -0.017 -6.802 0.883 -1.006 -1.140 0.267 D 64 62 3 65 3 0 0 51 70 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 1 53 73 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 38 - A - - MR 66 65 3 68 5 1 1 52 71 -7.215 -0.318 -7.030 -2.477 -8.134 1.018 -1.519 0.151 -0.955 D 67 65 3 68 5 0 0 50 70 -5.352 -0.707 -2.978 -4.409 -2.404 IR 68 68 3 68 5 1 1 52 71 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 2 37 G C - - MP 69 68 3 73 6 2 2 51 70 -9.038 -8.977 -0.022 -7.753 -8.033 -8.428 -4.401 -2.933 -4.475 0.421 -4.753 -4.556 -0.200 -4.689 -4.097 3.545 -4.459 -0.622 -0.596 -4.242 -2.220 -3.358 ML 70 68 3 73 6 1 1 49 68 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 3 73 6 1 1 49 69 -8.005 -6.734 -0.586 -6.712 -1.846 -4.926 -0.645 1.116 -1.403 -0.295 D 72 68 3 73 6 0 0 47 66 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 50 70 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 74 74 6 74 5 1 1 50 69 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 24 ] 3 36 G C - - MP 75 74 6 79 6 2 2 49 68 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -5.016 -3.226 -5.146 0.014 -5.618 -4.799 -0.914 -5.405 -4.502 3.698 -4.821 -0.937 -1.292 -4.646 -2.967 -4.019 ML 76 74 6 79 6 1 1 47 66 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 77 74 6 79 6 1 1 47 66 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 78 74 6 79 6 0 0 45 64 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 48 68 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 80 80 6 80 5 1 1 48 67 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 25 ] 4 35 U A - - MP 81 80 6 85 6 2 2 47 66 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -4.524 -4.356 -4.324 -0.628 -3.198 -4.857 1.136 -3.916 -4.326 -0.419 -4.683 -2.244 3.466 -4.661 -0.866 -3.114 ML 82 80 6 85 6 1 1 45 65 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 6 1 1 45 64 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 84 80 6 85 6 0 0 43 62 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 1 46 66 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 86 86 6 86 5 1 1 46 65 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 5 34 A U - - MP 87 86 6 91 6 2 2 45 64 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -4.047 -3.015 -4.045 3.475 -4.514 -5.603 -0.196 -4.069 -3.928 0.802 -4.488 -0.452 -0.613 -4.746 -2.136 -2.865 ML 88 86 6 91 6 1 1 43 63 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 89 86 6 91 6 1 1 43 63 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 90 86 6 91 6 0 0 41 60 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 44 64 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 92 92 6 92 5 1 1 44 63 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 6 33 G C - - MP 93 92 6 97 6 2 2 43 62 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -5.016 -3.226 -5.146 0.014 -5.618 -4.799 -0.914 -5.405 -4.502 3.698 -4.821 -0.937 -1.292 -4.646 -2.967 -4.019 ML 94 92 6 97 6 1 1 42 61 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 95 92 6 97 6 1 1 42 61 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 96 92 6 97 6 0 0 40 60 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 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 98 98 6 98 5 1 1 42 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 28 ] 7 32 A U - - MP 99 98 6 103 4 2 2 41 60 -7.097 -7.304 -0.048 -5.718 -4.047 -3.015 -4.045 3.475 -4.514 -5.603 -0.196 -4.069 -3.928 0.802 -4.488 -0.452 -0.613 -4.746 -2.136 -2.865 ML 100 98 6 103 4 1 1 41 61 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 101 98 6 103 4 1 1 41 60 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 102 98 6 103 4 0 0 40 59 -4.568 -4.250 -2.265 -0.520 IL 103 103 5 103 4 1 1 43 62 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 104 104 6 104 3 1 1 42 61 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 29 ] 8 - A - - - ML 105 104 6 107 3 1 1 38 57 -8.103 -0.019 -6.757 1.773 -2.653 -2.257 -2.223 D 106 104 6 107 3 0 0 37 56 -6.174 -1.687 -0.566 IL 107 107 3 107 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 30 ] 9 - A - - - ML 108 107 3 110 3 1 1 37 56 -8.103 -0.019 -6.757 1.773 -2.653 -2.257 -2.223 D 109 107 3 110 3 0 0 36 55 -6.174 -1.687 -0.566 IL 110 110 3 110 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 10 - A - - - ML 111 110 3 113 3 1 1 36 55 -8.103 -0.019 -6.757 1.773 -2.653 -2.257 -2.223 D 112 110 3 113 3 0 0 35 54 -6.174 -1.687 -0.566 IL 113 113 3 113 3 1 1 38 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 11 - G - - - ML 114 113 3 116 3 1 1 35 54 -8.103 -0.019 -6.757 -1.874 -3.138 1.782 -2.526 D 115 113 3 116 3 0 0 34 53 -6.174 -1.687 -0.566 IL 116 116 3 116 3 1 1 37 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 12 - a - - - ML 117 116 3 119 3 1 1 34 53 -8.485 -0.017 -6.802 0.883 -1.006 -1.140 0.267 D 118 116 3 119 3 0 0 33 51 -5.620 -0.734 -1.403 IL 119 119 3 119 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 34 ] - 31 - U - - MR 120 119 3 122 3 1 1 33 52 -8.485 -0.017 -6.802 -0.849 0.152 -1.621 1.006 D 121 119 3 122 3 0 0 31 50 -6.390 -1.568 -0.620 IR 122 122 3 122 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 35 ] - 30 - C - - MR 123 122 3 125 3 1 1 32 51 -8.485 -0.017 -6.802 -2.081 1.704 -2.912 -1.427 D 124 122 3 125 3 0 0 30 49 -6.390 -1.568 -0.620 IR 125 125 3 125 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 36 ] - 29 - C - - MR 126 125 3 128 3 1 1 31 50 -8.485 -0.017 -6.802 -2.081 1.704 -2.912 -1.427 D 127 125 3 128 3 0 0 29 48 -6.390 -1.568 -0.620 IR 128 128 3 128 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 37 ] - 28 - G - - MR 129 128 3 131 3 1 1 30 49 -8.485 -0.017 -6.802 -1.874 -3.138 1.782 -2.526 D 130 128 3 131 3 0 0 28 47 -6.390 -1.568 -0.620 IR 131 131 3 131 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 38 ] - 27 - C - - MR 132 131 3 134 5 1 1 29 48 -7.215 -0.036 -7.030 -7.243 -8.134 -2.081 1.704 -2.912 -1.427 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 39 ] 13 26 U A - - MP 135 134 3 139 6 2 2 28 47 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -4.524 -4.356 -4.324 -0.628 -3.198 -4.857 1.136 -3.916 -4.326 -0.419 -4.683 -2.244 3.466 -4.661 -0.866 -3.114 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 24 43 -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 40 ] 14 25 G C - - MP 141 140 6 145 6 2 2 26 45 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -5.016 -3.226 -5.146 0.014 -5.618 -4.799 -0.914 -5.405 -4.502 3.698 -4.821 -0.937 -1.292 -4.646 -2.967 -4.019 ML 142 140 6 145 6 1 1 25 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 26 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 41 ] 15 24 G C - - MP 147 146 6 151 6 2 2 24 43 -9.166 -9.105 -0.020 -7.882 -8.162 -8.557 -5.016 -3.226 -5.146 0.014 -5.618 -4.799 -0.914 -5.405 -4.502 3.698 -4.821 -0.937 -1.292 -4.646 -2.967 -4.019 ML 148 146 6 151 6 1 1 23 42 -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 23 42 -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 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 151 151 5 151 6 1 1 24 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 42 ] 16 23 U A - - MP 153 152 6 157 4 2 2 22 41 -7.097 -7.304 -0.048 -5.718 -4.524 -4.356 -4.324 -0.628 -3.198 -4.857 1.136 -3.916 -4.326 -0.419 -4.683 -2.244 3.466 -4.661 -0.866 -3.114 ML 154 152 6 157 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 155 152 6 157 4 1 1 22 41 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 156 152 6 157 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520 IL 157 157 5 157 4 1 1 24 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 158 158 6 158 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 43 ] 17 - g - - - ML 159 158 6 161 3 1 1 19 37 -8.103 -0.019 -6.757 -0.533 -1.220 0.845 0.116 D 160 158 6 161 3 0 0 18 37 -6.174 -1.687 -0.566 IL 161 161 3 161 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 44 ] 18 - U - - - ML 162 161 3 164 3 1 1 17 36 -8.103 -0.019 -6.757 -0.849 0.152 -1.621 1.006 D 163 161 3 164 3 0 0 17 36 -6.174 -1.687 -0.566 IL 164 164 3 164 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 45 ] 19 - u - - - ML 165 164 3 167 3 1 1 16 35 -8.103 -0.019 -6.757 -0.495 -0.961 -0.116 0.891 D 166 164 3 167 3 0 0 16 34 -6.174 -1.687 -0.566 IL 167 167 3 167 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 20 - u - - - ML 168 167 3 170 3 1 1 15 33 -8.103 -0.019 -6.757 0.199 -0.917 -1.228 0.923 D 169 167 3 170 3 0 0 15 33 -6.174 -1.687 -0.566 IL 170 170 3 170 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 47 ] 21 - A - - - ML 171 170 3 173 3 1 1 13 31 -8.103 -0.019 -6.757 1.773 -2.653 -2.257 -2.223 D 172 170 3 173 3 0 0 13 32 -6.174 -1.687 -0.566 IL 173 173 3 173 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 48 ] 22 - A - - - ML 174 173 3 176 2 1 1 1 1 * 0.000 1.018 -1.519 0.151 -0.955 D 175 173 3 176 2 0 0 0 0 * 0.000 IL 176 176 3 176 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 49 ] - - - - - - E 177 176 3 -1 0 0 0 0 0 // HMMER3/f [3.3.2 | Nov 2020] NAME PK-PYVV ACC RF01078 DESC 3'-terminal pseudoknot in PYVV LENG 58 MAXL 139 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Thu Jun 6 12:05:06 2019 COM [1] /nfs/production/xfam/rfam/rfam_rh7/software/bin/cmbuild -F CM SEED NSEQ 3 EFFN 2.469727 CKSUM 1850675342 STATS LOCAL MSV -7.9607 0.72156 STATS LOCAL VITERBI -8.6089 0.72156 STATS LOCAL FORWARD -3.3712 0.72156 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.08075 1.61925 1.46792 1.46011 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 1.17439 0.90332 2.32918 1.66923 1 c - - : 1.38629 1.38629 1.38629 1.38629 0.27796 3.95124 1.49861 1.46634 0.26236 1.09861 0.40547 2 2.33305 2.82116 0.24759 2.76810 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.04954 3.72283 3.72283 1.46634 0.26236 0.15883 1.91831 3 2.61810 3.29419 0.16205 3.22992 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 4 3.02769 1.95393 2.79157 0.28964 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 5 0.31858 2.84287 1.88468 2.76963 5 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 6 2.61867 3.29488 0.16193 3.23087 6 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 7 0.31844 2.84347 1.88479 2.77050 7 A - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 8 0.14501 3.30053 3.01864 3.01073 8 A - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 9 0.14501 3.30053 3.01864 3.01073 9 A - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 10 0.14501 3.30053 3.01864 3.01073 10 A - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 11 2.76307 3.64941 0.13797 3.22473 11 G - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 12 0.76389 2.10368 2.19768 1.20038 12 a - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 13 3.03650 1.95448 2.79557 0.28864 13 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 14 2.62459 3.30208 0.16065 3.24084 14 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 15 2.62483 3.30237 0.16060 3.24124 15 G - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 16 3.03882 1.95462 2.79661 0.28838 16 U - - < 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 17 1.78159 2.26047 0.78230 1.30942 17 g - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 18 2.00821 1.27390 2.54553 0.67806 18 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 19 1.75203 2.07532 1.46282 0.75613 19 u - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 20 1.24936 2.04361 2.26082 0.73504 20 u - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 21 0.14501 3.30053 3.01864 3.01073 21 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 22 0.66926 2.47540 1.27438 2.08602 22 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 23 0.32697 2.98281 1.79158 2.78792 23 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 24 3.44739 0.18994 3.14091 2.32362 24 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 25 3.45218 0.18954 3.14304 2.32453 25 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 26 0.32607 2.98738 1.79210 2.79339 26 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 27 2.92063 0.18702 3.49694 2.44892 27 C - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 28 2.76307 3.64941 0.13797 3.22473 28 G - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 29 2.92063 0.18702 3.49694 2.44892 29 C - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 30 2.92063 0.18702 3.49694 2.44892 30 C - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 31 2.00821 1.27390 2.54553 0.67806 31 U - - - 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 32 2.97103 2.18271 2.64627 0.26775 32 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 33 3.36267 0.19740 3.10233 2.30707 33 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 34 2.92299 2.17624 2.62704 0.27382 34 U - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 35 0.34140 2.91321 1.78347 2.70500 35 A - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 36 3.09920 0.22559 2.97090 2.24795 36 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 37 2.70400 0.32955 2.62060 1.95859 37 C - - > 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 38 0.66926 2.47540 1.27438 2.08602 38 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 39 0.76389 2.10368 2.19768 1.20038 39 a - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 40 1.21998 2.03986 2.24902 0.75669 40 u - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 41 0.14501 3.30053 3.01864 3.01073 41 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 42 2.66751 2.62172 3.18719 0.20259 42 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 43 0.14501 3.30053 3.01864 3.01073 43 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 44 1.11649 2.55266 0.73819 2.14796 44 g - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 45 2.66751 2.62172 3.18719 0.20259 45 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 46 0.14501 3.30053 3.01864 3.01073 46 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 47 0.66926 2.47540 1.27438 2.08602 47 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 48 0.14501 3.30053 3.01864 3.01073 48 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 49 2.66751 2.62172 3.18719 0.20259 49 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 50 0.14501 3.30053 3.01864 3.01073 50 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 51 0.14501 3.30053 3.01864 3.01073 51 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 52 0.14501 3.30053 3.01864 3.01073 52 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 53 2.66751 2.62172 3.18719 0.20259 53 U - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 54 0.14501 3.30053 3.01864 3.01073 54 A - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 55 2.76307 3.64941 0.13797 3.22473 55 G - - : 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547 56 2.76307 3.64941 0.13797 3.22473 56 G - - : 1.38629 1.38629 1.38629 1.38629 0.24369 3.95124 1.62437 1.46634 0.26236 1.09861 0.40547 57 2.44891 0.30295 3.01459 2.07219 57 C - - : 1.38629 1.38629 1.38629 1.38629 0.04791 3.75547 3.75547 1.46634 0.26236 2.50518 0.08519 58 2.35357 3.17850 0.22369 2.75270 58 G - - : 1.38629 1.38629 1.38629 1.38629 0.31018 1.32168 * 0.17084 1.85123 0.00000 * //