INFERNAL1/a [1.1.5 | Sep 2023] 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 Jul 4 17:10:04 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/RF01078/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 2.317383 CKSUM 1850675342 NULL 0.000 0.000 0.000 0.000 GA 65.00 TC 74.60 NC 36.50 EFP7GF -8.6684 0.72157 ECMLC 0.55272 -9.60741 1.49119 1600000 553762 0.002167 ECMGC 0.41139 -17.15395 -2.29095 1600000 180942 0.002211 ECMLI 0.52216 -8.27141 2.67662 1600000 364662 0.003291 ECMGI 0.42837 -12.99454 0.19402 1600000 113667 0.003519 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 73 92 -7.099 -7.306 -0.048 -5.720 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 -8.486 -0.276 -2.545 0.316 0.662 -1.314 -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 -8.231 -0.020 -6.548 -1.296 -2.469 1.649 -1.854 D 7 5 3 8 3 0 10 70 89 -7.702 -2.880 -0.219 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 -8.231 -0.020 -6.548 -1.423 1.526 -2.234 -0.903 D 10 8 3 11 3 0 10 69 89 -7.702 -0.448 -1.932 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 -8.486 -0.017 -6.804 -1.879 -3.143 1.783 -2.530 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 -8.486 -0.017 -6.804 -1.879 -3.143 1.783 -2.530 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 -1.750 -1.701 -2.496 1.686 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 -1.750 -1.701 -2.496 1.686 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 1.011 -1.520 0.163 -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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 -1.750 -1.701 -2.496 1.686 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 -8.486 -0.017 -6.804 0.399 -1.626 0.904 -1.039 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 -1.750 -1.701 -2.496 1.686 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 -8.486 -0.017 -6.804 1.774 -2.657 -2.260 -2.228 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 -8.486 -0.017 -6.804 0.250 -0.912 -1.209 0.885 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 -8.486 -0.017 -6.804 0.876 -1.003 -1.139 0.278 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 -7.217 -0.321 -7.032 -2.460 -8.136 1.011 -1.520 0.163 -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 -9.037 -8.976 -0.022 -7.753 -8.032 -8.427 -4.397 -2.931 -4.471 0.424 -4.747 -4.554 -0.195 -4.684 -4.093 3.543 -4.457 -0.620 -0.591 -4.239 -2.215 -3.353 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 -8.015 -6.744 -0.581 -6.722 -1.856 -4.936 -0.657 1.124 -1.415 -0.303 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -5.020 -3.228 -5.151 0.011 -5.624 -4.800 -0.919 -5.409 -4.505 3.698 -4.823 -0.939 -1.297 -4.649 -2.972 -4.023 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -4.529 -4.361 -4.329 -0.633 -3.201 -4.861 1.133 -3.919 -4.331 -0.424 -4.687 -2.249 3.468 -4.666 -0.869 -3.118 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -4.051 -3.018 -4.048 3.477 -4.519 -5.609 -0.201 -4.072 -3.932 0.798 -4.492 -0.454 -0.618 -4.752 -2.141 -2.868 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -5.020 -3.228 -5.151 0.011 -5.624 -4.800 -0.919 -5.409 -4.505 3.698 -4.823 -0.939 -1.297 -4.649 -2.972 -4.023 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 -7.099 -7.306 -0.048 -5.720 -4.051 -3.018 -4.048 3.477 -4.519 -5.609 -0.201 -4.072 -3.932 0.798 -4.492 -0.454 -0.618 -4.752 -2.141 -2.868 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 -8.105 -0.019 -6.759 1.774 -2.657 -2.260 -2.228 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 -8.105 -0.019 -6.759 1.774 -2.657 -2.260 -2.228 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 -8.105 -0.019 -6.759 1.774 -2.657 -2.260 -2.228 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 -8.105 -0.019 -6.759 -1.879 -3.143 1.783 -2.530 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 -8.486 -0.017 -6.804 0.876 -1.003 -1.139 0.278 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 -8.486 -0.017 -6.804 -0.849 0.163 -1.621 1.000 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 -8.486 -0.017 -6.804 -2.086 1.705 -2.917 -1.431 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 -8.486 -0.017 -6.804 -2.086 1.705 -2.917 -1.431 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 -8.486 -0.017 -6.804 -1.879 -3.143 1.783 -2.530 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 -7.217 -0.036 -7.032 -7.244 -8.136 -2.086 1.705 -2.917 -1.431 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -4.529 -4.361 -4.329 -0.633 -3.201 -4.861 1.133 -3.919 -4.331 -0.424 -4.687 -2.249 3.468 -4.666 -0.869 -3.118 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -5.020 -3.228 -5.151 0.011 -5.624 -4.800 -0.919 -5.409 -4.505 3.698 -4.823 -0.939 -1.297 -4.649 -2.972 -4.023 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 -9.167 -9.106 -0.020 -7.883 -8.162 -8.557 -5.020 -3.228 -5.151 0.011 -5.624 -4.800 -0.919 -5.409 -4.505 3.698 -4.823 -0.939 -1.297 -4.649 -2.972 -4.023 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 -7.099 -7.306 -0.048 -5.720 -4.529 -4.361 -4.329 -0.633 -3.201 -4.861 1.133 -3.919 -4.331 -0.424 -4.687 -2.249 3.468 -4.666 -0.869 -3.118 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 -8.105 -0.019 -6.759 -0.542 -1.236 0.866 0.093 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 -8.105 -0.019 -6.759 -0.849 0.163 -1.621 1.000 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 -8.105 -0.019 -6.759 -0.502 -0.963 -0.140 0.906 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 -8.105 -0.019 -6.759 0.180 -0.920 -1.237 0.937 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 -8.105 -0.019 -6.759 1.774 -2.657 -2.260 -2.228 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 1.011 -1.520 0.163 -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 [3.4 | Aug 2023] 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 Jul 4 17:10:04 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/RF01078/CM NSEQ 3 EFFN 2.469727 CKSUM 1850675342 STATS LOCAL MSV -7.8607 0.72157 STATS LOCAL VITERBI -8.6118 0.72157 STATS LOCAL FORWARD -3.3727 0.72157 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.08113 1.61933 1.46768 1.45975 1.38629 1.38629 1.38629 1.38629 0.03922 3.95124 3.95124 1.46634 0.26236 0.00000 * 1 1.16672 0.91029 2.32581 1.66866 1 c - - : 1.38629 1.38629 1.38629 1.38629 0.28094 3.95124 1.48856 1.46634 0.26236 1.09861 0.40547 2 2.32958 2.81510 0.24896 2.76222 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.04968 3.71998 3.71998 1.46634 0.26236 0.15736 1.92690 3 2.61808 3.29416 0.16205 3.22988 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 3.02764 1.95393 2.79155 0.28965 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 0.31859 2.84285 1.88467 2.76960 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 2.61864 3.29485 0.16193 3.23083 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 2.84346 1.88479 2.77048 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 0.76972 2.10088 2.19627 1.19306 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 3.24083 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 3.24123 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 1.78761 2.27033 0.76803 1.32637 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 2.00676 1.26634 2.54448 0.68280 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 1.75624 2.07561 1.48015 0.74608 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 1.26299 2.04555 2.26653 0.72523 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 0.67429 2.47450 1.26613 2.08460 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 2.00676 1.26634 2.54448 0.68280 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 2.97088 2.18269 2.64621 0.26777 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 3.36228 0.19744 3.10215 2.30699 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 2.92258 2.17619 2.62688 0.27387 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 0.34148 2.91286 1.78343 2.70458 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 3.09765 0.22579 2.97007 2.24757 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 2.70030 0.33069 2.61688 1.95647 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 0.67429 2.47450 1.26613 2.08460 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 0.76972 2.10088 2.19627 1.19306 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 1.21297 2.03906 2.24631 0.76197 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 1.10874 2.54942 0.74487 2.14469 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 0.67429 2.47450 1.26613 2.08460 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 0.24620 3.95124 1.61444 1.46634 0.26236 1.09861 0.40547 57 2.44330 0.30476 3.00874 2.06774 57 C - - : 1.38629 1.38629 1.38629 1.38629 0.04803 3.75307 3.75307 1.46634 0.26236 2.51350 0.08445 58 2.34852 3.17260 0.22507 2.74677 58 G - - : 1.38629 1.38629 1.38629 1.38629 0.30390 1.33915 * 0.17412 1.83383 0.00000 * //