INFERNAL1/a [1.1.5 | Sep 2023] NAME PK-SPCSV ACC RF01091 DESC 3'-terminal pseudoknot in SPCSV STATES 187 NODES 51 CLEN 61 W 76 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 6 20:55:56 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/RF01091/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 1.589844 CKSUM 998912730 NULL 0.000 0.000 0.000 0.000 GA 36.00 TC 36.40 NC 35.90 EFP7GF -5.2250 0.72491 ECMLC 0.57092 -8.14555 2.42361 1600000 500949 0.002395 ECMGC 0.41818 -15.46715 -1.47856 1600000 138856 0.002881 ECMLI 0.54901 -6.41120 3.90096 1600000 345088 0.003477 ECMGI 0.44386 -11.13110 1.29693 1600000 99491 0.004020 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 76 95 -6.802 -7.009 -0.059 -5.423 IL 1 1 2 1 4 1 16 80 100 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 16 79 99 -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 15 76 95 -8.229 -0.020 -6.546 -1.418 1.524 -2.229 -0.898 D 4 2 3 5 3 0 11 75 94 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 15 77 96 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 61 - C - - MR 6 5 3 8 3 1 14 75 94 -8.229 -0.020 -6.546 -1.418 1.524 -2.229 -0.898 D 7 5 3 8 3 0 9 73 93 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 14 76 95 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 60 - U - - MR 9 8 3 11 3 1 14 74 93 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 10 8 3 11 3 0 8 72 92 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 13 75 94 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 59 - G - - MR 12 11 3 14 3 1 13 73 92 -8.229 -0.020 -6.546 -1.291 -2.463 1.647 -1.849 D 13 11 3 14 3 0 7 71 91 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 12 74 93 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 58 - G - - MR 15 14 3 17 3 1 12 72 91 -8.229 -0.020 -6.546 -1.291 -2.463 1.647 -1.849 D 16 14 3 17 3 0 6 70 90 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 11 73 92 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 57 - A - - MR 18 17 3 20 3 1 11 71 90 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 19 17 3 20 3 0 5 69 89 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 10 72 91 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 56 - U - - MR 21 20 3 23 3 1 10 70 89 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 22 20 3 23 3 0 4 68 88 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 10 71 90 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 55 - C - - MR 24 23 3 26 3 1 10 69 88 -8.229 -0.020 -6.546 -1.418 1.524 -2.229 -0.898 D 25 23 3 26 3 0 4 67 87 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 9 70 89 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 54 - A - - MR 27 26 3 29 3 1 9 68 87 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 28 26 3 29 3 0 3 66 86 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 8 69 88 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 53 - A - - MR 30 29 3 32 3 1 8 67 86 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 31 29 3 32 3 0 2 65 85 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 7 68 87 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 52 - U - - MR 33 32 3 35 3 1 7 66 85 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 34 32 3 35 3 0 1 64 84 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 6 67 86 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 51 - A - - MR 36 35 3 38 3 1 7 65 84 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 37 35 3 38 3 0 1 63 83 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 5 66 85 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 50 - A - - MR 39 38 3 41 3 1 6 64 83 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 40 38 3 41 3 0 0 62 82 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 5 65 84 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 49 - A - - MR 42 41 3 44 3 1 5 63 82 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 43 41 3 44 3 0 0 61 81 -6.390 -1.568 -0.620 IR 44 44 3 44 3 1 4 64 83 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 15 ] - 48 - U - - MR 45 44 3 47 3 1 5 62 81 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 46 44 3 47 3 0 0 60 80 -6.390 -1.568 -0.620 IR 47 47 3 47 3 1 3 63 82 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 16 ] - 47 - U - - MR 48 47 3 50 3 1 4 61 80 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 49 47 3 50 3 0 0 59 79 -6.390 -1.568 -0.620 IR 50 50 3 50 3 1 3 62 81 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 17 ] - 46 - U - - MR 51 50 3 53 3 1 4 60 79 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 52 50 3 53 3 0 0 58 78 -6.390 -1.568 -0.620 IR 53 53 3 53 3 1 2 61 80 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 18 ] - 45 - A - - MR 54 53 3 56 3 1 3 59 78 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 55 53 3 56 3 0 0 57 77 -6.390 -1.568 -0.620 IR 56 56 3 56 3 1 2 60 79 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 19 ] - 44 - U - - MR 57 56 3 59 3 1 3 58 77 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 58 56 3 59 3 0 0 56 76 -6.390 -1.568 -0.620 IR 59 59 3 59 3 1 1 59 78 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 20 ] - 43 - G - - MR 60 59 3 62 3 1 2 57 76 -8.229 -0.020 -6.546 -1.291 -2.463 1.647 -1.849 D 61 59 3 62 3 0 0 55 75 -6.390 -1.568 -0.620 IR 62 62 3 62 3 1 1 58 77 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 21 ] - 42 - A - - MR 63 62 3 65 3 1 2 56 75 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 64 62 3 65 3 0 0 54 74 -6.390 -1.568 -0.620 IR 65 65 3 65 3 1 1 57 76 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 22 ] - 41 - U - - MR 66 65 3 68 5 1 1 55 74 -6.976 -0.042 -6.791 -7.004 -7.895 -1.240 -1.281 -1.960 1.540 D 67 65 3 68 5 0 0 54 73 -5.352 -0.707 -2.978 -4.409 -2.404 IR 68 68 3 68 5 1 1 55 74 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 23 ] 2 40 G C - - MP 69 68 3 73 6 2 2 54 73 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -4.481 -2.971 -4.560 0.371 -4.865 -4.589 -0.293 -4.781 -4.152 3.569 -4.509 -0.661 -0.686 -4.295 -2.317 -3.441 ML 70 68 3 73 6 1 1 52 72 -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 52 72 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 3 73 6 0 0 50 69 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 54 73 -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 53 72 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 24 ] 3 39 G C - - MP 75 74 6 79 6 2 2 52 71 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -4.481 -2.971 -4.560 0.371 -4.865 -4.589 -0.293 -4.781 -4.152 3.569 -4.509 -0.661 -0.686 -4.295 -2.317 -3.441 ML 76 74 6 79 6 1 1 50 70 -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 50 70 -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 48 67 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 52 71 -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 51 70 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 25 ] 4 38 U A - - MP 81 80 6 85 6 2 2 50 69 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -3.916 -3.731 -3.784 -0.047 -2.787 -4.373 1.534 -3.463 -3.792 0.252 -4.178 -1.639 3.179 -4.077 -0.470 -2.642 ML 82 80 6 85 6 1 1 48 68 -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 48 68 -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 46 65 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 85 85 5 85 6 1 1 50 69 -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 49 68 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 26 ] 5 37 U A - - MP 87 86 6 91 6 2 2 48 67 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -3.916 -3.731 -3.784 -0.047 -2.787 -4.373 1.534 -3.463 -3.792 0.252 -4.178 -1.639 3.179 -4.077 -0.470 -2.642 ML 88 86 6 91 6 1 1 46 66 -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 46 66 -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 44 63 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 91 91 5 91 6 1 1 48 67 -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 47 66 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 27 ] 6 36 U A - - MP 93 92 6 97 6 2 2 46 65 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -3.916 -3.731 -3.784 -0.047 -2.787 -4.373 1.534 -3.463 -3.792 0.252 -4.178 -1.639 3.179 -4.077 -0.470 -2.642 ML 94 92 6 97 6 1 1 44 64 -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 44 64 -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 42 61 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 97 97 5 97 6 1 1 46 65 -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 45 64 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 28 ] 7 35 U A - - MP 99 98 6 103 6 2 2 44 63 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -3.916 -3.731 -3.784 -0.047 -2.787 -4.373 1.534 -3.463 -3.792 0.252 -4.178 -1.639 3.179 -4.077 -0.470 -2.642 ML 100 98 6 103 6 1 1 43 62 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 101 98 6 103 6 1 1 42 62 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 102 98 6 103 6 0 0 40 60 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 103 103 5 103 6 1 1 44 63 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 104 104 6 104 5 1 1 43 62 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 29 ] 8 34 C G - - MP 105 104 6 109 6 2 2 42 61 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -4.280 -4.160 -4.014 -0.419 -2.794 -4.460 3.458 -3.577 -4.055 -0.136 -4.344 -2.104 0.745 -4.366 -0.495 -2.905 ML 106 104 6 109 6 1 1 41 61 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 107 104 6 109 6 1 1 41 60 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 108 104 6 109 6 0 0 39 59 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 109 109 5 109 6 1 1 42 61 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 110 110 6 110 5 1 1 41 61 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 30 ] 9 33 C G - - MP 111 110 6 115 4 2 2 40 59 -6.802 -7.009 -0.059 -5.423 -4.280 -4.160 -4.014 -0.419 -2.794 -4.460 3.458 -3.577 -4.055 -0.136 -4.344 -2.104 0.745 -4.366 -0.495 -2.905 ML 112 110 6 115 4 1 1 40 60 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 113 110 6 115 4 1 1 40 59 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 114 110 6 115 4 0 0 39 58 -4.568 -4.250 -2.265 -0.520 IL 115 115 5 115 4 1 1 42 61 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 116 116 6 116 3 1 1 41 60 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 31 ] 10 - U - - - ML 117 116 6 119 3 1 1 37 56 -7.829 -0.023 -6.483 -1.240 -1.281 -1.960 1.540 D 118 116 6 119 3 0 0 36 55 -6.174 -1.687 -0.566 IL 119 119 3 119 3 1 1 40 59 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 32 ] 11 - A - - - ML 120 119 3 122 3 1 1 36 55 -7.829 -0.023 -6.483 1.653 -2.101 -1.760 -1.617 D 121 119 3 122 3 0 0 35 54 -6.174 -1.687 -0.566 IL 122 122 3 122 3 1 1 39 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 33 ] 12 - A - - - ML 123 122 3 125 3 1 1 35 54 -7.829 -0.023 -6.483 1.653 -2.101 -1.760 -1.617 D 124 122 3 125 3 0 0 34 53 -6.174 -1.687 -0.566 IL 125 125 3 125 3 1 1 38 57 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 34 ] 13 - A - - - ML 126 125 3 128 3 1 1 34 53 -7.829 -0.023 -6.483 1.653 -2.101 -1.760 -1.617 D 127 125 3 128 3 0 0 33 52 -6.174 -1.687 -0.566 IL 128 128 3 128 3 1 1 36 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 35 ] 14 - U - - - ML 129 128 3 131 3 1 1 33 52 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 130 128 3 131 3 0 0 32 50 -5.620 -0.734 -1.403 IL 131 131 3 131 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 36 ] - 32 - U - - MR 132 131 3 134 3 1 1 32 51 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 133 131 3 134 3 0 0 30 49 -6.390 -1.568 -0.620 IR 134 134 3 134 3 1 1 33 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 37 ] - 31 - U - - MR 135 134 3 137 3 1 1 31 50 -8.229 -0.020 -6.546 -1.240 -1.281 -1.960 1.540 D 136 134 3 137 3 0 0 29 48 -6.390 -1.568 -0.620 IR 137 137 3 137 3 1 1 32 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 38 ] - 30 - C - - MR 138 137 3 140 3 1 1 30 49 -8.229 -0.020 -6.546 -1.418 1.524 -2.229 -0.898 D 139 137 3 140 3 0 0 28 47 -6.390 -1.568 -0.620 IR 140 140 3 140 3 1 1 31 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 39 ] - 29 - C - - MR 141 140 3 143 3 1 1 29 48 -8.229 -0.020 -6.546 -1.418 1.524 -2.229 -0.898 D 142 140 3 143 3 0 0 27 46 -6.390 -1.568 -0.620 IR 143 143 3 143 3 1 1 30 48 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 40 ] - 28 - A - - MR 144 143 3 146 3 1 1 28 47 -8.229 -0.020 -6.546 1.653 -2.101 -1.760 -1.617 D 145 143 3 146 3 0 0 26 45 -6.390 -1.568 -0.620 IR 146 146 3 146 3 1 1 29 47 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 41 ] - 27 - G - - MR 147 146 3 149 5 1 1 27 45 -6.976 -0.042 -6.791 -7.004 -7.895 -1.291 -2.463 1.647 -1.849 D 148 146 3 149 5 0 0 25 44 -5.352 -0.707 -2.978 -4.409 -2.404 IR 149 149 3 149 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 42 ] 15 26 C G - - MP 150 149 3 154 6 2 2 26 44 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -4.280 -4.160 -4.014 -0.419 -2.794 -4.460 3.458 -3.577 -4.055 -0.136 -4.344 -2.104 0.745 -4.366 -0.495 -2.905 ML 151 149 3 154 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 152 149 3 154 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 153 149 3 154 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 154 154 5 154 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 155 155 6 155 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 43 ] 16 25 G C - - MP 156 155 6 160 6 2 2 24 42 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -4.481 -2.971 -4.560 0.371 -4.865 -4.589 -0.293 -4.781 -4.152 3.569 -4.509 -0.661 -0.686 -4.295 -2.317 -3.441 ML 157 155 6 160 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 158 155 6 160 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 159 155 6 160 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 160 160 5 160 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 161 161 6 161 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 44 ] 17 24 U A - - MP 162 161 6 166 6 2 2 22 40 -9.053 -8.993 -0.022 -7.769 -8.049 -8.444 -3.916 -3.731 -3.784 -0.047 -2.787 -4.373 1.534 -3.463 -3.792 0.252 -4.178 -1.639 3.179 -4.077 -0.470 -2.642 ML 163 161 6 166 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 164 161 6 166 6 1 1 21 40 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 165 161 6 166 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 166 166 5 166 6 1 1 22 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 167 167 6 167 5 1 1 21 40 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 45 ] 18 23 C G - - MP 168 167 6 172 4 2 2 20 38 -6.802 -7.009 -0.059 -5.423 -4.280 -4.160 -4.014 -0.419 -2.794 -4.460 3.458 -3.577 -4.055 -0.136 -4.344 -2.104 0.745 -4.366 -0.495 -2.905 ML 169 167 6 172 4 1 1 21 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 170 167 6 172 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 171 167 6 172 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 172 172 5 172 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 173 173 6 173 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 46 ] 19 - G - - - ML 174 173 6 176 3 1 1 16 35 -7.829 -0.023 -6.483 -1.291 -2.463 1.647 -1.849 D 175 173 6 176 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 47 ] 20 - U - - - ML 177 176 3 179 3 1 1 15 33 -7.829 -0.023 -6.483 -1.240 -1.281 -1.960 1.540 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 48 ] 21 - G - - - ML 180 179 3 182 3 1 1 13 32 -7.829 -0.023 -6.483 -1.291 -2.463 1.647 -1.849 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 49 ] 22 - A - - - ML 183 182 3 185 2 1 1 1 1 * 0.000 1.653 -2.101 -1.760 -1.617 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 50 ] - - - - - - E 186 185 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME PK-SPCSV ACC RF01091 DESC 3'-terminal pseudoknot in SPCSV LENG 61 MAXL 148 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 6 20:55:56 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/RF01091/CM NSEQ 2 EFFN 1.566406 CKSUM 998912730 STATS LOCAL MSV -7.6545 0.72491 STATS LOCAL VITERBI -9.0258 0.72491 STATS LOCAL FORWARD -3.1768 0.72491 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.28159 1.53616 1.44582 1.30325 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.35334 0.33560 2.91455 1.99651 1 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.32247 2.80274 0.25179 2.75016 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.32503 2.80515 0.25099 2.75372 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 2.55507 1.60774 2.25104 0.48340 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.55538 1.60773 2.25114 0.48335 5 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.55526 1.60773 2.25110 0.48337 6 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.55498 1.60774 2.25101 0.48342 7 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.79335 0.36456 2.51208 1.81290 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.79293 0.36463 2.51191 1.81284 9 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.23380 2.26407 2.73185 0.32317 10 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 0.24398 2.82877 2.59391 2.49273 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 0.24398 2.82877 2.59391 2.49273 12 A - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 0.24398 2.82877 2.59391 2.49273 13 A - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.23380 2.26407 2.73185 0.32317 14 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.78771 0.36551 2.50983 1.81206 15 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.32514 2.80526 0.25095 2.75387 16 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 2.55516 1.60773 2.25107 0.48338 17 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.79441 0.36438 2.51250 1.81306 18 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 2.26683 3.07680 0.24893 2.65052 19 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.23380 2.26407 2.73185 0.32317 20 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.26683 3.07680 0.24893 2.65052 21 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 0.24398 2.82877 2.59391 2.49273 22 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.08681 2.67896 0.31562 2.55169 23 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 0.55063 2.42776 1.44419 2.31022 24 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.97955 0.29192 2.63764 2.03387 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 2.08852 2.68087 0.31488 2.55428 26 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 27 2.26683 3.07680 0.24893 2.65052 27 G - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 28 0.24398 2.82877 2.59391 2.49273 28 A - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 29 2.35334 0.33560 2.91455 1.99651 29 C - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 30 2.35334 0.33560 2.91455 1.99651 30 C - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 31 2.23380 2.26407 2.73185 0.32317 31 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 32 2.23380 2.26407 2.73185 0.32317 32 U - - - 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 33 2.08557 2.67758 0.31617 2.54982 33 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 34 2.08579 2.67782 0.31607 2.55016 34 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 35 0.55096 2.42687 1.44424 2.30894 35 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 36 0.55087 2.42711 1.44423 2.30928 36 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 37 0.55076 2.42739 1.44421 2.30970 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 0.55063 2.42774 1.44419 2.31019 38 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 39 2.97943 0.29194 2.63760 2.03385 39 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 40 2.98162 0.29164 2.63844 2.03427 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 2.23380 2.26407 2.73185 0.32317 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 0.24398 2.82877 2.59391 2.49273 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 2.26683 3.07680 0.24893 2.65052 43 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 44 2.23380 2.26407 2.73185 0.32317 44 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 45 0.24398 2.82877 2.59391 2.49273 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 2.23380 2.26407 2.73185 0.32317 46 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 47 2.23380 2.26407 2.73185 0.32317 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 2.23380 2.26407 2.73185 0.32317 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 0.24398 2.82877 2.59391 2.49273 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 0.24398 2.82877 2.59391 2.49273 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 0.24398 2.82877 2.59391 2.49273 51 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 52 2.23380 2.26407 2.73185 0.32317 52 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 53 0.24398 2.82877 2.59391 2.49273 53 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 54 0.24398 2.82877 2.59391 2.49273 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 2.35334 0.33560 2.91455 1.99651 55 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 56 2.23380 2.26407 2.73185 0.32317 56 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 57 0.24398 2.82877 2.59391 2.49273 57 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 58 2.26683 3.07680 0.24893 2.65052 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 2.26683 3.07680 0.24893 2.65052 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 2.23380 2.26407 2.73185 0.32317 60 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 61 2.35334 0.33560 2.91455 1.99651 61 C - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //