# STOCKHOLM 1.0
#=GF ID IRES_Pesti
#=GF AC RF00209
#=GF DE Pestivirus internal ribosome entry site (IRES) including 5'UTR SLI
#=GF AU Tautz N; 0000-0002-2398-4968
#=GF GA 180.0
#=GF NC 71.2
#=GF TC 185.8
#=GF PI Pesti_IRES
#=GF SE Kevin Lamkiewicz, Sandra Triebel, Manja Marz
#=GF SS AnchoRNA, LocARNA, ViennaRNA Package, manual curation
#=GF TP Cis-reg; IRES;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF CL CL00017
#=GF DR SO; 0000243; internal_ribosome_entry_site;
#=GF DR GO; 0043022; ribosome binding;
#=GF RN [1]
#=GF RM 11142379
#=GF RT Ribosomal binding to the internal ribosomal entry site of classical swine
#=GF RT fever virus.
#=GF RA Kolupaeva VG, Pestova TV, Hellen CU
#=GF RL RNA 2000;6:1791-1807.
#=GF RN [2]
#=GF RM 8388102
#=GF RT 5' and 3' untranslated regions of pestivirus genome: primary and secondary
#=GF RT structure analyses.
#=GF RA Deng R, Brock KV
#=GF RL Nucleic Acids Res. 1993;21:1949-1957.
#=GF RN [3]
#=GF RM 35380920
#=GF RT Insights into the secondary and tertiary structure of the Bovine Viral
#=GF RT Diarrhea Virus Internal Ribosome Entry Site.
#=GF RA Gosavi D, Wower I, Beckmann IK, Hofacker IL, Wower J, Wolfinger MT,
#=GF RA Sztuba-Solinska J
#=GF RL RNA Biol. 2022;19:496-506.
#=GF RN [4]
#=GF RM 7831836
#=GF RT Pestivirus translation initiation occurs by internal ribosome entry.
#=GF RA Poole TL, Wang C, Popp RA, Potgieter LN, Siddiqui A, Collett MS
#=GF RL Virology. 1995;206:750-754.
#=GF RN [5]
#=GF RM 32512856
#=GF RT Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by 
#=GF RT Horizontal Gene Transfer.
#=GF RA Arhab Y, Bulakhov AG, Pestova TV, Hellen CUT
#=GF RL Viruses. 2020;12:612.
#=GF RN [6]
#=GF RM 10846062
#=GF RT A stem-loop motif formed by the immediate 5' terminus of the bovine viral 
#=GF RT diarrhea virus genome modulates translation as well as replication of the
#=GF RT viral  RNA.
#=GF RA Yu H, Isken O, Grassmann CW, Behrens SE
#=GF RL J Virol. 2000;74:5825-5835.
#=GF CC This family represents the internal ribosome entry site (IRES) of the the
#=GF CC pestiviruses. The pestivirus IRES allows cap and end-independent
#=GF CC translation of mRNA in the host cell. The IRES achieves this by mediating
#=GF CC the internal initiation of translation by recruiting a ribosomal 43S
#=GF CC pre-initiation complex directly to the initiation codon and eliminates the
#=GF CC requirement for eIF4F [1]. The classical swine virus UTR described in [1]
#=GF CC appears to be longer at the 5' end than other pestivirus UTRs. This family
#=GF CC represents the conserved core.
#=GF WK Pestivirus_internal_ribosome_entry_site_(IRES)
#=GF SQ 42

NC_076029.1/1-385 --------GUAUACGAGAACUAGAUAAAAUA------------------------CUCGUAUAC-AUAUUGGACAACAGAAAAUAACU------------------------------AUUAGGCC--UAGGGAAUGAAUC-----------CCUCUC---AGCGAAGGCCGAAAGGAGGCUAGCCA-UGCCCUUAGUAG
NC_001461.1/1-385 --------GUAUACGAGAAUUAGAAAAGGCA------------------------CUCGUAUAC-GUAUUGGGCAAUUAAAAAUAAUA------------------------------AUUAGGCC--UAGGGAACAAAUC-----------CCUCUC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
KC853440.1/1-384  --------GUAUACGAGAUUUAGAAAAGUCU------------------------CUCGUAUAC-ACAUUGGACAUAACAAAAUAACA------------------------------AUUAGGCC--UAGGGAACGAAUC-----------CCUCUC---AGCGAAGGCCGAAAAGAGGUUAACCA-UACCCUUAGUAG
M96687.1/1-383    ------AUGUAUACGAGAAUUUGCCUAAC--------------------------CUCGUAUAC-AUAUUGGGCAUUCUAAAA-AUAA------------------------------AUUAGGCC--UAAGGGACAAAUC-----------CUCCUU---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
KT951841.1/1-376  ----------------GAAUUAGAAAAAGCU------------------------CCUGUAUAC-AGAUUGGGCAAUUAAAAAUUGAAG-----------------------------AUUAGGCC--UAGGGAA-AAAUC-----------CCUCUC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
KX577637.1/1-376  ---------------AGAUUUAGG-AAAGCU------------------------CUCGUAUGC-AUAUUGGGCAAUCUAAAAUAAUA------------------------------AUUAGACC--UAGGGAAC-AAUC-----------CCUCUC---AGCGAAGGCCGAAAGGAGGCUAGCCA-UGCCCUUAGUAG
MW054939.1/1-350  -----------------------------------------------------------------GGAUUGGGCAAACUAAAUAAUA-------------------------------AUUAGGCC--UAGGGAACAAAUC-----------CUCCAC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
NC_076032.1/1-385 --------GUAUACGAGAUUAGCUAAAGUA-------------------------CUCGUAUAU-GGAUUGGACGUCAACAAAUUUUU-----------------------------AAUUGGCAAGUCAGGGAACCUU-------------CCCCUC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
NC_039237.1/1-385 --------GUAUACGAGAUUAGCUAAAGUA-------------------------CUCGUAUAC-GGAUUGGACGUCGACAAACUUUG-----------------------------AAUUGGCAACACAGGGAACCUU-------------CCCCUC---GGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
MH231152.1/1-356  -----------------------------------------------------------------GGAUUGGGUGUUGGCAAACAGUU-----------------------------AAUUAGUGAAGUAGGGAACCUUCC-----------CCCCUC---UGCGAAGGCCGAAAAGAGGCUAACCA-UGCCCUUAGUAG
MH806436.1/1-371  ------------------------AAAGUA-------------------------CUCGUAUAC-GGAUUGGACGUUGACAAAAUAUUG----------------------------AAUUGAAAAUGUAGGGAAUCUU-------------CCCCUC---AGCGAAGGCCGAAAAGAGGCUAACCA-CGCCCUUAGUAG
HG426490.1/1-379  ----------------GAUUAGAUAAAGUA-------------------------CUCGUAUAC-AGAUUGGAUAUUGACAAAACAUUG----------------------------AAUUGGCGAAGUAGGGAACUUUU------------CCCCUC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
MK599227.1/1-343  -----------------------------------------------------------------------------GGCAAAACAUUG----------------------------AAUUGAUAAGGUAGGGAACUUU-------------CCCCUC---AGCGAAGGCCGAAAAGAGGCUAGCCA-UGCCCUUAGUAG
NC_003678.1/1-382 --------GUAUACGAGUUUAGCUCAAUC--------------------------CUCGUAUACAAUAUUGGGCGUCACCAAAUAUAG------------------------------AUUUGGCA--UAGGCAACA---------------CCCCGA---UGCGAAGGCCGAAAAG-GGCUAACCA-UGCCCUUAGUAG
NC_012812.1/1-383 ------GUAUACGCCCAGUUAGUUCAGG---------------------------UGGACGUGUACGAUUGGGUAUCCCAAAUUAAUA------------------------------AUUUGGUU--UAGGGACUAAA-------------UCCCCU---GGCGAAGGCCGAAACA-GGUUAACCA-UACCUUUAGUAG
NC_038912.1/1-373 --------GUAUACGAGGUUAGUUCAUU---------------------------CUCGUAUGCAUGAUUGGACAAAUUAAAAUUUCA------------------------------AUUUGGAU--CAGGG--CCU--------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCACAGUAG
NC_002657.1/1-373 --------GUAUACGAGGUUAGUUCAUU---------------------------CUCGUAUGCAUGAUUGGACAAAUCAAAAUUUCA------------------------------AUUUGGUU--CAGGG--CCU--------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCACAGUAG
OM817567.1/1-312  --------------------------------------------------------------------------------------------------------------------------------CAGGG--CCU--------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCUCACAGUAG
GU233732.1/1-373  --------GUAUACGAGGUUAGCUCGUU---------------------------CUCGUAUACGAUAUCGGAUACACU-AAAUUUCG------------------------------AUUUGGUC--UAGGGCAC----------------CCCUCC---AGCGACGGCCGAAAUG-GGCUAGCCA-UGCCCAUAGUAG
KP343640.1/1-372  --------GUAUACGAGGUUAGCUCGUC---------------------------CUCGUGUACAAAAUUGGACAAAUU-AAAUUCUG------------------------------AUUCGACC--UAGGGCAU----------------CCCUCC---AGCGACGGCCAACCUG-GGCUAGCCA-UGCCCACAGUAG
AY805221.1/1-374  --------GUAUACGAGGUUAGUUCAUU---------------------------CUCGUAUACACGAUUGGACAAAUCAAAAUUAUA------------------------------AUUUGGUU--CAGGG--CCU--------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCAUAGUAG
AY775178.1/1-373  --------GUAUACGAGGUUAGUUCAUU---------------------------CUCGUAUGCAUGAUUGGACAAAACAAAAUUUCA------------------------------AUUUGGUU--CAGGG--CCC--------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCAUAGUAG
MG387218.1/1-372  --------GUAUACGAGGUUAGUUCAUU---------------------------CUCGUAUACAAUAUUGGACAAACA-AAAUUCCU------------------------------AUUUGGCU--UAGGACAC----------------CCCUCC---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCACAGUAG
NC_003679.1/1-372 --------GUAUACGGGAGUAGCUCAUG---------------------------CCCGUAUACAAAAUUGGAUAUUCCAAAACUC-------------------------------GAUU-GGGU--UAGGGAGC----------------CCUCCU---AGCGACGGCCGAACCG-UGUUAACCA-UACACGUAGUAG
MF102261.1/1-377  --------GUAUACGAGAGUAGUUCAUG---------------------------CUCGUAUACAGAAUUGGAUAUUCUAAAAUUUGUU----------------------------AAUU-GGAC--UAGGGUCU----------------CCUCCU---GGCGACGGCCGAACCG-GGUUAGCCA-UACCCGUAGUAG
NC_018713.1/1-377 --------GUAUACGAGAUUAGCUCAUA---------------------------CUCGUGUACAA-AUUGGACGUAGCAAAUUUAAA-----------------------------AAUU-CGGA--UAGGGUCC----------------CCAUCC---AGCGACGGCCGAACGG-GGUUAACCA-UACCUCUAGUAG
MZ664274.1/1-374  --------GUAUACGAAGUUAGCUCAUUU--------------------------UUCGUAUACAAAAUUGGACAGUGAAAAUUUUGU-----------------------------GAUU-CGAC--UAGGGACC----------------CCCUCC---AGCGACGGCCGAACUA-GGCUAGCCA-UGCCUAUAGUAG
NC_077023.1/1-351 -------------------------------------------------------CUCGUGUACAAAAUUGGGCAUAU-AAAUUUCU------------------------------GAUU-CGAU--UAGGGAAU----------------CCCUCU---AGCGACGGCCGAACUG-GGCUAGCCA-UGCCCAUAGUAG
NC_023176.1/1-399 UACGCGGGGUAUAACGACAGUAGUUCAAGUG------------------------UCGUUAUGCAUCAUUGGCCAUAACAAAUUAUCU-----------------------------AAUUUGGAA--UAGGGACCUG--------------CGACCU--GUACGAAGGCCGAGCGU-CGGUAGCCAUUCCGACUAGUAG
NC_035432.1/1-381 --------GUAUAGCAGCAGUAGCUCAAGG-------------------------CUGCUAUACGA--UUGGACAUACC-AAAUUCCA------------------------------AUUGGUGU--UAGGGA------------------CCACCU--AGGUGAAGGCCGACGAC-AGGUAGCCAUUCCUGUUAGUAG
NC_077026.1/1-382 ------GUAUACACAAGGUUAGCUCAAUCC-------------------------AUUGUGUGUACGAUUGGAUGUUGCAAAUUUAUA------------------------------AUUUGAGAUAUAGGGACCCAU-------------UCAUCA--CAGCGAAGGCCGAACAA-GGGUAGCCAAUCCCUUCAUUAG
NC_077024.1/1-412 --------GUAUGAAGAUAAAUCAAAGAGGUGAGAGUGGAUUACCACAGCAACCCGCUUCAUACACAUUGGACUAUACCAAACUGAUCUUUAGG---------------------UAGAUUGG--AUAUGUAAAAAGAAC------------AGCAUUAGGGGUGAAGGGCGAAAGGAUGUUAGCCA-UACACCGAGUAG
ON024093.1/1-359  -----------------------------------------------------------UCAUACAUAUUGGUUAUACCAAAUUAAAGUUUAGG---------------------UAAAUUGG--AUAUACCAAACAAU-------------AGCAUUAGGGGUGAAGGGCGAAAGGACGUUAGCCA-UACGCCAAGUAG
ON024108.1/1-360  ---------------------------------------------------------CUUCAUACACAUUGGCCAUGUCCAAAGAGUU---AGG---------------------CAAAUUGGAAA--UACCAAAUGAAC------------AGCACUAGGGGUGAAGGGCGAAAGAAUGCUAGCCA-UGCAUCAAGUAG
MK216749.1/1-385  AUAUGGGGCAUAAUGCAUAGAUUGGC-----------------------------UGCAUUAUG--UGUAUAACAUCCCAA-------------------------------------AUUGCCAUAG------------------------GCUCUGUGGUGAG--UGGGGGAAAGGGGUUAACCA-GGCCUCUAGUAC
MN099165.1/1-376  --------CAUAAUGCUUAGAUUGGC-----------------------------UGCAUUAUG--UGUGGGACAUCCUAA-------------------------------------AUUUUUAUGA------------------------GCCCUGUGGUGAG--UGGGGGAAAGGGGUUAACCA-GGCCUCUAGUAC
MN584738.1/1-353  ----------------------------------------------------------------AAUGUAAGGGACUCCUAA------------------------------------AUUGCUAUAA------------------------GCCCUGCGGUGAG--UGGGGGAAAGGGGUUAACCA-GGCCUCUAGUAC
NC_077015.1/1-391 -------UGCAUAACCCUGAUUGUAAUUGGCU-----------------------GGGUUAUGCAUGUGAGAACG---CAAAAUUUUU---------------------------UAAAUUAUGUUA-------------------------CCGGCUUUGAGGU--UGGCGGACCAGAGUUAACCA-GGCUCUCAGUAC
OU592965.1/1-358  --------------------------------------------------------------------UGUAACAUCACAAAGUCACC----------------------------AAAUUUGCU---------------------------CCAGCUACGAGGU--UGGCGGACCGGAGUUAACCA-GGCUCCCAGUAC
NC_077001.1/1-426 --------GUAUAAGGGAUGGGA--------------------------------UCCUUGUACAUUUCAUACCUCUACCGAACAGUAUUUGGGAGUUCUUUUUACCUGCCGUACAGUAUUGGG-AUUUAAACAACUAAAUGUUUACAAAU-CACGUGUGUGGUG--GCGGGGAUAGACCGU-GCCA-GCGGUUGUGUAC
NC_025677.1/1-399 --------GUAUAAGGGUUGGGA--------------------------------ACCUUGUACCAAGCUACCUC-UGCCAUUCAGU-------------------------------AUUUGGG-AGUAGAAGUAGAUGUGUUUACAAACUCACACGUGUGGGG--GCGGGGAUAGACUGU-GCCA-GCGGUCGUGUAC
NC_077000.1/1-383 -------UGUAUAAGGAAGGGGUGGGAG------------------------CCUUCCCUAUACUUGUUUACAAA-UACCAUACAGUG-------------------------------UUACAGCAGUGUGUA-------GUUUACUAU--GCAGGUUUGAAGG--GCGGGGAUAGUCUGU-GCCA-GCAGACGUGUAC
#=GC SS_cons      ........<<<<<<<<<___________...........................>>>>>>>>>::::::::::::::::::::::::..............................::::::::..::::::::::..............<<<<<<..--<<---<<<<---<<<-<<<______._>>>>>>---->
#=GC RF           ........GuauAcgggauuaguuaaau...........................cccgUauaCaauaUuGgacAuuacaAAauuaua..............................AUUuggau..UAgGgAacaa..............cccccc..gaGcGAagGccGAAaggagGcUAGCCA.ugCcccuAGUAg

NC_076029.1/1-385 GACUAGC-------AUAAUGAGGGGGGUAGCAACAGUGGUGAGUUCGUUGGAUGGCUUA-AGCCCUGAGUACAGGGUAGUCGUC-AGUGGUUCGACGCCUCGGUAU---------------AAAGGUCUCGAGAUGCCAC-GUGGACGAGGGCACGCCC-AAAGC-ACAUCUUAACCUGAGCGGGGGUCGCCCAGGCAA-
NC_001461.1/1-385 GACUAGC-------AUAAUGAGGGGGGUAGCAACAGUGGUGAGUUCGUUGGAUGGCUUA-AGCCCUGAGUACAGGGUAGUCGUC-AGUGGUUCGACGCCUUGGAAU---------------AAAGGUCUCGAGAUGCCAC-GUGGACGAGGGCAUGCCC-AAAGC-ACAUCUUAACCUGAGCGGGGGUCGCCCAGGUAA-
KC853440.1/1-384  GACUAGC--------AAACGAGAGGGGUAGCAAUGGUGGUGAGUUCGUUGGAUGGCUGA-AGCCCUGAGUACAGGGUAGUCGUC-AAUGGUUCGACACCUAUGGAA--------------CGUAGGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-ACAGC-ACAUCUUAACUUUGGCAGGGGUCGCCAAAGUGA-
M96687.1/1-383    GACUAGC-------AAAACAAGGAGGGUAGCAACAGUGGUGAGUUCGUUGGAUGGCUGA-AGCCCUGAGUACAGGGUAGUCGUC-AGUGGUUCGACGCUUCGUGUG---------------ACAAGCCUCGAGGUGCCAC-GUGGACGAGGGCAUGCCC-ACAGC-ACAUCUUAACCUGAGCGGGGGUCGUUCAGGUGA-
KT951841.1/1-376  GACUAGC-------AAAAUGAGAGGGGUAGCAACAGUGGUGAGUUCAUUGGAUGGCUGA-AGCCCUGAGUACAGGGUAGUCGUC-AGUGGUUCGACACCUCGGAAA---------------GAAGGUCUCGAGAUGCCAC-GUGGACGAGGGCAUGCCC-ACAGC-ACAUCUUAACCUGGACGGGGGUCGCCCAGGUAA-
KX577637.1/1-376  GACUAGC-------AAAAUGAGGGGGGUAGCAUCAGUGGUGAGUUCGUUGGAUGGCUGA-AGCCCUGAGUACAGGGCAGUCGUC-AGUGGUUCGACGCCUAGGAU---------------GAUAGGUCUCGAGAUGCCAC-GUGGACGAGGGCAUGCCC-ACAGC-ACAUCUUAGCCCGAGCGGGGGUCGCCCGGGUGA-
MW054939.1/1-350  GACUAGC-------AUAUUGUGGAGGGUAGCAACAGUGGUGAGUUAGUUGGAUGGCUGA-AGCCCUGAGUACAGGGUAGUCGUC-AGUGGUUCGACGCCU-UGGGA--------------UAUAGGCCUCGAGAUGCCAC-GUGGACGAGGGCAUGCCC-ACAGC-ACAUCUUAGCCUGAGCAGGGGUCGCCCAGGCAA-
NC_076032.1/1-385 GACUAGC-------CAAAGGAGGGGACUAGCGGUAGCAGUGAGUUCAUUGGAUGGCCGA-ACCCCUGAGUACAGGGGAGUCGUC-AAUGGUUCGACACUCCAUCAGC------------UGAGGAGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-ACGGC-ACAUCUUAACCUAUGCGGGGGUUGCAUGGGUGA-
NC_039237.1/1-385 GACUAGC-------CAAAGGAGGGGACUAGCGGUAGCAGUGAGUCCAUUGGAUGGCCGA-ACCCCUGAGUACAGGGGAGUCGUC-AAUGGUUCGACACUCCUUUAGU------------CGAGGAGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-ACGGC-ACAUCUUAACCCACGCGGGGGUUGCGUGGGUGA-
MH231152.1/1-356  GACUAGC-------AAAAAGAGGGGGCUAGCGGUAGCAGUGAGUUUAUUGGAUGGCCGA-AUCCCUGAGUACAGGGAAGUCGUC-AAUGGUUCGACACUCUGGUAAU------------AUAAGAGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-ACGGC-ACAUCUUAACCUAUGCGGGGGUUGCAUGGGUGA-
MH806436.1/1-371  GACUAGC-------AAAAGGAGGGGACUAGCGGUAGCAGUGAGUUCAUUGGAUGGCCGA-ACCCCUGAGUACAGGGGAGUCGUC-AAUGGUUCGACACUCCUUCAGU------------UGAGGAGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-ACGGC-ACAUCUUAACCCAUGCGGGGGCUGCAUGGGUGA-
HG426490.1/1-379  GACGAGC-------AAAAUGAGGGGACUAGCGGUAGCAGUGAGUUCAUUGGAUGGCCUA-AUCCCUGAGUACAGGGAAGUCGUC-AAUGGUUCGACACUCCAUCAGU------------UGAGGAGUCUCGAGAUGCCAU-GUGGACGAGGGCAUGCCC-AAGGC-ACAUCUUAACCUAUGCGGGGGUUGCAUAGGCAA-
MK599227.1/1-343  GACUAGC-------AAAAGGAGGGGACUAGCGGUAGCAGUGAGUUCAUUGGAUGGCCGA-AUCCCUGAGUACAGGGAAGUCGUC-AAUGGUUCGACACUCCAUCAGU------------CGAGGAGUCUCGAGAUGCCAU-GUGGACGAGGGCUUGCCC-ACGGC-ACAUCUUAACCUAUGCGGGGGUUGCAUAGGUGA-
NC_003678.1/1-382 GACUAGC------AAAAAAUCGGGGACUAGCCCAGGUGGUGAGCUUCCUGGAUGACCGA-AGCCCUGAGUACAGGGCAGUCGUC-AACAGUUCAACACGCAGAAUAG------------GUUUGCGUCUUGAUAUGCUGU-GUGGACGAGGGCAUGCCC-ACGGU-ACAUCUUAACCUAUCCGGGGGUCGGAUAGGCGA-
NC_012812.1/1-383 GACGAGC--------AUAAUGGGGGACUAGUGGUGGCAGUGAGCUCCCUGGAUCACCGA-AGCCCCGAGUACGGGGUAGUCGUC-AAUGGUUCGACGCAUCAAGG-----------------AAUGCCUCGAGAUGCCAU-GUGGACGAGGGCGUGCCC-ACGGU-GUAUCUUAACCCAGGCGGGGGCCGCUUGGGUGA-
NC_038912.1/1-373 GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGAA---------------GCCCACCUCGAUAUGCUAU-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
NC_002657.1/1-373 GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGAA---------------GCCCACCUCGAGAUGCUAU-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
OM817567.1/1-312  GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCGGAA---------------GCCCACCUCGAGAUGCUAU-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
GU233732.1/1-373  GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCACCA---------------GCCCACCUCGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
KP343640.1/1-372  GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGGA---------------GCCCACCUUGAGAUGCUAU-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUGGCGGGGGUCGCUAGGGUGA-
AY805221.1/1-374  GACUAGC-------AAAACGGAGGGACUAGCCAUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGAA---------------GCCCACCUCGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
AY775178.1/1-373  GACUAGC--------AAACGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGAA---------------GCCCACCUCGAGAUGCUAU-GUGGACGAGGGCAUGCCC-AAGAC-GCACCUUAACCCUAGCGGGGGUCGCUAGGGUGA-
MG387218.1/1-372  GACUAGC--------AGAUGGAGGGACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUUUA-AGUCCUGAGUACAGGACAGUCGUC-AGUAGUUCGACGUGAGCAGGA---------------GCCCACCUCGAGAUGCUAU-GUGGACGAGGGCAUGCCC-AAAAC-ACACCUUAACCCUGGCGGGGGUCGCCAGGGUGA-
NC_003679.1/1-372 GACUAGC--------AGACGGGAGGACUAGCCAUCGUGGUGAGAUCCCUGAGCAGUCUA-AAUCCUGAGUACAGGAUAGUCGUC-AGUAGUUCAACGCAGGCACGG---------------UUCUGCCUUGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-UUGCUUUAAUCUCGGCGGGGGUCGCCGAGGUGA-
MF102261.1/1-377  GACUAGC--------AUAUGGGAGGACUAGCUUUCGUGGUGAGGUUCCUGAGUGGUCUA-AGUCCUGAGUACAGGAUAGUCGUC-AGUAGUUCGACACAAACGGAG--------------UUUUAGUCUCGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-UCACUUUAAUCCUGGCGGGGGUCGCCAGGGUGA-
NC_018713.1/1-377 GACUAGC--------AGACGGAUGGACUAGCCACAGUGGUGAGCUCCCUGGGAGGUCUA-AGUUCUGAGUACAGAACAGUCGUC-AGUAGUUCAACGCUGGUAAAC---------------CCCAGCCUUGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-ACACCUUAACCUGGACGGGGGUCGUCCAGGUGA-
MZ664274.1/1-374  GACUAGC--------AAACGGAGGGACUAGCCACAGUGGUGAGCUCCCUGGGUAGUCUA-AGCCCUGAGUACAGGGCAGUCGUC-AGUAGUUCGACACAGGCAAGG---------------GCCUGUCUCGAGAUGCUAC-GUGGACGAGGGCGUGCCC-AAGAC-AUACCUUAACCCGGGCGGGGGUCGCUCGGGUAA-
NC_077023.1/1-351 GACUAGC--------AAACGGAGGGACUAGCCGUAGCGGUGAGCUCCCUGGGAAGUCUA-AGCCCUGAGUACAGGGUAGUCGUC-AGUAGUUCGACGUGGACGAGA---------------GUCCAUCUCGAGAUGCUAC-GUGGACGAGGGCAUGCCC-AAGAC-AUACCUUAACCCAGGCGGGGGUCGUCUGGGUGA-
NC_023176.1/1-399 GACUAGU------ACAAAUAGGUCAACUGGUUGAGCAGGUGAGUGUGCUGCAGCGGCUA-AGCGGUGAGUACACCGUAUUCGUCAACAGGUGCUACUGGAAAGGAU---------------CACCCACUAGCGAUGCCUGUGUGGACGAGGACAUGUCC-AAGCC--AAUGUUAUCAGUAGCGGGGGUCGUUACUGAGA-
NC_035432.1/1-381 GACGAAC-------CGUUAUGGUGGACUGGUUGCUCAGGUGAGCAGGCUGCAAUGCGUA-AGUGGUGAGUACACCACAGCCGUC-AAAGGUGCCACUGGUAAGGAU---------------CACCCACUGGCGAUGCCUU-GUGGACGGGGGCGUGCCC-AACGC--AAUGUUAGCGGUGGCGGGGGCUGCCAUCGUGA-
NC_077026.1/1-382 GACUAGC-------ACAAGUGAUGGACUGGAGACGUGGAUGAGUGAGCUGUAGAGAGGA-AGUGGUGAGUACACCACAGUCGUC-AAGAGUACUACCGGUAAGGAU---------------CACCCGCUAGUUAUGCUCU-GUGGACGAGGGCAUGCCC-ACCUU-CUCUACUAGAUACCCCGGGGGUUGGGGUGUCGA-
NC_077024.1/1-412 CACUAGC----CCUGAUAAUAUGCGAGAGCCCCAACC--UGAGUAGAUGAGGAAGGCCGUAGCAGUGAGUACACUGUAGCCAAC-AAGGUUCCUACUGGUAAGGAU---------------CACCCACUAGGUAUGACCU-GUAGUUGGGGGCAUGCCC-AGGCC--AUCCUUAAUGCAACCGGGGGUUGGUUGCAUGA-
ON024093.1/1-359  CACUAAC----CCUGAUCAUAUGCGAGAGCCCCAACC--UGAGUAGAUGAGGA-GGCCGUAGCAGUGAGAACACUGCAGCCAAC-AAGGUUCCUACUGGUAAGGAU---------------CACCCACUAGGUAUGACCU-GUAGUUGGGGGCGUGCCC-AGGCC--AUCCUUAAUGCAAUCGGGGGUCGGUUGCAUGA-
ON024108.1/1-360  CACAAAC----CCUGAAGAUGUGCGAGAGCCCCAACC--UGAGUAGAUGAGGGAAGCCGUAGCAGUGAGUACACUGUAGCCAAC-AAGGUUCCUACUGGUAAGGAU---------------CACCCACUAGGUAUGACCU-GUAGUUGGGGGCGUGCCC-AGGCU--UACCUUAAUGUAACUGGGGGUCGGUUACAUGA-
MK216749.1/1-385  CACAGGC--ACC-AUUUAACAGGGCAACUCAAACCUGAGAGAGAGGUA-CCGAACUCUUAAGCCUCGAGUACGGGGCAGACGUCACCGAGUAGUACACCCAACGACCACCACAUUUAGGUGUAGGGUCUACUGAGGCUCGGGUGGACGUGGGCAUGCCCAAAGAGAAAACGGUGGGGGACCUGGGGGUCGGGUCCGCCA-
MN099165.1/1-376  CACAGGC--ACC-AAUGGACAGGGCAACUCGAACCUGAGAGAGAGGUA-CCGAACUCUUAAGUCCCGAGUACGGGGCAGACGUCACCGAGUAGUACACCCAAAGACCACCACUUUUAGGUGUAGGGUCUACUGAGGCUCGGGUGGACGUGGGCGUGCCCAAAGAGAAAUCGGUGGUGGACCCGGGGGUCGGGACCACCA-
MN584738.1/1-353  CACAGGC--ACC-UAUGGACAGGGCAACUCAAACCUGAGAGAGAGGUA-CCGAACUCUUAAGUCCCGAGUACGGGGCAGACGUCACCGAGUAGUACACCCAAAGACCACCAUUUGUAGGUGUAGGGUCUACUGAGGCUCGGGUGGACGUGGGCGUGCCCAAAGAGAAAUCGGUGGUGGACCCGGGGGUCGGGGCCACCA-
NC_077015.1/1-391 GACACCC--UCCUAAACAAAGUCGGAACUGCUGACUAGGAGACUAUGC-ACUCAGCACUAAGCCCGGAGUACCGGGCAUUCUACU-ACAGCUCUGCACUCAACGACGGCU--CUUGAGGCCUAGAGUCCAGGAUGGCUGUGUAAGUAGAGGACAUGUCCAAGUGUGA--GGUGUAAUCCGGUGGGGGUUGCCGGAUUUG-
OU592965.1/1-358  GACACCCUCUCGACUAAAUGGCUGGAACUGCUAACUAGGAGACCAUGC-AUGAAGCACUAAGUCCGGAGUACCGGGCAUUCUACU-GCAGCUCUGCACUCAACGACGGUCUCGGAACGGCCUAGAGUCCAGGAUAGCUGUGUAGGUAGAGGACAUGUCCAAGUGUGU--AGUGUGGCCCAGCGGGGGUUGCUGGGUCUG-
NC_077001.1/1-426 CAGCAAU---CACAAACAACACGUGGACUGCAAUCCAGGAGAGCACCU-AGGUCUGUU-AAGUUGUGAGUACACGACAU-UCGUCAAUGAGUCAGCUGGUAAGGAU---------------CACCCACCUGGAUACUCAUGUGGACGAGGGA-GUUUCCCAAACAGUAACCUACUCUGGGGGAGGGG-UCCCCCAGAGAC
NC_025677.1/1-399 CAGCACC----UACGCAUACGUGUGGACUGCGAACCAGGAGAGCACCU-AGGUCUGAC-AAGCUGUGAGAACACAGUAG-UCGUCAGUGAGUCAGCUGGUAAGGAU---------------CACCCACCUGGAUACUCACGUGGACGAGGGA-GUUUCCCAGUCAGAAACCUACACCAGAGGAGGGG-UCCUCUGGAGAC
NC_077000.1/1-383 CAGCACU---UCAGAAGGAACCUGCAACUGCGAACCGGGAGAGCAUCU-AGAGCCCCU-AAGCUGUGAGUACACAGCAG-CCGUCAGAGAGUCAGCUGGAAAGGAU---------------CACCCACCUGGAAGCUCUCGUGGACGGGGUC-AUAGACCAAGGGCAACUCUAUUGAGGAGGUGGGGUACCUCUUCA---
#=GC SS_cons      >->>->>.......----->>>>>>{{{{{{{{{{{{{{[[-[[[[[[,(((((((((,.,<<<<<<____>>>>>>,,<<<<<.-<<<<<<<<<-<<<<<<____...............>>>>>>->>>>--->>>>>.--->>>>><<<____>>>.,)))).-))))),,<<<<<<<<<<___>>>>>>>>>>,,.
#=GC RF           gACcAgC.......aAaAaggggggacugGccaccgcGGuGAgcucccUggguggccua.AgcccuGAGUACagggcAGuCguC.AgugGuuCgaCgcgcccggAu...............gggcgcCucGagAugCcac.GUGGacGaGGGCAUGCCC.Aaggc.AcaccuUagcccgggcgGGGGUcgcccgggcgA.

NC_076029.1/1-385 ---AAGCAGAUCGACCA-AUCUGUU------ACGAAUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGUAU-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
NC_001461.1/1-385 ---AAGCAGUUUUAACC-GACUGUU------ACGAAUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGUAU-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
KC853440.1/1-384  ---AAGUGGCCUAACC--AACCACU------ACGAACACAGCCUGAUAGGGU-GCUGCAGAGGCCCACCUUCU-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
M96687.1/1-383    ---AAGCGGUUUAACC--AACCGCU------ACGAAUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGUAU-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
KT951841.1/1-376  ---AAGCAGUUUAACU--AACUGUU------AUGGACACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGCAU-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
KX577637.1/1-376  ---AAACGGUAAAUACA-GACCGCU------ACGAAUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGUAA-UGCUACUAAAAA---ACUCUGCUGUACAUGGCAC
MW054939.1/1-350  ---AAGCGGAUAAAA---UACCGUU------ACUAACACAGCCUGAUAGGGU-GCUGCAGAGGCCCACUGCAC-UGCUACUAAAAA---UCUCUGCUGUACAUGGCAC
NC_076032.1/1-385 ---AAGCGCCAUUC---GUGGCGUU------AUGGACACAGCCUGAUAGGGU-GUAGCAGAAGCCUGCUAUUC-CGCUAGUAAAA----ACUCUGCUGUACAUGGCAC
NC_039237.1/1-385 ----AAGCGCCAUUCG-UGGCGUC-------AUGGACACAGCCUGAUAGGGU-GUAGCAGAGACCUGCUACUC-CGCUAGUAAAA----ACUCUGCUGUACAUGGCAC
MH231152.1/1-356  ----AAGCACCAUUUA-CGGUGUU-------AUAAACACAGCCUGAUAGGGU-GUAGCAGAGACCUGCUAUCC-CGCUAGUAAAA----ACUCUGCUGUACAUGGCAC
MH806436.1/1-371  ----AAGCGCCAUUCG-UGGCGUU-------AUGGACACAGCCUGAUAGGGU-GUAGCAGAGACCUGCUAUCC-CGCUAGUAAAAA---ACUCUGCUGUACAUGGCAC
HG426490.1/1-379  ----AAGCACCACUCA-CGGUGUU-------GUGGACACAGCCUGAUAGGGU-GUAGCAGAGACCUGCUAUUC-CGCUAGUAAAA----ACUCUGCUGUACAUGGCAC
MK599227.1/1-343  ----AAGCACCAUUCA-UGGUGUU-------AUGGACACAGCCUGAUAGGGU-GUAGCAGAGACCUGCUAUUC-CGCUAGUAAAA----ACUCUGCUGUACAUGGCAC
NC_003678.1/1-382 -----AAGUCCAGUAU-UGGACU--------GGGAGUACAGCCUGAUAGGGU-GUUGCAGAGACCCAUCUGAUAGGCUAGUAUAAAAA-ACUCUGCUGUACAUGGCAC
NC_012812.1/1-383 --AAUAGGGUUGUUAUACAAGCCUUU-----GGGAGUACAGCCUGAUAGGGU-GUUGCAGAGACCUGCUACAC-CACUAGUAUAAAAA--CUCUGCUGUACAUGGCAC
NC_038912.1/1-373 ------AAUCACACCACGUGAU---------GGGAGUACGACCUGAUAGGGU-GCUGCAGAGGCCCACUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
NC_002657.1/1-373 ------AAUCACACCACGUGAU---------GGGAGUACGACCUGAUAGGGC-GCUGCAGAGGCCCACUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
OM817567.1/1-312  ------AAUCACACCAGGUGAU---------GGGGGUACGACCUGAUAGGGU-GCUGCAGAGGCCCACUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
GU233732.1/1-373  ------AAUCACAUUAUGUGAU---------GGGGGUACGACCUGAUAGGGU-GCUGCAGAGGCCCACUAUCA-GGCUAGUAUAAAAAAUCUCUGCUGUACAUGGCAC
KP343640.1/1-372  ------AAUCACACCAUGUGAU---------GGGGGUACGACCUGAUAGGGU-GCUGCAGAGGCCCACUAACA-GGCUAGUAUGAAAA-UCUCUGCUGUACAUGGCAC
AY805221.1/1-374  ------AAUCACACCACGUGAU---------GGGAGUACGACCUGAUAGGGC-GCUGCAGAGGCCCACUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
AY775178.1/1-373  ------AAUCACACCACGUGAU---------GGGAGUACGACCUGAUAGGGC-GCUGCAGAGGCCCACUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
MG387218.1/1-372  ------AAUCACAUCAUGUGAU---------GGGGGUACGACCUGAUAGGGU-GCUGCAGAGGCCCACUAACA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
NC_003679.1/1-372 -----AAACACCUAAC-GGUGUU--------GGGGUUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACGAAUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
MF102261.1/1-377  -----AAACGCCCAAU-GGCGUU--------GGAACUACAGCCUGAUAGGGU-GCUGCAGAGGCCCACGCAAC-AGCUAGUAUAAAAAAUCUCUGCUGUACAUGGCAC
NC_018713.1/1-377 ---AAGUACCCAUCUU-UGGGUGCU------GGGAGUACAGCCUGAUAGGGC-GCUGCAGAGGCCCACUGACA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGAAC
MZ664274.1/1-374  ------AACCACCUUGUGUGGU---------GGGAGUACAGCCUGAUAGGGU-GUUGCAGAGACCCACUAGUA-GGCUAGUAUAAAAU-ACUCUGCUGUACAUGGCAC
NC_077023.1/1-351 ------AAUCACUUAGCGUGAU---------GGGGGUACAACCUGAUAGGGU-GCUGCAGAGGCCCGCUAUUA-GGCUAGUAUAAAAA-UCUCUGCUGUACAUGGCAC
NC_023176.1/1-399 ---AAGCUGCCCAGAAUGGGUAGUU------GCACAUACAGUCUGAUAGGAUGCCGGCGGAUGCCCUGUAUUUUGACCAGUAUAAAUAUUAUCCGUUGUAA--AGCAU
NC_035432.1/1-381 -AAGCUAGGUCUUGAU-GGACCUUGUU----GCCUGUACAGUCUGAUAGGAUGCCGGCGGAUGCCCUGUGAC--AGCCAGUAUAAAGAAUAUCCGUUGUG-AUUGCAC
NC_077026.1/1-382 -----AAGUCGAAAUG-UCGAUU--------GCUCACACAGUCUGAUAGGAUGCCGGCGGAUGCUCCACGUA--UACCAGUAUAAAA---AUCCGUUGA--AUAGCAC
NC_077024.1/1-412 --------AUCCAAUAGGGAA----------AUCUACACAGCCUGAUAGGGUAUCGGCGCCGAUGGGGAAA----GGCUCUAUAAAA---UGGCGUGGAACAUAGCAC
ON024093.1/1-359  --------AUCCACUAGGGAG----------AUCUACACAGCCUGAUAGGGUAUCGGCGCCGAUGGGGAAA----GGCUCUAUAAAA---UGGCGUGGAUCAUAGCAC
ON024108.1/1-360  --------AUCCACUAGGGAU----------AUCUACACAGCCUGAUAGGGUAUCGGCGCCGAUGGGGAAA----GGCUCUAUAAAA---UGGCGUAGCACAUAGCAC
MK216749.1/1-385  ------UGCCCCUCAAUGGGGUA--------GACCUUACUGCUUGAUAGAGUGCCGGCGGAUGCCUCAGGUA---AGAGU-AUAAA----AUCCGUUGUUUAU-UAAC
MN099165.1/1-376  ------UGCCCUUCAC-GGGGCA--------GACCUUACUGCUUGAUAGAGUGCCGGCGGAUGCCUCGGGUG---AGAGU-AUAAA----AUCCGUUGUUUAU-UAAC
MN584738.1/1-353  ------UACCCCGUUAUGGGGUA--------GACCUUACUGCUUGAUAGAGUGCCGGCGGAUGCCUCGGGUA---AGAGU-AUAAA----AUCCGUUGUCUAU-UAAC
NC_077015.1/1-391 -----CUACUGGUAGA-CCAGUAG-------UCAUAGACUGCCUGAUAGGGUCCCGGCGGACGGCCUAGGCUU-AGCAGU-AUAAUA---GUCCGUUGUAUU--CAAC
OU592965.1/1-358  -----CUACUGCGGAU-GCAGUAG-------UCAUGGACUGCCUGAUAGGGUCUCGGCGGACAGCCUAGUGUUUAGCAGU-AUAAUA---GUCCGUUGUAAC--CAAA
NC_077001.1/1-426 A-AUUUGUCUCAAAUA-UGGGAUAAGU--UGGGGUGUGCUGCCUGACAGGGUCUCGGCUGAUAGCCUGGAA---AGCAGU-AUAAU----AUCAGUUGAAUUG-GCAU
NC_025677.1/1-399 AUGGAUGGUCUGAGUAACAGACUAUCUACUGGGGUGUGCUGCCUGACAGGGUCUCGGCUGAUAGCCUGGCU---AGCAGU-AUAAAA---AUCAGUUGAAUUG-GCAU
NC_077000.1/1-383 ------UACACCCCAGUGGUGUG----------AUGUGCUGCCUGACAGGGUCCCGGCUGAUGGCCCGGCU---AGCAGU-AUAAAA---AUCAGUUGUAAUG-GCAC
#=GC SS_cons      .....,<<<<<<_____>>>>>>........]]]]]]-]]<<<<____>>>>,,AAAAAAAA,,}}}}}}}--.}}}}}}}::::::..:aaaaaaaa::::::::::
#=GC RF           .....acgccccaaaauggggcg........gggagcACagCCUGAUAGGGuagCgGCaGAggcCCgcgguuu.ggCcaguAUAAAA..uaUCuGuUGUAcAUgGCAC
//
