# STOCKHOLM 1.0
#=GF ID Pestivirus-3UTR-SLI
#=GF AC RF04322
#=GF DE Pestivirus 3' UTR SLI
#=GF AU Tautz N; 0000-0002-2398-4968
#=GF GA 37.0
#=GF NC 36.8
#=GF TC 42.5
#=GF SE Kevin Lamkiewicz, Sandra Triebel, Manja Marz
#=GF SS AnchoRNA, LocARNA, ViennaRNA Package, manual curation
#=GF TP Cis-reg;
#=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 DR SO; 0000655; ncRNA;
#=GF RN [1]
#=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 [2]
#=GF RM 15383680
#=GF RT Complex signals in the genomic 3' nontranslated region of bovine viral
#=GF RT diarrhea virus coordinate translation and replication of the viral RNA.
#=GF RA Isken O, Grassmann CW, Yu H, Behrens SE
#=GF RL RNA. 2004;10:1637-1652.
#=GF RN [3]
#=GF RM 15994806
#=GF RT Essential and nonessential elements in the 3' nontranslated region of
#=GF RT Bovine  viral diarrhea virus.
#=GF RA Pankraz A, Thiel HJ, Becher P
#=GF RL J Virol. 2005;79:9119-9127.
#=GF RN [4]
#=GF RM 28811507
#=GF RT Global mapping of miRNA-target interactions in cattle (Bos taurus).
#=GF RA Scheel TKH, Moore MJ, Luna JM, Nishiuchi E, Fak J, Darnell RB, Rice CM
#=GF RL Sci Rep. 2017;7:8190.
#=GF RN [5]
#=GF RM 32374844
#=GF RT Evolutionary selection of pestivirus variants with altered or no microRNA
#=GF RT dependency.
#=GF RA Kokkonos KG, Fossat N, Nielsen L, Holm C, Hepkema WM, Bukh J, Scheel TKH
#=GF RL Nucleic Acids Res. 2020;48:5555-5571.
#=GF WK Pestivirus
#=GF SQ 36

NC_076029.1/12248-12308 AGCUGUAUGAGGAU-----ACA-CCCGACGUCUA-UAGUUGGACUAGGG----AAGACCUCUAACAGCCCCC
NC_001461.1/12518-12573 AGCUGUAUGAGGAU-----ACG-CCCGACGUCUA-UAGUUGGACUAGGG----AAGACCUCUAACAG-----
KC853440.1/12212-12271  AGCUGUAUGAGGGU-----AUA-CCCGACGUCUA-CAGUUGGACUAGGG----AAGACCUCUAACAGCCCC-
KX577637.1/12199-12258  AGCUGUACGAGGGU-----AUA-CCCGACGUCUA-CAGUUGGACUAGGG----AAAACCUCUAACAGCCCC-
MW054939.1/12176-12225  AGCUGUAUGAGGGU-----ACA-CCCGACGUCUA-CAGUUGGACUAGGG----AAUACCCC-----------
AF526381.3/12160-12220  AGCUGUAUGAGGGU-----ACA-CCCGACGUCUA-UAGUUGGACUAGGG----AAGACCCUUAACAGCCCCC
NC_076032.1/12226-12284 AGCUGUGUGAGGUU------AA-CUCGACGUCCA-CGGUUGGACUAGAG----GAUGGCUCUAACAGCCCC-
NC_039237.1/12453-12512 AGCUGUGUGAGGUU------AA-CUCGACGUCCA-UGGUUGGACUAGAG---GAUGGCUCUA-ACGGUCCCC
MH231152.1/12196-12254  AGCUGUUUGAGGUU------AA-CCCGACGUCCA-UGGUUGGACUAGGG---AAUACCUCUA-ACGGCCCC-
MH806436.1/12572-12629  AGCUGUGUGAGGUU------AA-CUCGACGUCCA-UGGUUGGACUAGAG---GAAG-CCUC-UACAGCCCC-
NC_003678.1/12544-12602 AGCUGGAAG-GGGA-----UAU-UCCGACGUCCA-CUGUUGGUCUAGGA----AAAAACCCUGAAGGCCCC-
NC_012812.1/12280-12337 AGCUGUUUG-GGAA-----AGA-CCCGACGUCCA-CAGUUGGACUAGGG----AAAAUCCCUAACGGCCC--
NC_038912.1/12241-12298 AGCUGGAAG-GAAA-----AUU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
NC_002657.1/12244-12301 AGCUGGAAG-GAAA-----AUU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
GU233732.1/12241-12297  AGCUGGAGG-GAAA------AC-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
KP343640.1/12240-12296  AGCUGGAGG-GAAA------AU-CCUGACGUCCA-UAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
KC533775.2/12242-12298  AGCUGGAGG-GAGA------AU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
AY805221.1/12254-12310  AGCUGGAAG-GAAA-----AUU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUU-CUAACGGCCC--
AF099102.3/12251-12310  AGCUGGAAG-GAAA-----AUU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCCCC
AY775178.1/12240-12297  AGCUGGAAG-GAAA-----AUU-CCUGACGUCCA-CAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
MG387218.1/12239-12295  AGCUGGAGG-GAAA------AU-CCUGACGUCCA-UAGUUGGACUAAGG----UAAUUUCCUAACGGCCC--
NC_003679.1/12275-12333 AGCUGGAAG-GGAA-----AAG-CCUGAAGUCCA-GAGUUGGAUUAAGG----AAAAACCCUAACAGCCCC-
MF102261.1/12254-12311  AGCUGAAAG-GGA------AUU-CCUGACGUCCA-AAGUUGGACUAAGG----UAAAACCCUAACAGCCCC-
NC_018713.1/12234-12292 AGCUGGAAG-GAAA-----ACC-CCUGACGUCCA-CAGUUGGACUAAGG----UAAGUUCCUAACAGCCCC-
MZ664274.1/12229-12286  AGCUGGAAG-GAAG-----AAU-CCUGACGUCCA-UAGUUGGACUAAGG----UAAAUUCCUAACAGCCC--
NC_024018.2/12213-12273 AGCCGAAUG-GAGG-----GAA-CCCGACGUCCUUU-GUAGGACUAGGA--AAAAUCUUCCACUAGGCCCC-
NC_023176.1/12596-12656 AGCUGAUUG-GGAC-GU-AAGU-GCAGACGUCCUGUAGGAGGACUAUGC----ACAGUUCCAAAAAGCC---
NC_035432.1/12552-12614 AGCUAAUUG-GGAC-AUAAAGU-AAGGACGUCCUAG-GGAGGACUACUU----ACAGUUCCAAGAGGCCCC-
NC_077026.1/11817-11880 AGCUAAUUG-GGAU-GUAAAGU-AGAGACGUCCUUCAGGAGGACUAUCU----ACAAUUCCAAGAGGCCCC-
NC_077024.1/12374-12436 AGCUGAGCA-GGGU---AAGAA-GGGUACACUCC-UAGGGGAGUUGACC---AAUAAUCCUGCAAGGCCCCC
ON024108.1/12334-12394  AGCUGAGCA-GGGU-UUUAC---GGGUACACUCC-UAGGGGAGUUGACC---AACAAUCCUGCAAGGCCC--
MN099165.1/11500-11564  -GCCCCAUU-UGCU-UUGUAGU-GGUGACGACCU-GUAUAGGUCUGAUCUAGAUGAAGCAAG-GGGGCCCC-
NC_077015.1/11857-11921 -ACCCCAGU-CGACACUGUAGU-UCUGACGUUCCUGAAUGGGACUGAAGUAGAUAGGUCGA-UGGGGCC---
NC_077001.1/13161-13220 AGUGCUU-A-GGGU-UGAAA----GUGACAACCAUUUUUUGGUUCGAAC---AAAAAUCCUAAAGCACCC--
NC_077000.1/12704-12767 UGUGUUUUU-GGGU-CGUAAC--GCUGACUUACC-GUAUGGUGACGAUG---CUUGAUCCAAUAGCACCACC
OM030319.1/12495-12556  AGCUGGUU--AGGU-CGUAAAAGCUUGACGUCCU-UUGUAGGACUAAA----GCUGAUCUAAACUGGCCC--
#=GC SS_cons            :<<<<<<<<.<<<<.....---.<<<---<<<<<.____>>>>>-->>>...---->>>>>>>>>>>>:::.
#=GC RF                 AGCuguuuG.GGgu.....Aau.ccuGACGUCCa.uAGUuGGACUAagg...AaAAauCCCaaacgGCCCC.
//
