# STOCKHOLM 1.0
#=GF ID Flavi_CRE
#=GF AC RF00185
#=GF DE Flavivirus 3' UTR cis-acting replication element (CRE)
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 42.0
#=GF NC 40.9
#=GF TC 42.2
#=GF PI Flavi_pk3
#=GF SE Bateman A, Moxon SJ, Weinberg Z
#=GF SS Published; PMID:9696848; Bateman A, Moxon SJ, Weinberg Z
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 24.00 -Z 2958934 CM SEQDB
#=GF DR GO; 0019079; viral genome replication;
#=GF DR SO; 0000837; UTR_region;
#=GF RN [1]
#=GF RM 9696848
#=GF RT Identification of specific nucleotide sequences within the conserved 3'-SL
#=GF RT in the dengue type 2 virus genome required for replication.
#=GF RA Zeng L, Falgout B, Markoff L
#=GF RL J Virol 1998;72:7510-7522.
#=GF RN [2]
#=GF RM 8672458
#=GF RT Evidence for the existence of a pseudoknot structure at the 3' terminus of
#=GF RT the flavivirus genomic RNA.
#=GF RA Shi PY, Brinton MA, Veal JM, Zhong YY, Wilson WD
#=GF RL Biochemistry 1996;35:4222-4230.
#=GF CC This family represents the Flavivirus 3'-SL cis-acting replication element
#=GF CC (CRE). The family is thought to play a crucial role in replication and is
#=GF CC thought to be needed for the formation of a "replication complex" [1].
#=GF CC Although evidence has been presented for an existence of a pseudoknot
#=GF CC structure in this RNA [2], it does not appear to be well conserved across
#=GF CC flaviviruses. Deletions of the 3' UTR of flaviviruses have been shown to
#=GF CC be lethal for infectious clones.
#=GF WK Flavivirus
#=GF SQ 84

AY585243.1/10869-10968 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF306516.1/477-576     CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF022438.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCC-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF169684.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF069076.1/10878-10977 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGU-AAGAACACAGGAUCU
U47032.1/10877-10976   CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAAGAUCU
AF022439.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UUUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF217620.1/10865-10964 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AACAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AY099346.1/2415-2507   CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF204177.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAGCGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCC
M19197.1/10611-10703   CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGGACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AB074760.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAGCGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF416457.1/10877-10976 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UACGUGGUG-GUGAGG-AAGAACACAGGAUCU
AY184212.1/10878-10978 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAAGCCACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF075723.1/10877-10976 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UGGCUGGUG-GUGAGG-AAGAACACAGGAUCU
L48961.1/10877-10976   CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
AF045551.2/10864-10963 CUGG-GAAUAGAGUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
U14163.1/10877-10976   CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUA-GUGAGG-AAGAACACAGGAUCU
AF226686.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF119661.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUC-CUGUUG-AAUC-AACAGGUUCU
U88537.1/10643-10735   CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAA--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF022440.1/10631-10723 AUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF204178.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCCG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF098737.1/10877-10976 CUGGAGAU-AGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF306514.1/473-572     CUGG-GAAUAGAGUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-UUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF350498.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCG
AF486638.1/10878-10977 CUGG-GAAUAUACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
M14933.1/102-200       CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUA-CUAGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
AF326825.1/10557-10649 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUG-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--AAGAUG-GAU-UGGUG-UUG-UU-GAUCCAACAGGUUCU
AY145122.1/10643-10733 CUGG-GAG-AGACCAG---AGAU-CU-GCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AAC-GGAUCU
AF161266.1/10915-11014 CUGG-GAAAAGACUAGG--AGAU-CUU-CUGC-UCUAUU-----C-CAACAUCAG-UCACAAGGCACCGAGCGCCGA--ACACUG-UGACUGAUGGGGG-AG-AAGACCACAGGAUCU
AB074761.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--AUC-CAGGCACAGAGCACCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
M84728.1/10631-10723   CUGG-GAA-AGACCAG---AAAU-ACUACUA--UCUACU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF289029.1/10573-10665 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--GAGAUG-GAU-UGGUG-UUG-UU-GAUCCAACAGGUUCU
AY688948.1/10964-11057 CUGG-GAU-AGACUAGG--GGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--UAUAGG-UGGCUGGUG-GUG-CU-AGAA-CACAGGAUCU
M12294.2/10869-10962   CUGG-GAU-AGACUAGG--GGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAUAGG-UGGCUGGUG-GUG-CU-AGAA-CACAGGAUCU
Y07863.1/10770-10871   CCUC-GAC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
M84727.1/10631-10723   CUGG-GAC-AGACCAG---AAAU-CCAACUA--UCUACU-----C-AG-CAUCA--UUC-UAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AY274505.1/10929-11022 CUGG-GAU-AGACUAGG--AGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUG-CG-AGAA-CACAGGAUCU
AB185914.2/10936-11029 CUGG-GAU-AGACUAGG--AGAU-CCU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUG-CG-AGAA-CACAGGAUCU
U21056.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
L40361.3/10825-10927   CCCU-CAACAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049391.1/623-725     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGAGUGACUCGGAAAAACACCCGCU
U27496.1/624-726       CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049400.1/627-729     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGCGUGACUCGGAAAAACACCCGCU
AB049398.1/628-730     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--AGAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
M76660.1/535-636       CCUC-GGU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AY640589.1/10762-10860 CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U52417.1/345-443       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUCUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AF069066.1/10825-10927 CCCU-CAACAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGACAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049396.1/620-721     CCUC-AAU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
U52423.1/369-467       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGC--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U27494.1/1000-1101     CCUC-GGC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
U52399.1/343-441       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CG-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U17066.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-ACAAACACAAAACCA
U52393.1/369-467       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGU--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U54798.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGUUG-ACAAACACAAAACCA
L06436.1/10738-10839   CCAG-G---AAACUGGGGGGGC--GGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUGUGUGACUCGGAAAAACACCCGCU
AB049399.1/627-729     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGACAGUCUG--ACAAGG-AAG-UGAUGUGUGACUCGGAAAAACACCCGCU
U27495.1/11040-11141   CCUC-GGU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGGUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AY326413.1/368-466     CAAG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGC--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AF253420.1/10842-10943 CCUC-GUC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCU--AGACACAGAUAGUCUG--AAAAGG-AGG-UGAUGCGUGUCUCGGAAAAACACCCGCU
AF357219.1/530-631     CCAG-G---AAACUGGGGGGGC--GGUUCUUGUUCUCCCUGAGCC-AC-CGCCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUGAGUGACUCGGAAAAACACCCGCU
AY326415.1/368-467     CAGG-GAA-AGACCGGAG-UGG--UCU-CUGCUUUUCCU-----C-CA-AGGGUC-UGC--GAGCACAGUUUGCUU-UUAAAAGAAGCAGACCUUUUGGAUG-AAAAACACAAAACCA
AY193805.1/10685-10787 CCCU-CAUCUGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGGCAGUCUA--ACAAGG-AGG-UGAUGUGUGACUCGGAACAACACCCGCU
AY679147.1/10615-10703 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACGGG----
AY303796.1/10878-10969 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AAGAACA
AY303795.1/10878-10969 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AGAAACA
AF254453.1/10878-10969 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AAGAACA
AY326414.1/369-467     CAGG-GAA-AGACCGGAG-UGGG-UCU-UUGCUUUUUCU-----U-CA-AGGGUC-UGC--GAGCACAGUUUGCUUU--AUAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AY303794.1/10878-10969 CUGG-GAAUAGACUGGG--AGA--UCUUCUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGGAAAAACA---------
AF310149.1/353-435     CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUC-GAA-UGGUG-CUGUUGAAUC------------
AF310147.1/373-455     CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUC-GAA-UGGUG-CUGUUGAAUC------------
AF310153.1/295-377     CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUG-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--AAGAUC-GAA-UGGUG-CUGUUGAAUC------------
AY262283.1/10899-10984 CUGG-GAU-AGACUAGG--AGA--UCUUCUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUGCGAGAACA-----------
AF310926.1/379-460     CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
AF310933.1/378-458     CCAG-G---AAACUGGGG-GGG-CGUU-CUUGUUCUCCCUGAGCC-AC-CGCCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--AGU------------------
AF310931.1/380-461     CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCU-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
AF310930.1/376-457     CCCA-GGA-AGCUGGGGG-GGC--GUU-CUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGACAGCCUG--ACAAGG-AGA-UGGUG--AGU------------------
AF310929.1/376-458     CCCA-GGA-AGCUGGGGG-GGC--GGUUCUUGUUCUCCCUGAUCC-AC-CACCA--UCC--AGGCACAGACAGCCUG--ACAAGG-AGA-UGGUG--AUU------------------
EU670438.1/10738-10819 CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
U87412.1/10631-10697   CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--A------AAA-UGGA------------------------
EF571854.1/10936-11009 CUGG-GAU-AGACUAGG--AGAU-CU-UCUGC-UCUGCA-----CAAC-CAGC---CAC-ACGGCACAGUGCGCC-G--ACAAUG-GUG--GCUG---GU------------------
FJ850060.1/10610-10676 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--A------AAA-UGGA------------------------
#=GC SS_cons           <<<<.___.___>>>>:..<<<-.<<<-----.------.....<.<<.<<<<<..<<<.--<<<_______>>>--..------.>>>.>>>>>.>>>---.-------->>>->>>
#=GC RF                Ccgg.GAa.AGAccgGG..gGgU.ccUuCUgc.UCUccu.....C.ag.cAcca..ccc.uAGGCACAGaucGCCug..AaAAuG.ggg.uggUg.cuGaug.AaaAAaACAggacCc
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