# STOCKHOLM 1.0
#=GF ID Bacteria_large_SRP
#=GF AC RF01854
#=GF DE Bacterial large signal recognition particle RNA
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 60.0
#=GF NC 59.9
#=GF TC 60.0
#=GF PI SRP_bact_l; SRP_bact
#=GF SE Published; PMID:19838050
#=GF SS Published; PMID:19838050
#=GF TP Gene;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 2958934 CM SEQDB
#=GF CL CL00003
#=GF DR URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR SO; 0000590; SRP_RNA;
#=GF DR GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR GO; 0048501; signal recognition particle, plasma membrane targeting;
#=GF RN [1]
#=GF RM 12520023
#=GF RT SRPDB: Signal Recognition Particle Database.
#=GF RA Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL Nucleic Acids Res 2003;31:363-364.
#=GF RN [2]
#=GF RM 12140321
#=GF RT Prediction of signal recognition particle RNA genes.
#=GF RA Regalia M, Rosenblad MA, Samuelsson T
#=GF RL Nucleic Acids Res 2002;30:3368-3377.
#=GF RN [3]
#=GF RM 19838050
#=GF RT Kinship in the SRP RNA family.
#=GF RA Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL RNA Biol. 2009;6:508-516.
#=GF CC The signal recognition particle (SRP) is a universally conserved
#=GF CC ribonucleoprotein involved in the co-translational targeting of proteins
#=GF CC to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA
#=GF CC (RFAM:RF00017) and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal
#=GF CC SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54
#=GF CC proteins. In most bacteria, the SRP consists of a 4.5S RNA and the Ffh
#=GF CC protein (a homologue of the eukaryotic SRP54 protein). Some Gram-positive
#=GF CC bacteria (e.g. Bacillus subtilis) have a longer eukaryote-like SRP RNA
#=GF CC that includes an Alu domain [2]. The Alu domain of the longer SRP RNAs is
#=GF CC not included in this model and therefore the reported bounds of some
#=GF CC members are incorrect. The Signal Recognition Particle Database (SRPDB)
#=GF CC [1] provides compilations of SRP components, with phylogenetic data and
#=GF CC structural illustrations.
#=GF WK Signal_recognition_particle_RNA
#=GF SQ 92

CP000764.1/25247-25511       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUACU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUACG---CAACGAGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
AE015929.1/2386853-2386584   CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-ACUUA---AUUCCUUUGUU-GAGGGCGU-AUUUUU-GUGAAG-UCUGCC-CGAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000730.1/508055-508324     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000485.1/25122-25386       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-----AGCGAGGCCGAAUCCCUUCUCG--AGGUUAU-GUUGCU-GUAAGG-CCUGCCUUAAGUA--AGUGGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP000029.1/101125-101225     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
X06802.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
D26185.1/90020-90284         CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP000728.1/33073-33316       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGGCUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGC
AE001437.1/136141-136243     -------------------------------------------------------------------------------------------------------------------------------------GAAUUGGGU---CCCACG---CAACGGAAA--UUC-AUGAACUCCGUCAGGUCCGGAAGGAAGCAGC
CP000736.1/536869-536969     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
BX571857.1/485579-485679     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
BA000017.4/525852-525952     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
D11420.1/5-270               CCGUGCUAAGCAGGCGAGGUAGCGGUGCCCCAUA--CCCGCAAUCCGCUCU-AGGAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-GUAAGG-UCUGCC-UUAAGUAAGU-GGC---GUU-GA-CGUCUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
D12926.1/388-490             -------------------------------------------------------------------------------------------------------------------------------------GGAGCGGGU---CCUGUG---CAACGCG---AACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGC
AE016879.1/25115-25379       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
U15684.1/154-183             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAUGUCAGGUCCGGAAGGAAGCAGC
AL596173.1/263987-263721     UCGUGCUAGAC-GGGGAGGUAGCGGCGCCCUGUAA-CCCGCAAUCCGCUCU-AGCGGG-GUUGA---AUUCCU-CAUUUGAGGCAUC-GUAAUU-GUUUGGUCU-GCC-CUUGACAAGU-GGU---GUU-GA-AGGUUGGGU---CUUGCG---CAAUGGGAA--CCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AF269831.1/1333-1433         --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
BA000018.3/501420-501689     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000716.1/1385812-1385778   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACCGGGUCAGGUCCGGAAGGAAGCAGC
CP000726.1/37731-37974       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGC
CP000448.1/35764-35828       CCGUGCUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCUGCAACCCGCUAU-AGCAGG-GUCGA---AUUCC--------------------------------------------------------------------------------------------------------------------------------
AF269814.1/2629-2729         --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
X52144.1/697-961             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP001186.1/24962-25226       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP000227.1/25236-25338       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP001175.1/2823285-2823387   -------------------------------------------------------------------------------------------------------------------------------------AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AE017225.1/25229-25331       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP000246.1/54302-54566       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGC
CP000002.3/30682-30947       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUAC-UC-GCAAUCCGCUCG-AGCGAG-GCCGA---AUCCCUUUCUC-GAGGUUCG--UUUACUUUAAGG-UCUGCC-UUAAGCAAGU-GGU---GUU-GA-CGCUUGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
ACHE01000060.1/4624-4355     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-ACUUA---AUUCCUUUGUU-GAGGACGU-AUUUUU-GUGAAG-UCUGCC-CGAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
D11419.1/5-270               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUUCCU-UUCU-GAGGCUGG-UAUCCU-GUAGGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUCCGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP000560.1/27594-27646       ----------------------------------------------------------------------------------------------------------------------------------------------------------------GA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AM180355.1/20131-20368       --GUACUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCUGCAAUCCGCUAU-AGCAGG-AUUGA---AUUCCAUCUAA--AGGCUUA-UUUUCU-GUAGG--GCCG--CCCUAAAUAAGUGGU---GUU-GA-UGCUUAGGU---CCUGCG---CAAUGAAAG--CUC-AUGAACCCCGUCAGAUCCGGAAGGAAGCAGC
AF368293.1/5-274             CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
D11417.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP001215.1/24988-25252       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGG---ACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP000255.1/508278-508378     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
AP006627.1/47077-47179       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---UCUGCG---CAACGGA---AACCCAUGAACCCUGUCAGGUCCGGAAGGAAGCAGC
CP001185.1/1535075-1535038   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGAACCGGGUCAGGUCCGGAAGGAAGCAGC
D13041.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AE017194.1/25229-25331       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
X12642.1/292-556             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
ACFR01000004.1/173539-173639 --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
D11412.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
D11416.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AE015927.1/24077-23975       -------------------------------------------------------------------------------------------------------------------------------------GAAUUGGGU---CCCACG---CAACGGAAA--CUC-AUGAAACCCGUCAGGUCCGGAAGGAAGCAGC
AE017333.1/30486-30751       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUAC-UC-GCAAUCCGCUCG-AGCGAG-GCCGA---AUCCCUUUCUC-GAGGUUCG--UUUACUUUAAGG-UCUGCC-UUAAGCAAGU-GGU---GUU-GA-CGCUUGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AM412317.1/37716-37959       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGC
D11415.1/5-268               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UCAAGG-UCUGCC-UUAAAUAAGU-GGU---GUU-GA-CGUCUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AL591984.1/65413-65311       -------------------------------------------------------------------------------------------------------------------------------------AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP000382.1/2507879-2507649   -CGUGCUAGAC-GGGAAGUUAGCGGUGUCCUGU--ACCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCUCGUUG--AGGCUUU-AAAAUG-GGAGG--UCUG--GCUUAUAUAAGUGGC---GUU-GA-GAAUUGGGC---CCUACG---CAAUAGGAA--CUC-AUGAACCCCGUCAGGUCCGGAAGGAAGCAGC
CP000727.1/37731-37974       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGC
BA000043.1/27043-27145       -------------------------------------------------------------------------------------------------------------------------------------CGUCUGGGU---CCCGCG---CAAUGGG---AUUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGC
BA000004.3/46485-46751       CCGUGCUAGGU-GGGGAGGUAGCGGUGCCCUGUCA-CUCGCAAUCCGCUAU-AGCGAG-GCUGA---AUCCCU-UCUA-GAGGUUUU--GUCACCGUAGGG-UCUGCC-CUAAGUAAGU-GGU---GUU-GA-CGCUUGGGU---UCUACG---CAACGAAA--ACCC-ACGAACCCUGUCAGGUCCGGAAGGAAGCAGC
CP000702.1/1631640-1631756   --------------------------------------------------------------------------------------------------------------------------------GGGGGCGAUGAAGA-CCGGGUCCCACGCAACGGA-ACCCU-GUGAACCUGGUCAGGCCCGGGAGGGAGCAGC
CP000253.1/444208-444308     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000046.1/524416-524685     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000001.1/25120-25384       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
CP001283.1/25232-25334       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGG---ACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
AE017262.2/2736493-2736285   --------------------------------------------------------------GA---AUUCCU-CAUUUGAGGCAUC-GUAAUU-GUUUGGUCU-GCC-CUUGACAAGU-GGU---GUU-GA-AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
D11421.1/5-270               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP001598.1/25015-25279       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
D14472.1/475-743             CCGUGCUAGAC-GGGGAGGUUGCGGUGCCCUGUAA-CCUGCAAUCCGCAAUAGCCAGG-GUGUG-A-AUUCCU-AUCC-UAGGUUUU--CUUAU-GUGAGG--CUGCCGUUGAUGGCGGCGGU---GUU-GA-GGAGCGGGU---CCUGUG---CAACGCGA--ACCC-AUGAACCUGGUCAGGUCCGGAAGGAAGCAGC
CP000703.1/536798-536898     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
AP009324.1/527299-527399     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
D11422.1/5-266               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUAU-AGCAGG--CUGA---AUCCCU-UCUA-GAGGUUUU--GUCACCGUAGGC-UCUGCC-CUAAGUAAGU-GGU---GUU-GA-CG-UUGGGU---UCUACG---CAACGAAA--ACCC-ACGAACCCUGUCAGGUCCGGAAGGAAGCAGC
CP000141.1/2376482-2376447   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAACCGUGUCAGGUCCGGAAGGAAGCAGC
D49784.1/286-550             CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGC
AL009126.3/26420-26684       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AP006716.1/2548377-2548277   --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAAUCAUGUCAGGUCCUGACGGAAGCAGC
D11413.1/5-264               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA---CCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGC
D11414.1/5-268               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUUCCU-UCUU-GAGGUUAG-CUCAUC-UUAGGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUACG---CAAUGGGA--AUCU-GUGAACCCUGUCAGGUCCGGAAGGAAGCAGC
X14796.1/291-555             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
CP000557.1/25310-25574       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUCCCU-UCUC-GAGGUUAG-UCUGUU-GUGAGG-UCUGUC-UCAAGCAAGU-GGU---GUU-GA-CGUCUGGGU---CCCGCG---CAAUGGG---AUUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGC
CP000232.1/28709-28775       CCGUGCUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCCGCAAACCGCUAU-AGCGGG-GUUGA---AGUCCCA------------------------------------------------------------------------------------------------------------------------------
BA000016.3/54529-54793       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGC
CP000721.1/5829625-5829394   ---UGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAU-AGCAGG-AUUGA---AUUCCUCGCUU--AGGUAUU--AGCGAUUUAUAG-UCUG--ACUUUUGUAAGUGGU---GUU-GA-UGACUGGGU---CCCACG---CAAUGGAAG--CCC-AUGAACCUCGUCAGAUCUGGAAGGAAGCAGC
AE008691.1/46248-46514       CCGUACUAGAU-GGGGAGGUAGCGGUGCCCUGUAG-CCUGCAACCCGCUAU-AGCAGG-GUCGA---AUUCCCAGGCU-GAGGCCUGA-UUUCU-GUAAGG-CCUG--GCGCAAGUAAGUGGCGUU-GA-UACUUGA-GU--CCUGCG------CAACGGAGA--UUU-GCGAACCCCGUCAGGUCCGGAAGGAAGCAGC
X15523.1/2-266               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUCCCU-UCUC-GAGGUUAG-UCUGUU-GUGAGG-CCUGUC-UCAAGUAAGU-GGU---GUU-GA-CGUCUGGGU---CCCGCG---CAAUGGGA--UUCC-GUGAACCCUGUCAGGUCCGGAAGGAAGCAGC
BA000028.3/30821-31086       ACGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUAU-AGCGGG-GCCGA---AUUCCC-ACUC-GAGGUGGG-ACGACU-UUAUGG-UCUGAC-UUAAGGGAUU-GGU---GUU-GA-CGCCCGGGU---CCUGCG---CAACAGGA--ACCC-ACGAAUCCUGUCAGGUCCGGAAGGAAGCAGC
CP000724.1/39593-39767       --GUGCUAGAC-GGGGAGGUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCU-CAUG-GAGGCUUG-UUGCUU-GUAGGG--CUGGC-CUAGAUAAGU-GGU---GAU-GA-GAAUUGGGU---CCUACG---CAAUGAA---AACUCAUGAACUCCGUCAGAUCCGGAAGGAAGCAGC
CP000813.1/551215-551244     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAUGUCAGGUCCGGAAGGAAGCAGC
D11418.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGC
AE000512.1/1124728-1124612   --------------------------------------------------------------------------------------------------------------------------------GGGGGCGAUGAAGA-CCGGGUCCCACGCAACGGA-ACCCU-GUGAACCUGGUCAGGCCCGGGAGGGAGCAGC
AC025951.19/16428-16528      --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
AJ938182.1/468421-468690     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000568.1/2549377-2549203   --GUGCUAGAC-GGGGAGGUAGCGGUGCCCUGUU-ACCUGCAAUCCGCUAU-AGCAGG-GUCGA---AUUCCUAUAAU--AGGCAUG-CUUCUG-UAAGG--UCUG--CCCUUUGCAAGUGGC---GAU-GA-AAAUUGGGU---CCUACG---CAACGGAAG--CCU-AUGAACCCCGUCAGGUUCGGAAGAAAGCAGC
AP008934.1/2359274-2359174   --------------------------------------------------------------------------------------------------------------------------------------AUCUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAAUCAUGUCAGGUCCUGACGGAAGCAGC
AP009351.1/497755-498024     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGC
CP000312.1/54097-54361       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGC
AP009049.1/3810996-3810763   -CGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUA-ACCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCUGGCUU--AGACUUU-AAAAUG-UGAGG--CCUG--CCCCAUAAAAGUGGC---GUU-GA-GAGCUUGGU---CCCACG---CAACAAGAA--CUC-AUGAACCCCGUCAGGUCCGGAAGGAAGCAGC
#=GC SS_cons                 [[[[[[[((((.<<<<<<<<___>>>>>>>>,,,..<<<<<<_________.>>>>>>.)))),...,,,<<<.<<<<.-<<<<<<-..<<<<<.<<<<<-.--<<...<<<<<<--<<.<<<...---.--.<<<<<<<<<...<<<<<<...<<-<<<<<..<<<<.<<<---<<<<<----<<<____>>>---->>
#=GC RF                      cCGuGCcgggc.gGGGggcuAGCggucCCCuGUA..CccGCgAUCCGCUau.cGCggG.gcccA...AUuCCu.ccuc.GcGgcccu..ccccc.gugggG.uCug...ccgagcaAgg.gGc...GUu.GA.cgcccgGGc...cCugcG...caAcggga..accc.gugAACccuGuCAGGuCCGGAAGGaAGCAgC

CP000764.1/25247-25511       AAUAAGCGGGUUCUCUCG-UGUG---CCGUAGG--AGUGC-CUGAACUG-----AGCU-AACU-GCUUGA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
AE015929.1/2386853-2386584   AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-GUCG-ACUUCG--GUAACGUUUAU--GAUAU--GCGUUCGAUACAAAGGUGCAUGG
CP000730.1/508055-508324     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000485.1/25122-25386       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCUAACUG--CUUAA--GUAACGCUUAU--GGUAC--GUAAUCGACAGA-AGGUGCACGG
CP000029.1/101125-101225     AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
X06802.1/5-269               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
D26185.1/90020-90284         AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP000728.1/33073-33316       GGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
AE001437.1/136141-136243     GGUAAGUGAAAUCUUCCG-UGUG---CCGUGGA--UAAAU-CUGAUUUG-----AGU----------------------------------------------------------
CP000736.1/536869-536969     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
BX571857.1/485579-485679     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
BA000017.4/525852-525952     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
D11420.1/5-270               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGAGCACGG
D12926.1/388-490             CAUAAGUGGAUCAUCGCG-UGUG---CCGCAGG--GUAGC-CUGCUCUG-----AGC----------------------------------------------------------
AE016879.1/25115-25379       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
U15684.1/154-183             AU-----------------------------------------------------------------------------------------------------------------
AL596173.1/263987-263721     AUUAAUCAGUGCUUCUCA-UGUG---CCGCGAG--GUUGC-CUGGCCCG-----AGCU-AACU-AUCAAG--GUAACGCAGGU--GAUUG--CAUGUCGAGGUG-AGGUGCGCGA
AF269831.1/1333-1433         AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
BA000018.3/501420-501689     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000716.1/1385812-1385778   CCUAAG-------------------------------------------------------------------------------------------------------------
CP000726.1/37731-37974       GGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
CP000448.1/35764-35828       -------------------------------------------------------------------------------------------------------------------
AF269814.1/2629-2729         AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
X52144.1/697-961             AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001186.1/24962-25226       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUGA--GUAACGCUUAUG-G-UAC--GUAAUCGACGGA-GGGUGCACGG
CP000227.1/25236-25338       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
CP001175.1/2823285-2823387   AUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGC----------------------------------------------------------
AE017225.1/25229-25331       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
CP000246.1/54302-54566       GAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
CP000002.3/30682-30947       AUUAAGUGGAACCUUCCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
ACHE01000060.1/4624-4355     AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-GUCG-ACUUCG--GUAACGUUUAU--GAUAU--GCGUUCGAUACAAAGGUGCAUGG
D11419.1/5-270               AUUAAGUGGACACCCCCA-UGUG---CCGCAGG--GUUAC-CUGGACUG-----AGCU-AACU-ACUUAA--GUAACGCUUAU--GGGUG--CCAGUCGACAGA-AGGUGCACGG
CP000560.1/27594-27646       AUUAAGUGAAACCUCU---------------------------------------------------------------------------------------------------
AM180355.1/20131-20368       GGUAAGUGAUCACUUUUG-UGUG---CCGUGGG--GGUGC-CUAAGUUG-----AGCUAACU-GUUUUGGUAACG---CCUAUGG------------------------------
AF368293.1/5-274             AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
D11417.1/5-269               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001215.1/24988-25252       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAA-CGCUUAU-GGUAC--GUAAUCGACAGA-AGGUGCACGG
CP000255.1/508278-508378     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AP006627.1/47077-47179       AGUAAGUGGACCCUUCCG-UGUG---CCGCAGA--GGUGC-CUGGAUCG-----AGC----------------------------------------------------------
CP001185.1/1535075-1535038   CCUAAGC------------------------------------------------------------------------------------------------------------
D13041.1/5-269               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE017194.1/25229-25331       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
X12642.1/292-556             AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
ACFR01000004.1/173539-173639 AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
D11412.1/5-269               AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUGC--GUAACGCUUAUG-GCUAC--GCAAUCGACAGA-AGGUGCACGG
D11416.1/5-269               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE015927.1/24077-23975       GGUAAGUGAUAAUUUUCG-UGUG---CCGUGGA--UAAAC-CUGGUUUG-----AGU----------------------------------------------------------
AE017333.1/30486-30751       AUUAAGUGGAACCUUCCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AM412317.1/37716-37959       GGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
D11415.1/5-268               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GUUUAA--GUAACGCUUGG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AL591984.1/65413-65311       AUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGC----------------------------------------------------------
CP000382.1/2507879-2507649   GGUAAGUGAGAACUCCUA-UGUG---CCGUAGG--UAAAC-CUGGUUUG-----AGUUAACU-AUAUAAGUAACG----------------------------------------
CP000727.1/37731-37974       GGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
BA000043.1/27043-27145       AGUAAGCGGAUGCUCCCA-UGUG---CCGCGGG--GACGC-CUGGGCUG-----AGC----------------------------------------------------------
BA000004.3/46485-46751       AGUAAGUGGCCCCUUUCG-UGUG---CCGUAGA--GUCGC-CUGGGCCG-----AGCU-AACU-GCUCAG--GUAACGCCUAGG-GUGGC--AUGAUCGAAGGA-AGGUGCACGG
CP000702.1/1631640-1631756   CAUAAGCAGGUGUUUCCGUGUG---CCGUGGGGG-AG-CC-CGGUUGGAGCCUU-------------------------------------------------------------
CP000253.1/444208-444308     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
CP000046.1/524416-524685     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000001.1/25120-25384       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
CP001283.1/25232-25334       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
AE017262.2/2736493-2736285   AUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGCU-AACU-AUCAGG--GUAACGCAGAU--GAUUGC--AUGUCGAUGUG-AGGUGCGCGA
D11421.1/5-270               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001598.1/25015-25279       AAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
D14472.1/475-743             CAUAAGUGGAUCAUCGCG-UGUG---CCGCAGG--GUAGC-CUGCUCUG-----AGCU-GCUA-CCAUAA--GUAACGCUCGG--AUAAG-GAUUAUCGAAGAU-AGGUGCACGG
CP000703.1/536798-536898     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AP009324.1/527299-527399     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
D11422.1/5-266               AGUAAGUGGCCCCUUUCG-UGUG---CCGUAGA--GUCGC--UGGGCCG-----AGCU-AACU-GCUCAG--GUAACGCUAGG--GUGGC--AUGAUCGACAGA-AGGUGCACGG
CP000141.1/2376482-2376447   ACUAAG-------------------------------------------------------------------------------------------------------------
D49784.1/286-550             GAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
AL009126.3/26420-26684       AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AP006716.1/2548377-2548277   AUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
D11413.1/5-264               AAUAAGCGGU-CUUCUCG-UGUG---CCG-AG---AGUGC-CUGAACCG-----AGCU-AACU-GCUUGA--GUAACG-UUAU--GGUAC--GUAAUCGACAGA-AGGUGCACGG
D11414.1/5-268               AGUAAGCAGAACCUCUCA-UGUG---CCAUGGG--GUCGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCCUGG--GGUGG--CUAAUCGACAGA-AGGUGCACGG
X14796.1/291-555             AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP000557.1/25310-25574       AGUAAGCGGAUGCUCCCA-UGUG---CCGCGGG--GGUGC-CUGGGCUG-----AGCUA-ACU-ACUUGA--GCAACGCUCGG--GGCAGC--UAAUCGACAGA-AGGUGCACGG
CP000232.1/28709-28775       -------------------------------------------------------------------------------------------------------------------
BA000016.3/54529-54793       GAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
CP000721.1/5829625-5829394   GAUAAGUGGUUCCUUCCA-UGUG---CCGUGGA--UCAAU-CUGGUCUG-----AGCUAACU-GCAUUAGUAACG---U------------------------------------
AE008691.1/46248-46514       GGUAAGCAAACACCUCCG-UGUGCCGCAGG--GGU-GCUUGAGUGG--------AGCUAACU-GCUUGCGUAACG---CUUAU--GGGGA--CAGGUCG-AAGCUGGGUGUACGG
X15523.1/2-266               AGUUAGCGGAUGCUCCCA-UGUG---CCGCGGG--GGCGC-CUGGGCUG-----AGCC-AACU-GCUUGA--GCAACGCUCGG--GGCAG--CUAAUCGACAGA-AGGUGCACGG
BA000028.3/30821-31086       AGUAAGUGGUUAUUCUUG-UGUG---CCGCAGG--GAAGC-CUAGGCCG-----AGCC-AUGA-ACUUAU--GUAGCGCAUAG--GGUCG-UUUCAUCGACAGU-GGGUGCACGU
CP000724.1/39593-39767       GGUAAG-------------------------------------------------------------------------------------------------------------
CP000813.1/551215-551244     AU-----------------------------------------------------------------------------------------------------------------
D11418.1/5-269               AUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--UUGCC-UUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE000512.1/1124728-1124612   CAUAAGCAGGUGUUUCCGUGUG---CCGUGGGGG-AG-CC-CGGUUGGAGCCUU-------------------------------------------------------------
AC025951.19/16428-16528      AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AJ938182.1/468421-468690     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000568.1/2549377-2549203   GGUAAG-------------------------------------------------------------------------------------------------------------
AP008934.1/2359274-2359174   AUUAAGUGGAUCAUCGUA-UGUG---CCGUAGG--GUUGC-CGAGAUUUAG----------------------------------------------------------------
AP009351.1/497755-498024     AUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000312.1/54097-54361       GAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
AP009049.1/3810996-3810763   GGUAAGUGAAUAUUUUUG-UGUG---CCGUGGA--UAAAC-CUGGUUUG-----AGUUAACU-AUAUGGGUAACG---CU-----------------------------------
#=GC SS_cons                 >>>->>>>>>>-->>>>>.>>--...->>>>>>..--->>.>>>>>>>-.....->>>.->>..>>>>>>..->>...>>>>>..>>>>>...>>>>>>.>>>>.>>>]]]]]]]
#=GC RF                      aguAagcgggucuucccg.ugUG...CCgcaGg..guugC.Ccgggcgg.....AgCc.Acc..gcucgg..gca...cccac..ggggg...gggcCg.gagg.aGGgGCaCGg
//
