# STOCKHOLM 1.0
#=GF ID PK-repZ
#=GF AC RF01087
#=GF DE Pseudoknot of the regulatory region of the repZ gene
#=GF AU Wilkinson A; 0000-0001-7406-0151
#=GF GA 44.0
#=GF NC 41.2
#=GF TC 173.2
#=GF SE Pseudobase
#=GF SS Pseudobase
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.73 -Z 2958934 CM SEQDB
#=GF DR PKBASE; PKB00170;
#=GF DR SO; 0005836; regulatory_region;
#=GF DR GO; 0006417; regulation of translation;
#=GF RN [1]
#=GF RM 9565606
#=GF RT An RNA pseudoknot as the molecular switch for translation of the repZ gene
#=GF RT encoding the replication initiator of IncIalpha plasmid ColIb-P9.
#=GF RA Asano K, Mizobuchi K
#=GF RL J Biol Chem. 1998;273:11815-11825.
#=GF WK Regulatory_region_of_repZ_gene
#=GF SQ 6

AB021078.1/294-442   AAGGAAAACCCCCACUAUCUUUCUUACGAACUUGGCGGAACG-ACGAAAGAUAGUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M20413.1/189-337     AAGGAAAACCCCCACUAUCUUUCUUACGAACUUGGCGGAACG-ACGAAAGAUAGUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M20412.1/189-336     AAGGAAAACCCCCACAAUCUUUC-GACGAACUUGGCGGGACG-GAGAAAGAUUAUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M93062.1/561-709     AAGGAAAACCCCCACUAUUUUUCCU-CGAACUUGGCGGAACG-CAGAAAAAUAAUGGGGGC-CUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
AY686591.1/9038-8888 AAGGAAAACCCCCACUAUCUUUCCUCGAACUUUGGCGGACUC-GUGAAAGAUAGUAGGGGCGUUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M93064.1/561-711     AAGGAAAACCCCCAUAAUCUUCCUGUCGAACUUGGCGGAACGCACAGAAGAUUAUGGGGGC-CUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUGUCAGAGAUUCAACCCUUCGCAGUGUAUUAACGCACGGCAUUCUGUUUCCGCCAU
#=GC SS_cons         :<<<----<<<<<<<<<<<<<<<_________AAAAAAA_AA.A_>>>>>>>>>>>>>>>>.>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::aaa:aaaaaaa:
#=GC RF              AaGGAAAACCCCCacuaucuuuCuuacGAAcUUGGCGGAAcg.aaGaaagauaguGGGGGC.CuCACAGAAUACGGGauAAGUAUAUAUGAAACCGUAcCAGAGAUUCAACCCUgUGCAGUGUAUAAAUACACGGCAcAAUcgcUCCGCCAU
//
