# STOCKHOLM 1.0
#=GF ID sRNA71
#=GF AC RF03534
#=GF DE Staphylococcus sRNA71 small RNA
#=GF AU Morice E; 0000-0001-8113-3769
#=GF GA 50.0
#=GF NC 49.4
#=GF TC 65.0
#=GF SE Published; PMID:23733475;
#=GF SS Predicted; LocARNA;
#=GF TP Gene; sRNA;
#=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 GO; 0003729; mRNA binding;
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 23733475
#=GF RT Analysis of the small RNA transcriptional response in multidrug-resistant
#=GF RT Staphylococcus aureus after antimicrobial exposure.
#=GF RA Howden BP, Beaume M, Harrison PF, Hernandez D, Schrenzel J, Seemann T,
#=GF RA Francois P, Stinear TP
#=GF RL Antimicrob Agents Chemother. 2013;57:3864-3874.
#=GF CC sRNA71 is a Bacterial small RNA discovered by RNA-seq analysis of the
#=GF CC multiresistant Staphylococcus aureus strain ST239 grown in the presence of
#=GF CC antibiotics [1] and found throughout the Staphylococcus genus. It is
#=GF CC thought to be a trans-encoded small RNA expressed in diverse conditions
#=GF CC and media. The 5' position is uncertain, this record adds 12 bases to the
#=GF CC initial sRNA71 sequence to include additional conserved nucleotides.
#=GF WK SRNA71
#=GF SQ 13

AP006716.1/2609631-2609736   AA-CA--UGAUAGUAUUAGGGUGUAGUUAAUUAAUAACUACAAAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGGUGACGCCUUAACCCGACGUCACCCUCUUUUUA
CVUF01000027.1/94633-94531   AAUCA--UGAUACUAUUAGAGUGUAGUUAGU-AGUAACUACAAAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGGCG---UAACCCAGCGCCAUCCUCUUUUUU
AP008934.1/2423050-2423151   AGAUA--UGAUAUAUUAAAGGUGUAGUUGGAAACCGACUAC-UAGUCUUUUAUAUUCAUGAACAUAUUACUCUU--AAGGCGACACGGA-----UGUGUCGUCUUUUUUUAU
LTWW01000021.1/81501-81397   UG-CA--UGAUACUAUUAACUUGUAGUUAUUUAAUAACUACA-AGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGACGUCUUAACCCGACGUCAUCCUCUUUUUU
AGUA01000094.1/7609-7707     UUUUA--UGCUAGAAUGAAGGUGUAGUUAGU--UUAACUAC-UAGUCUUUUAUAUUCAUGAACAUAUUACUCUU--AGGGUGGCU------CUUGUAGCCACCUUUUUUUUA
CP000029.1/43036-42934       AAUC---UGAUAAUAUUAAAUUGUAGUUAUUUAGUAACUACAAAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGGCG---UAACCCAGCGCCAUCCUUUUUUAU
AEUN01000498.1/22638-22537   AA--A--UGGUAAGAUAAAGUUGUAGUUGAGAAACAGCUACACAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGACG---UUUCCCUGCGUCAUCCUUUUUUAU
LNPF01000016.1/396663-396565 AAUUG--UUAUAUUAUAGAU--GUAGUUGAAAAUCAACUAC-UAGUCUUUUAUAUUCAUGAACAUAUUACUCUU---AGGCGACACAA-----AUGUGUCGUCUUUUUUCAA
CP000253.1/367225-367123     GA-UG--UGUUACUAUAUGGGUGUAGUUCUUAAAUGACUACACAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGGCG---CAACCCAACGUCAUCCUUUUUUUA
LUGM01000002.1/960931-960827 AAUCAUAUGCUAUAUUAAGAAUGUAGUUAAU-ACUAACUAC-UAGUCUUUUAUAUUCAUGAACAUAUUACUCUUUGAGAGCGACACAU-----CAGUGUCGCUCUUUUUUUU
CP023966.1/2236122-2236224   AAUCA--UGAUACUAUUAGAGUGUAGUUAGU-AGUAACUACAAAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGGCG---UAACCCAGCGCCAUCCUCUUUUUU
CP041722.1/885520-885415     AAUCA--UGCUAAAAUAUAACUGUAGUUA-GAGAUAACUACAUAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGACGCCUUAACCCGACGUCAUCCUCUUUUUU
CP054017.1/2020481-2020378   AUUCA--UGAUAUUAUAUACAUGUAGUUAAUAAGUAACUACAAAGUCUUUUAUAUUCAUGAACAUAAUACUCCU---GGAUGGCG---UUACCCAGCGUCAUCCUCUUUUUU
#=GC SS_cons                 ::<<<..<<<--<<<<<<<<<<<<<<<<<_____>>>>>>>>---->>>>>>>>>>>>>>>:::::::::::::...<<<<<<<<...________>>>>>>>>::::::::
#=GC RF                      aauca..UGaUAcuaUaaagguGUaGuugauaAacaaCuACauAGUccuuuAuaguCAugaACAUAaUACUCcU...GGguGgCg...uaACccagcGcCacCCUuUUUUuu
//