# STOCKHOLM 1.0
#=GF ID RsaE
#=GF AC RF01820
#=GF DE RNA Staph. aureus E (RoxS)
#=GF AU Moore B; 0000-0002-4074-1933
#=GF GA 79.0
#=GF NC 78.9
#=GF TC 79.3
#=GF PI ncr22; ncr629
#=GF SE Published; PMID:19786493
#=GF SS Published; PMID:19786493
#=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; 0006446; regulation of translational initiation;
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 19786493
#=GF RT A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT conserved sequence motif for regulation.
#=GF RA Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL Nucleic Acids Res. 2009;37:7239-7257.
#=GF RN [2]
#=GF RM 25643072
#=GF RT A nitric oxide regulated small RNA controls expression of genes involved
#=GF RT in redox homeostasis in Bacillus subtilis.
#=GF RA Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N,
#=GF RA Nicolas P, Romby P, Condon C
#=GF RL PLoS Genet. 2015;11:e1004957.
#=GF CC It was shown to be regulated by the presence of nitric oxide (NO). In
#=GF CC Bacillus subtilis it controls expression of genes with functions related
#=GF CC to oxidative stress and oxidation-reduction reactions and it was renamed
#=GF CC RoxS (for related to oxidative stress).[2]
#=GF WK Rsa_RNA
#=GF SQ 15

ABQL01000005.1/214304-214418 GUGAAAUUGAUCACA-AA-CAAAC---A-----UU--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--GUUAA-----GACAUA--UGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUU
ABFU01000021.1/68350-68459   GUGAAGUUGAUCACA-AA-CAAAC---A------UAUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUU--C--GUAAA-----G-GAAA--ACCCCUUGUAAC-----------CUAGUUACAAGGGGUUU
CP000922.1/2095013-2094892   GUGAAGUGAAUCACA-AU-CAAAC---AAACUUAU--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--UUUAU-----GACAAAGAAAAAGGACUCGG---C-----AUCCCCCGAGUCCUUUUUC
ABCF01000041.1/14193-14301   AAGAAGUUGAUCACA--A-CAAAC---A------UAUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUU-----UGUAU--------AAG--AAAACCCGUUGU---C-----UUCGGACAACGGGUUUUCU
AP009484.1/660819-660915     AUGAAAUUGAUCACA-UACCAAAC---A------U--AC--CCCUUUGUUUGA--GUGAAAGAUUUCUCCCAUCCCCUUUGU--------------------U---UAAUACCGUG-----U-----AUACAGACACGGUAUUUUU
AP008934.1/1857525-1857428   AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGCCGUGU----A-----AUCAG-ACACGGCGUUUUU
AM295250.1/605317-605414     AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGCCGUGUC---U-------GAAUACACGGCGUUUUU
CP000255.1/991517-991614     AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGUCGUG-----U-----AUUCAGACACGACGUUUUU
CP000817.1/1311650-1311762   GUGAAAUAAAUCACAAAA-CAAAC---A------U--ACACCCCUUUGUUUGAACGUGAAC-AUUUCUCCCAUCCCCUUUGU--------GAA---------AA--AGAAGCGUCUCUAUC-GGUCGAGGAUAGAGGCGUUUCUUU
ACNH01000027.1/21597-21717   GUGAACGAAUUCACA-UA-CAAAC---A------UAUAC--CCCUUUGUUUGAACGUGAAAAU-UUCUCCCAUCCCCUUUAAUAUUUUUAUAAGC-CGUAAAGA--AGAAGACCUGGU---G-----UUUACACCAGGUCUUCUUC
ACLW01000041.1/9530-9650     GUGAACGAAUUCACA-UA-CAAAC---A------UAUAC--CCCUUUGUUUGAACGUGAAAAU-UUCUCCCAUCCCCUUUAAUAUUUUUAUAAGCCGUAAAGAA--GAAGACCUGGUG---U-----UUU-ACACCAGGUCUUUUU
CP000002.3/1262536-1262653   GUGAAAUUGAUCACA-AA-CAAAC---A------UUUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGU--CGUUAAGA-CA--UAAU--AGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUA
ABRX01000001.1/691882-691767 GUGAAAUUAAUCACA-UA-CAAAC---A------U-UAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--GUUAA-----GACAUA-GUGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUC
CP001638.1/846669-846782     GUGAACGAAGUCACA-AA---AACCUUA------U--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--UUGGC-----AACAAG--GAAAAGCCCGGC---------AUUCAGCCGGGCUUUUCCU
CP002472.1/906962-907066     GUGAAGUUGAUCACA-AG-CAAAC---A------U--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGU--UC--GUGUU-----G---AA--AGAGGCCUUGCA---A-----A----CGCAAGGCCUCUUU
#=GC SS_cons                 ::<<<<<<--<<<<-.--.<<<<<...<......_..__.._____>>>>>>--->>>>-->>>>>>:::::::::::::::<.-<.._____.....>.->::..:<<<<<<<<<<<..._....._____>>>>>>>>>>>:::
#=GC RF                      gUGAAauuaaUCACA.aA.CAAAC...A......U..AC..CCCUUUGUUUGAaCGUGAAAaauUUCUCCCAUCCCCUUUGUu.Uc..uuuAa.....g.aaaa..agaggccgcgcc...u.....aUuaaggcgcggccucUUu
//