# STOCKHOLM 1.0
#=GF ID StyR-44
#=GF AC RF01830
#=GF DE Salmonella enterica Typhi npcRNA 44
#=GF AU Moore B; 0000-0002-4074-1933
#=GF GA 54.0
#=GF NC 53.8
#=GF TC 54.0
#=GF SE Published; PMID:20460466
#=GF SS Predicted; CMfinder
#=GF TP Gene;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 31.57 -Z 2958934 CM SEQDB
#=GF DR SO; 0001263; ncRNA_gene;
#=GF RN [1]
#=GF RM 20460466
#=GF RT Experimental identification and characterization of 97 novel npcRNA
#=GF RT candidates in Salmonella enterica serovar Typhi.
#=GF RA Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J,
#=GF RA Tang TH, Rozhdestvensky TS
#=GF RL Nucleic Acids Res. 2010;38:5893-5908.
#=GF WK Bacterial_small_RNA
#=GF SQ 34

AE014613.1/2690822-2690714   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG----AAAGAAACAUCUUCGG-
AY116932.1/331-439           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UC--GAA--ACAC---UGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-CUUUCGCAACAC-GAUGAUGAGUCG-----AAAGGGACAUCUUCGG
AF100900.1/239-352           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAAUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCGUAAGAAAAGAAACAUCUUCGG
ABHU01000059.1/3214-3111     -----AAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAACAACG------AGAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
CP000857.1/4171432-4171538   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAGAAUGUUUU-------ACGAAACAUCUUCGG
ABKX01000004.1/394099-393989 CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAAUAGUCG----AAAGAUUAUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
CP001113.1/4386681-4386779   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAAG---------------UGAAACAUCUUCGG
CP000468.1/4355748-4355847   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACUCUGAAG---------------UGAAACAUCUUCGG
CP000880.1/3459447-3459349   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACA------UAAGUUGUUC-----GUGGGUCUCUC-A---AA-UUUUUGCAACGU-GAAG---------------UGAAACAUCUUCGG
AB236014.1/275-381           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAAUG------CGAAUUGUUC----CGUGGGUCUCUC-A---AA-UUUUCGCAA-UU-GAUGGUGUUUU-------ACGAAACAUCUUCGG
FJ410388.1/548-654           CUUU-AAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGCU------CA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAGUC-GGUGAUGAAUCG-----AAAGAAACAUCUUCGG
AF259999.1/375-477           CACUUAAAAUCUG-AUCA-GCUGAAAU--U----GA--ACAC---UGAC--ACG------AACUUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
EU623145.1/240-345           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUG------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGAUGUUUC-------ACGAAACAUCUUCGG
CP000822.1/185538-185640     CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAC-GU-------AA-AGUGUGU-----AUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAAG-UGUUUC-------ACGAAACAUCUUCGG
BAAW01000727.1/1098-993      CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAUGU------UA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGAUGUUUU-------ACGAAACAUCUUCGG
EU623354.1/239-345           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAUCUUU------AAUGGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGGUGUUUU-------ACGAAACAUCUUCGG
CP000964.1/5488123-5488018   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACUGUU------UA-AGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGGUGUUUU-------ACGAAACAUCUUCGG
AJ010486.1/1772-1875         CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAC--UU------AA-GGUGUGU-----UCGAGUCUCUC-A---AA-UUAUCGCAAUGC-GGCGAUGUUUU-------ACGAAACAUCUUCGG
EU721606.1/377-485           CUUAAAAAAUCUGGAUCCUCCUGAAUA--UU--GAA--ACAC---UAAACAAAA------AAAGUAGUUC-----AUAAGGCACUC-A---CA-UUUGCGCAAUGC-GAAGAUUUAUCC-----UAUGAAAAAUCUGCUG
AY116919.1/393-498           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUC------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GUGGGUGUUUU-------ACGAAACAUCUUCGG
EU623213.1/394-491           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUU------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAACCA-GAAG---------------UGAAACAUCUUCGG
DQ399552.1/94-191            CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAUGU------UA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCA-GAAG---------------UGAAACAUCUUCGG
CP000647.1/3202639-3202542   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACUGUU------UA-AGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCA-GAAG---------------UGAAACAUCUUCGG
EU623091.1/238-331           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUU------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCU-GAAG-------------------ACAUCUUCGG
AF047424.1/240-332           CUUUAAAAAUCUGGAACAAGCUGAAAA--UU--GAA--ACAA---UAAACGCGU------AA--GCGUUU-----AUGAGUCUCUCUA---AA-UUAUCACA-CCU-GAAG-------------------ACAUCUUCGG
AY706746.1/462-568           CUUUAACAAUCUGGAACAAGCUGAAAA--UUCGAAA--ACAA--UCGAAUUGCUUUUAACAA-GUGAUUC-----GAGAGUCUCUC-A---AA-UGCUUGCAGCAC-GAAG---------------UGAAACACCUUCGG
AY591328.1/395-501           CUUUAACAAUCUGGAACAAGCUGAAAU--UC-GAAA--ACAC--UCGGAUUGCUUUUAAUAAAGUGAUCC-----GAGAGUCUCUC-A---AA-UGCUUACAGCAC-GAAG---------------UGAAACACCUUCGG
AY587142.1/1755-1856         CUUUAACAAUCUGGAACAAGCUGAAAA--UU--GAA--AC-A---CACAUUAUUG----AAAAAUAGUGU-----GGGGAACUCUC-A---AA-ACUCC--AAGUU-GAAGUGUUAUGC-----AAAUAG------GCAG
AF373202.1/1777-1883         CUUUAACAAUCCGGAACAAGCUGAAUAAUU--UGAA--ACGACGGCAUAUGAAUG----UGAAUUCAUGUGUUGUUCGAGUCUCUC-A--A-AAUACUCGCAUCCC-GAGA--------------------CACUUUCGG
AF548140.1/2032-2148         CUUUAACAAUCCGGAACAAGCUGAAAA--UU-UGAA--ACAC----AUGCUGAAGU-GCAAACUCAGUAU-----GCGAGUCUCUC-AAACGA-AGUAAGCAAACC-UGAGAUAACGCG-----CAAGCGUUAUCACUGU
EU285525.1/2391-2498         CUUUAACAAUCUGGAACAAGCUGAAAA--UUCGAAAAUACUC----GGAUUGCUUUUAAUAAAGUGAUCC-----GAGAGUCUCUC-A---AA-UGCUUACAGCAC-GAAG---------------UGAAACACCUUCGG
FJ517952.1/425-528           CUUUAACAAUCUGGAACAAGCUGAAAA-AUU-GAAA--ACAA--AUCAAUAUAUCA-CCGAGGUAUAUUG-----GUGAGUCUCUC-A---AA-AUCUCA-AAUCU-GAAAAGU-----------------ACUCUUCAG
FJ518551.1/451-563           CUUUAACAAUCUGGAACAAGCUGAAAA-AUU-GAAA--ACAA--AUCAAUAUAUCA-CCGAGGUAUAUUG-----AUGAGUCUCUC-A---AA-AUCUC--AAACU-UUGAAUGUGUU-------UUUCGACAUCGAAGU
ABWM02000001.1/211-104       CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAUCUAU------AA-GGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAGUC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
#=GC SS_cons                 :::::::::::::::::::<<-<<<<<..<<..---..-<<<...-<<<<<<<_......___>>>>>>>.....>>>--------.-...>>.>>>>>>>::::<.<<-<<<<____.......______>>>>->>>:
#=GC RF                      CUUUAAaAAUCUGGAuCAAGCUGaaaa..Uu..GAA..ACgc...ugcAcagcu......AAagcugUgc.....gcGAGUCUCUC.A...aA.uuuuCGCAAcac.gaaGauguaUu.......AuGAAAcauCUucgG
//
