# STOCKHOLM 1.0
#=GF ID isrF
#=GF AC RF01389
#=GF DE isrF Hfq binding RNA
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 40.0
#=GF NC 32.2
#=GF TC 46.2
#=GF SE Predicted; WAR; Infernal
#=GF SS Predicted; WAR
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 20.29 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 18725932
#=GF RT Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT global post-transcriptional regulator, Hfq.
#=GF RA Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA Hinton JC, Vogel J
#=GF RL PLoS Genet. 2008;4:e1000163.
#=GF RN [2]
#=GF RM 18267966
#=GF RT Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT host-induced expression and role in virulence.
#=GF RA Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA Margalit H, Altuvia S
#=GF RL Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK Hfq_binding_sRNA
#=GF SQ 3

CP000026.1/1399939-1400207 ACAAUAGCCUCACUACCAUCAAGCGA-UA-CUGCUGCUUACGAGAAAC------AAGGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGGUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGC
CP001144.1/1736669-1736962 AGAUUAUCCAGGAGAUACACGAAUUAAUUCUGGCGGGUGAAAUGGAAGUCGCCAAAAGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGCUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGC
CP000857.1/2246703-2246992 AUAACGACCUGGACGCCGGCGAAUUA----UGGCGGGUGAAAUGGAAGUGGCCAAAGGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGGUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGC
#=GC SS_cons               ::::::::::::::::::::::::::.::.::::[[[[,,,,,,,,,,,,,,,,,,((---(((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<______>>>,,,,,,,,,,,<<<<---<<<---<<<<<<____>>>>>>---->>>->>>>,,,,,,,,,,,,,,,,,,,
#=GC RF                    AuAauaaCCuggauaccaaCgAauuA.Ua.ugGCgggugAaauGgAAgUgGCCAAAgGGAUGCuGCGCACGCUGAUUAAAGUCACGUUCGgUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUgCGCAUGuuGUCGCCGGauGUGGauCCGGGUAUCaaAGCGuUUAUAGCCGUUGUCAGAGC

CP000026.1/1399939-1400207 UGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUUCG------UGUGCAGGAUAAGCGGGUG-CAAAUCAACA----------GAAUUCGC
CP001144.1/1736669-1736962 UGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUAAAACCCACUGAGCCAAAAACCUGCGCGACGAACCGGUCACAGUGGCCGGUUUUUUU
CP000857.1/2246703-2246992 UGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUAAAACCCACUGAGCCAAAAACCUGCGCGACGAACCGGUCACAGUGGCCGGUUUUUUU
#=GC SS_cons               ,,,,,,,,,,,,,,,,,,,,,,)))))---)),<<<_____>>>,,,,,,,,,,,,]]]]:::::::<<<<<<<<<_____>>>>>>>>>::::
#=GC RF                    UGCAGAACAUCAGUCAGAAAAAGCaGCGGACcAGGGUaaaACCCACUGaGCcaaAaacccGcGcGACaaacCGGcCACAGUGgCCGguuuUuuu
//
