# STOCKHOLM 1.0
#=GF ID isrQ
#=GF AC RF01399
#=GF DE isrQ Hfq binding RNA
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 50.0
#=GF NC 35.7
#=GF TC 94.3
#=GF SE Predicted; ClustalW; Infernal
#=GF SS Predicted; RNAalifold
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 28.23 -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 6

ABEJ01000001.1/95266-95427 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCAUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGUCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AL627284.1/6011-6172       UCAUGUGGUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGCACAGAGAACAUGUCACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AE017220.1/4670675-4670836 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGCCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCUCAAAAAUACGUGGCGCUGAAAGGCACAUUUUU
ABAN01000009.1/29307-29147 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGACGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAA-UACGUGGCGCUGAAAGGCGCAUUUUU
CP001138.1/4718718-4718879 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AE006468.1/4762997-4763158 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUAUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAUAACAUCUCACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
#=GC SS_cons               :::<<<<<<<____>->>>>>>:::::(((((-((((<<<<<<<-<<<<<<<<--<<<<<<<<<<______>>>->>>>>---->>-->>>>>>>>>>>->>>>,,,,,<<<<_________>>>>,))))-----))))):<<<<<____>>>>>::::::
#=GC RF                    UCAcGuGauCUAACGUauCaCgACUAAaCGuaAGGGcaaaGCgGCuggcguguCGuCCgGGCauaAAGUCAuauCGCCcGaACAGagAacacgccaCcGACuuuGAAACGCgaUUUUAUAAUucGCUgCCCAAAAAuaCGuGGcGCcGAAAgGCgCAUUUUU
//
