# STOCKHOLM 1.0
#=GF ID isrI
#=GF AC RF01392
#=GF DE isrI Hfq binding RNA
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 45.0
#=GF NC 39.2
#=GF TC 57.3
#=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 29.39 -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 30

ABEJ01000009.1/60520-60618   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AB104436.1/3199-3297         UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCUGG-GCCGUUACAGCCACCAGUUUAAAUGAC
AF021817.1/2883-2785         -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AL627269.1/34901-34999       -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABAO01000027.1/4186-4283     UAUU-GUCGGUGUCUGGCAUCUGCCAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
ABAO01000027.1/33813-33911   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP000026.1/1820880-1820782   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AE017220.1/1158057-1158155   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUGU
AY144492.1/557-460           -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
ABAN01000020.1/46731-46633   -AUGAGUAGGUGCCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABEL01000010.1/46545-46642   UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
ABEL01000010.1/109554-109652 -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AF060858.1/7527-7429         -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUGU
AY144491.1/557-460           -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUUUCUGCCAUAACGGUGAAGCAGGAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
AE014613.1/1892912-1892814   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABEJ01000008.1/1246-1344     UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGAGAUGAUAUCUGCCAUAACGGCGAAGCAGAAGUACUUUCCGG-ACCGUUACAAUCACCAGUUUAAAUGAU
ABEI01000017.1/65512-65609   -AUGGGUAUGUGUCUGGCACCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-GUAU
ABAO01000067.1/1169-1071     UAUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
FM200053.1/1816063-1815965   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001138.1/1047001-1047098   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
CP001113.1/1179781-1179879   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001120.1/1119161-1119257   -AUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
AE006468.1/2761461-2761364   -AUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
CP001113.1/1150121-1150217   -AUU-GUCGGUGUCUGGCAUCUGCCAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
CP001120.1/1182170-1182268   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001127.1/1136117-1136215   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AM933172.1/1055293-1055391   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001127.1/4328656-4328753   -AUU-GUCGGUGUCUGGCAUCUGACAAGGGGAGAUGAUAUCUGCCAUAACGGCGAAGCAGAAGUACUUUCCGG-ACCGUUACAAUCACCAGUUUAAAUGAU
CP001113.1/2761495-2761398   -AUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
ABEH02000010.1/15225-15322   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGGAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
#=GC SS_cons                 .:::::::<<<<<<---<-<<<______>>>->-->>>>>>:<<<_____>>>::::::::::::::::::::.::::::::::::::::::::::.::::
#=GC RF                      .AUgAGUaGgUgUCUGGCAuCuGACAAGaGgCGAUGAuAuCUgCCAUAACGGuGAAGCAGAAGUAaUaUCagg.GucguUAaaAacAccAucuUag.auAU
//
