# STOCKHOLM 1.0
#=GF ID STnc150
#=GF AC RF01402
#=GF DE STnc150 Hfq binding RNA
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 60.0
#=GF NC 58.7
#=GF TC 60.2
#=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 22.98 -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 17971080
#=GF RT A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT membrane protein synthesis from the Salmonella core genome.
#=GF RA Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL Mol Microbiol. 2007;66:1174-1191.
#=GF WK Hfq_binding_sRNA
#=GF SQ 9

AL627271.1/218020-218286     CCUUUUAUUGAAAUAAUCCCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGG-GUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGACUACUAUUGCGGUCUGAAUUGAGGACGUUUUGAUA
AY633740.1/1971-1706         CUUUUUAUUAAAAAAUUCUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAGUUUUGAUA
CP000026.1/1673567-1673844   CCUUUUAUUGAAAUAAUCCCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGG-UCUCAGGUUAUCAUGACGAUCGGCGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGGAGUUUUGAUA
CP001138.1/1888215-1888493   CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUAAUAAGGCACUUUCAAAAAAUAGCCAAACCACCCAUCAUAAAGAAAACCACACACAAUCAAAAUCGGUAACUAUCAGCUUUCAACGGG-GCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGAAGUUUUGAUA
CP001144.1/2041074-2041352   CUUUUUAUUAAAAAAUUAUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAGUUUUGAUA
ABEH02000010.1/181974-181708 CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAAUUUUCAGGGAA-UCUCAGGUUACCAUGACGAUCGGGGUAAAGGAUAGAUUACUAUUGCGGUCUGAAUUGAGGAAGUUUUGAUA
ABAK02000001.1/634826-634549 CCUUUUAUUGAAAUAUUAUCCUGAUAAUAAAAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAACUUUCAGCGGG-GCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGGAGUUUUGAUA
CP001120.1/1330954-1330700   CUUUUUAUUAAAAAAUUAUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAG--------
CP001127.1/1289610-1289344   CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAAUUUUCAGGGAG-UCUCAGGUUACCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCUGAAUUGAGAGAGUUUUGAUA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::<<<______________>>>::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::.:::::::::::::::::::<<<-<<_________________>>->>>:::::::::::::::::::::::
#=GC RF                      CcUUUUAUUgAAAuAuUaUCCUGAUAAUAAcAAuAAAUCUGaUAAGGCACUUUCAAAAAAUAGCCAAAcCACACAUcAUaAAGAAAACCAC.uACAAUCAAAAUCGGUAACUAUCAgcUUUCAGgGgG.uCUCAGGUUAUCAUGACGAuCGGggUAAAGGAUGgAuUACUAuuGCGgUCuGAAUUGAGGgAGUUUUGAUA

AL627271.1/218020-218286     AAUU-----------AUUUUGAUAACCGUUCGAAUACUAAUAAUAAAUAUCCUCCGGCAUAGCCGGAGGUUUUUCUGAUG
AY633740.1/1971-1706         AA-------------GUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP000026.1/1673567-1673844   AAUUUUUUUGAUAAAAUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001138.1/1888215-1888493   AAUUUUUUUGAUAAAAUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001144.1/2041074-2041352   AAUUUUUUUGAUAAAGUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUAGUUUUUA
ABEH02000010.1/181974-181708 AAUU-----------AUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGAACGUUAAGUCCCCGUUUUAGUUUUUA
ABAK02000001.1/634826-634549 AAUUUUUUUGAUAAAGUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001120.1/1330954-1330700   ----------------UUUUGAUAACCGUUCGAAUACUAAUAAUAAAUAUCCUCCGGCAUAGCCGGAGGUUUUUCAGAUG
CP001127.1/1289610-1289344   AAUU-----------AUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGAACGUUAAGUCCCCGUUUUUAUUUUAA
#=GC SS_cons                 ::::...........::::::::::::::::::::::::::<<<<<<<<<<<<-<<_____>>->>>>>>>>>>>>::::
#=GC RF                      AAUU...........aUUUUGAUAACCGUUCGAAUaCUAAUaacaaaaacggggaCGUuaAGuCcccguuuuuguuuuUA
//
