# STOCKHOLM 1.0
#=GF ID carA
#=GF AC RF04192
#=GF DE carA ncRNA motif
#=GF AU Ontiveros-Palacios N; 0000-0001-8457-4455
#=GF GA 100.0
#=GF NC 88.4
#=GF TC 101.5
#=GF SE Published;  PMID:33970790
#=GF SS Published;  PMID:33970790
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF DR GO; 0010468; regulation of gene expression;
#=GF RN [1]
#=GF RM 33970790
#=GF RT Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial
#=GF RT genomes.
#=GF RA Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X,
#=GF RA King N, White N, Breaker RR
#=GF RL RNA Biol. 2021; [Epub ahead of print]
#=GF CC carA ncRNA motif was reported as a Strong Riboswitch Candidate [1] CarA
#=GF CC ncRNA motif was located upstream of carA gene which codes for the small
#=GF CC subunit of carbamoyl phosphate synthase, which is an enzyme that catalyses
#=GF CC the first committed step in pyrimidine and arginine biosynthesis. It is
#=GF CC proposed as a possible cis-regulatory element.
#=GF WK CarA_ncRNA_motif
#=GF SQ 35

NZ_CP015018.1/1110809-1110609     GGUGGACUUCUCACUUUAAAGGC-UAA--UUGGCUAAGGGUUCAAG---GGCUUGCGGACCAAAACUGGUAUCAUUGCAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCUCGGGUUAGUAUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_CP015922.1/931078-931278       GGAGGAAAUCUGCCUUUAGAGCC-CAU--UUGGCUGGGGAUUCAAG---GGUUUAAGGACCAAAACUGGUAUGAUUGCAAGGUUCGAAACUUAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCCCGGGUUGGUCUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NC_009379.1/1020203-1020003       GGUGGACUUCUCACUUUAAAGGC-UAA--UUGGCUAAGGGUUCAAG---GGCUUGCGGACCAAAACUGGUAUCAUUGGAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCUCGGGUUAGUAUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_LZMQ01000003.1/558744-558543   GGAAGAAAACCCCUUUUUAAGCC-UGU--UUGGCUGGGAAUUCAAA---GGUUUAAGGACCAAAACUGGUAUGAUUGCAAGGUUCGAAACUUAUUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAAUACACCCCGGGUUGGUCUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_LOJI01000035.1/156322-156123   AGGGGCUUUUUCCUUUGUAAGCC-CCA-UUUGACUGGAUAUUCAAG---GGUUUACGA-GCAGAAAUGGUAUGAUUGCAAGGUUCGAAACUAAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUCUUUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_LZFI01000002.1/418693-418494   -GGGAGCUUUUUACCUUCCAGCCCCCA-UUUGGCUGUAUAUCCAAG---GGUUUACGA-GCAAAAAUGUUAUGAUUGCAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCACCCGCAAAAAU-AUCCCCGGGCUAGUCUUUUGU-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NC_010531.1/728061-728261         GGAGGGUGCCUCCCUGUGGACCC-CAU--UUGACAGAGUUUUCAAG---GGUUUACGA-GCAGAAAUGGUAUGAUCACAGGGUUCGAAACUAAUUAAAA-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUCUUUUUUGAGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_LVJO01000001.1/1020203-1020003 GGUGGACUUCUCACUUUAAAGGC-UAA--UUGGCUAAGGGUUCAAG---GGCUUGCGGACCAAAACUGGUAUCAUUGGAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCUCGGGUUAGUAUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_CP007501.1/771730-771924       ----GCUUAUUAGCUUGCAAGCC-CAA--UUGGCUGGGAAUCCAAG---GGUUUAUAA-GCAAAACUGGUAUGAUUGACCGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NC_020417.1/767597-767793         --GGGCUUAUUACCUUCUGAGCC-UAA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUACUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
NZ_LOJJ01000003.1/134636-134835   AGGGGCUUAUCCGCUUCUGAGCC-CAA--UUGGCUGGGAAUUCAAG---GGUUUAUA-CGUAAAACUGGUAUCAUUGUUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAUUCCA-GGGUUGGUCUUUUUU-GGGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP004348.1/767596-767793          -GGGGCUUAUUACCUUCUGAGCC-UAA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUACUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061288.1/990866-990675          --------UUUCCAUCUAAAGCC-CCA-UUUGGCUGGGUAUCCAAG---GGUUUACGA-GCAAAAAUGGUAUGAUUACAGGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUCUAUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP023277.1/1240050-1239907        --------------------------------------------------------------GAACUGGUAUCAUUACGCUAU-CAGUAACUAAUAAUU-UGCCCUAGCGCUUAAAGACACUUA--CCUCCC-CGCAAUUUCGCCUCGGGUUUGUCUUUU---GGGGCAA--AAAGUGUUGGACGGCAACAGGGUAUUGG
CP061292.1/1196831-1196687        --------------------------------------------------------------GAACUGGUAUCAUUACGACUAUCAGUAACUAAUAAUU-UGCCCUAGCGCUUAAAGACACUUA--CCUCCC-CGCAAUUUCGCCUCGGGUUUGUCUUUU---GGGGCAA--AAAGUGUUGGACGGCAACAGGGUAUUGG
LT606947.1/428675-428873          GGGGGCUUAUUACCUUCUAAGCC-CAA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUACUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP023276.1/758684-758862          UAAGGCU-----------GCGGC-UGG-UUUGGCGGG------AAG-------CGGACCUGCGAACUGGUAUUAUUGUUGGGUUCGUAACUCAAUAAAU-UACCCUAGCGCUUAAAAACACUCA--CCUCCCG--CAAC--CACUUCCGGGUAGGCUAUUUG-GGGGUGU--UGAGCGUUGGAUGGCAGCAG-GGAUUGG
LT615227.1/1561599-1561414        --------------UCCAAAGCC-CCA-UUUGGCUUGGUAUUCAAG---GGUUUACGA-GCAAAAAUGGUAUGAUUGCAAGGUUCGAAACUAAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUAGUCUUUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061304.1/942048-941889          -------------------------------------------AAG---GGUUUACGA-GCAAAACUGGUAUCAUUGCAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCCCGGGUUGGUCUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061297.1/724764-724962          UGGGGCUUAUUGCCUUCUGAGCC-UAA--UUGGCUGGGAAUUCAAG---GGUUUAUA-CGUAAAACUGGUAUCAUUGGCAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061290.1/967916-967757          -------------------------------------------AAG---GGUUUACGA-GCAAAACUGGUAUCAUUGCAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCCCGGGUUGGUCUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061316.1/813428-813626          GGGGGCUUAUUACCUUCCAGGCU-UGA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUGUUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061287.1/1064613-1064439        -------------------------AU--UUGACUGGAUAUUCAAG---GGUUUACGA-GCAGAAAUGGUAUGAUUGCAGGGUUCGAAACUAAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUCUUUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061299.1/1231687-1231479        G-----AUUUAUCCCCUAUUUUC-AUUUGUGGCAGAUGCGACAAAUGGGGUCAAACACCCCCGGUAAGGUAUAAUUUCUUAGUUAAAUUAUUAG-AUACUUGCCCUAGCGCUUAAAGACACAUAUACCUCCCG--AAAAUUCUCAGACCGGAGGUGUCUUUUCCGGAUGAGGGAUGUGUCGGAUGGCAGCAGGGCUUUGG
CP015018.1/1110770-1110609        ------------------------------------------CAAG---GGCUUGCGGACCAAAACUGGUAUCAUUGCAAGGUUCGAAACUUAAUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAUAAACAAGCCUCGGGUUAGUAUUUUUG-GGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061318.1/789323-789521          UGGGGCUUAUUCGCCUUCAAGCC-UCA--CCGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUACUAGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061309.1/950687-950519          ----------------------------------UGGGUAUUCAAG---GGUUUACGA-GCAAAAAUGGUAUGAUUACAGGGUUCGAAACUUAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCCAAAAACAUCCUCGGGUUGGUCUUUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061319.1/768516-768714          GGGGGCUUAUUACCUUCCAGGCU-UGA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUCAUUGUUAAGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061314.1/836618-836816          AGGGGCUUGUUACCUUGCAGGCC-UAA--UUGGCUGGGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUGAUUCAAGGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061285.1/974128-973927          AGGAGCUUUUUCCUUCUAGAGCC-CUA-UAUGGCUGGGUAUUCAAG---GGUUUACGA-GCAGAAAUGGUAUGAUUACAGGGUUCGAAACUAAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCCAAAAACAUCCUCGGGUUGGUCUUUUUUGAGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP049679.1/943249-943110          -----------------------------------------------------------------CUGGUAUCAUUGCAAGGUUCGAAACUCAAUAAU--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAACAGCCUU-GGGGUAGUCUUUUUG--AGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP007501.1/771726-771924          AGGGGCUUAUUAGCUUGCAAGCC-CAA--UUGGCUGGGAAUCCAAG---GGUUUAUAA-GCAAAACUGGUAUGAUUGACCGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
LT606949.1/869691-869493          GGGAGCUUUUUCCUUUUAGAGCC-CAU--UGGGCUGGGGAGUCAAG---GGUUUACGA-GUAAAAAUGGUAUGAUUUAAGGGUUCGAAACUAAUUAAA--UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUUUUUUUG-AGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP061317.1/839139-839337          AGGGGCUUAUUACCUUGCAAGCC-CAA--UUGGCUGCGAAUCCAAG---GGUUUAUA-CGCAAAACUGGUAUGAUUGAACGGUUCAAAACUUAAUAAAU-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCACAAACAGUCCU-GGGUUGGUCUUUUUG--GGGUGU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
CP001010.1/728061-728261          GGAGGGUGCCUCCCUGUGGACCC-CAU--UUGACAGAGUUUUCAAG---GGUUUACGA-GCAGAAAUGGUAUGAUCACAGGGUUCGAAACUAAUUAAAA-UACCCUAGCGCUUAAAGACACUCA--CCUCCCGCAAAAAC-AUCCUCGGGUUGGUCUUUUUUGAGGGUUU--UGAGCGUCGGAUGG-AGCAG-GGACUGG
#=GC SS_cons                      :::::::::::::::<<<-<<<<.___..__>>>>->>><<<____...>>>:::::::::::::<<<<<<____>>>>>>::::::::::::::::::.::<<<<---<<<<---<<<-<<<<..---<<<---<<<<----<<_______>>---->>>>.->>>---..>>>>->>>----->.>>>>>.>>:::::
#=GC RF                           gGgGGcuuuuuuccUuccaagcC.uaa..UuGgcugggagcccAAG...ggcUUAcaacgCAaAAcugguAUcAUUaccagGUUCaAAAcUUAaUAAAu.UAcCCUAGCGCUuAAAGACACuCa..CCUCCCGCAcAAacaauCcucGGGUUgGUcUUuUUg.gGGGUuU..uGaGCGUCGGAUGg.AGCAG.GgAcUGG

NZ_CP015018.1/1110809-1110609     AGAUGG--UUUGUCACCC
NZ_CP015922.1/931078-931278       AGAUGG--UUUGUCACCC
NC_009379.1/1020203-1020003       AGAUGG--UUUGUCACCC
NZ_LZMQ01000003.1/558744-558543   AGAUGG--UUUGUCACCC
NZ_LOJI01000035.1/156322-156123   AGAUGG--UUUGUCACCC
NZ_LZFI01000002.1/418693-418494   AGAUGG--UUUGUCACCC
NC_010531.1/728061-728261         AGAUGG--UUUGUCACCC
NZ_LVJO01000001.1/1020203-1020003 AGAUGG--UUUGUCACCC
NZ_CP007501.1/771730-771924       AGAUGG--UUUGUCACCC
NC_020417.1/767597-767793         AGAUGG--UUUGUCACCC
NZ_LOJJ01000003.1/134636-134835   AGAUGG--UUUGUCACCC
CP004348.1/767596-767793          AGAUGG--UUUGUCACCC
CP061288.1/990866-990675          AGAUGG--UUUGUCACCC
CP023277.1/1240050-1239907        AGAUUG--UUUGUCGCCC
CP061292.1/1196831-1196687        AGAUUG--UUUGUCGCCC
LT606947.1/428675-428873          AGAUGG--UUUGUCACCC
CP023276.1/758684-758862          AGAUGG--UUUGUCACCC
LT615227.1/1561599-1561414        AGAUGG--UUUGUCACCC
CP061304.1/942048-941889          AGAUGG--UUUGUCACCC
CP061297.1/724764-724962          AGAUGG--UUUGUCACCC
CP061290.1/967916-967757          AGAUGG--UUUGUCACCC
CP061316.1/813428-813626          AGAUGG--UUUGUCACCC
CP061287.1/1064613-1064439        AGAUGG--UUUGUCACCC
CP061299.1/1231687-1231479        AGAAUACCUUUGCUGCCA
CP015018.1/1110770-1110609        AGAUGG--UUUGUCACCC
CP061318.1/789323-789521          AGAUGG--UUUGUCACCC
CP061309.1/950687-950519          AGAUGG--UUUGUCACCC
CP061319.1/768516-768714          AGAUGG--UUUGUCACCC
CP061314.1/836618-836816          AGAUGG--UUUGUCACCC
CP061285.1/974128-973927          AGAUGG--UUUGUCACCC
CP049679.1/943249-943110          AGAUGG--UUUGUCACCC
CP007501.1/771726-771924          AGAUGG--UUUGUCACCC
LT606949.1/869691-869493          AGAUGG--UUUGUCACCC
CP061317.1/839139-839337          AGAUGG--UUUGUCACCC
CP001010.1/728061-728261          AGAUGG--UUUGUCACCC
#=GC SS_cons                      ::::::..::::::::::
#=GC RF                           AGAUGG..UUUGUCACCC
//
