# STOCKHOLM 1.0 #=GF ID DUF3800-VI #=GF AC RF02915 #=GF DE DUF3800-VI RNA #=GF AU Weinberg Z; 0000-0002-6681-3624 #=GF GA 35.0 #=GF NC 34.9 #=GF TC 35.6 #=GF SE Weinberg Z #=GF SS Published; PMID:28977401; #=GF TP Cis-reg; #=GF BM cmbuild -F CM SEED #=GF CB cmcalibrate --mpi CM #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.79 -Z 2958934 CM SEQDB #=GF DR SO; 0005836; regulatory_region; #=GF RN [1] #=GF RM 28977401 #=GF RT Detection of 224 candidate structured RNAs by comparative analysis of #=GF RT specific subsets of intergenic regions. #=GF RA Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, #=GF RA Sherlock ME, Breaker RR #=GF RL Nucleic Acids Res. 2017;45:10811-10823. #=GF CC Actinobacteria, Planctomycetes, Proteobacteria, Spirochaetes. Nearby to #=GF CC DUF3800 #=GF WK DUF3800_RNA_motifs #=GF SQ 87 URS0000D6ADF0_12908/1-52 CGAC-UAGAAGGGCUGC-ACAA-----GUGGCUCGUUAGGG--UUUAA-----CCCUGUCUG-GUUG URS0000D699E3_12908/1-51 UCGC-CGGGAGUGC----GUCAUUUA----GCACGCUGGGGC-UACG-----GCCUCACCCG-GCGU URS0000D66B14_12908/1-51 UCGC-CGGGAGUGCGU--CACA------GUGCACGGCGGGGC-UUCG-----GCCCCGCCCG-GCGU URS0000D6B946_12908/1-51 UCGC-CGGGAGUGCG---UCACAC-----UGCACGCUGGGAC-UGAG-----GUCCCACCCG-GCGU URS0000D6D3AA_12908/1-55 UGGU-UGAGAGGAUCGC-CCUCU----GCGGUCCGCCAAGG--CAUUCGU---CCUUGCUCG-GCCA URS0000D65F02_12908/1-52 CGAU-CAGGAGGGUUGC-AUUU-----GCGAUCCGUUAUGAA-GCA------UUCAUACCUG-GUUG URS0000D6D0FD_12908/1-49 -GGCCUGGGAGAUCC---UCUUU------GGAUCGUCGGAG--UUAA------CUCCGCCCGGGCCU URS0000D68C73_12908/1-56 CAGU-UGAGAGGCCUGC-CUUUUAU--GCGGGUCGCGAGAA--CAUAGU----UUCUCCUUG-ACUG URS0000D6AB1D_316056/1-53 UGGU-CGGGAGGUCCGC-CGUC-----GUGGACCGUUGGAAU-CUUU-----AUUCCACCCG-GCCG URS0000D69FD7_12908/1-47 UGGC-UGAGAGGGUAU--CUCG------AGGUUCGCUGGA---UUUU-------UCCACUCG-GCUG URS0000D67AB8_12908/1-54 -GAGUCGGGAGCGCUGU-CGAUU----ACGGUGCGUUGG-GC-GAUU-----GUUCCACCCGGCUUA URS0000D6D2E7_12908/1-51 --GU-UGGGAGCGCUGU-CGAUC----ACGGUGCGUUGG-AC-GAUU-----GUUCCACCUG-GCUC URS0000D673C5_565443/1-52 -GGC-CAGGAGUGCUGU-CGAUC----ACGGUGCGUUGG-AC-GAUU-----GUUCCACUUG-GCCU URS0000D6C406_12908/1-51 -CAGUUGGGAGAGCCG--CAGUUU----UGGUUCGUUGGA---AUUAU------UCCACCCGGCUGC URS0000D66180_12908/1-53 -CAGUUGGGAGGUCCGC-CGUA-----GCGGAUCGCAGGGG--UUUGU-----CCCCACCCGGCUGC URS0000D6C375_12908/1-55 -CGGUUGGGAGGUCCGC-CGAU-----GUGGACCGCUGGGGU-CUCGU----ACCCCGCCCGGCCGC URS0000D6A5CE_1187851/1-55 GCGGUUGGGAGGUCCGC-CGAU-----GCGGACCGUCGGGGU-CGUU-----ACCUCGCCCGGCCGC URS0000D66F43_12908/1-54 -CGGUUGGGAGAGCUGC-AUGAUU---GCGGUUCGUCGGGG--UCAU------CCCCGCCCGGCCGC URS0000D6B42A_12908/1-49 CAGU-UGGGAGAGCCG--CAGAG-----CGGUUCGCCGGA---CAAUG------UCCGCCUG-GCUG URS0000D65F74_12908/1-57 CGGU-CGAGAGGGCUGUGAUAUU---UACCGUCCGCUGUGGA-CAGGU----UCCACACUCG-GCUG URS0000D6616C_12908/1-52 UGGU-UGGGAGGGCCGC-AGGU-----GCGGUUCGUUGAAG--UUAUG-----CUUCACCUG-GCCU URS0000D695EF_12908/1-54 --GU-UGGGAGAGCUGC-AUUAUA---GCGGUUCGUUGGGG--UUUCAAU---CCCCACUUG-GCAC URS0000D6616B_12908/1-55 -GGU-UGGGAGAGCUA--UAUUGU----UGGUUCGUUGGAUGAUUUGA---UCAUCCACCCG-GCUG URS0000D6BA4E_12908/1-55 AGGU-CAGGAAGGCUGC-AUUAA----GCGGUCUGCUGGGGA-GUAAA----UGCCCACCUG-GCUA URS0000D67641_12908/1-53 GGGU-CAGGAGGGCUAC-AUUA-----GUGGUCCGCUGGG---GCUCCUUA---CCCACCUG-GCUA URS0000D68067_12908/1-54 CGGU-UGGGAGAGCUGC-GGUUGC---GCGGCUCGUUAGAG--UAAGU-----CUCUACCCG-GCUG URS0000D6B266_12908/1-51 CGGU-CGGGAGAGCUGC-AUGA-----GCGGUUCACUGGAC--AGAG------GGCCACUCG-GCUG URS0000D68C83_12908/1-47 --GU-UGAGAGAGCCG--CCUUUUUU--CGGUUCGUUGG----GAAA--------CCACUCG-GCUG URS0000D68B60_12908/1-53 CGGU-UGAGAGGGCC---CGUUGUGC---GGUCCGUUGGGGU-UGAA-----ACCUCACUCA-GCUG URS0000D676C7_12908/1-53 UGGU-CGGGAGAGCCGC-AUACA----GCGGUUCGCUGGAG--AUAAC-----CUCCACCCG-GCUU URS0000D68C5F_262489/1-54 UGGU-CGCGAGGGCUGU-AUUCG----GCGGUCCGCUGGGG--AUAAAA----CCUCACCCG-GCUA URS0000D6BA05_12908/1-52 CAGU-UGAGAGAGCCGU-AUCAG----ACGGUUCGCUAGGC--AUAA------GCCUACUCG-GCUG URS0000D6A8C5_12908/1-52 CAGU-UGAGAGGGCCGC-AUUAG----GCGGUUCGCUAGGC--AGCA------GCCUACUCG-GCUG URS0000D6C5C8_12908/1-52 CAGU-UGAGAGGGCCGC-AUCAG----GCGGUUCGCCAGGC--ACAA------GCCUACUCG-GCUG URS0000D691CC_12908/1-52 CAGU-UGAGAGGGCCGC-AUCAG----GCGGUUCGCUAGGC--AUAA------GCCUACUCG-GCUG URS0000D688E5_12908/1-52 CAGU-UGAGAGAGCCG--CAUCAGA---CGGUUCGCUAGGC--AUAA------GCCUACUUG-GCUG URS0000D6938C_12908/1-52 CAGU-UGGGAGGGCCG--CAUCAGA---CGGUUCGCUAGGC--AUAA------GCCUACUCG-GCUG URS0000D6A059_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGUUCGCUAGGC--AUAA------GUCUACUCG-GCUG URS0000D6B3EC_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGUUCGCUAGGC--AUAA------GCCUACUCG-GCUG URS0000D66824_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGUUCGCUAGGC--AUAA------GCCUACUCU-GCUG URS0000D65A58_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGCUCGCUAGGC--AUAA------GCCUACUCG-GCUG URS0000D678C5_12908/1-52 CAGU-UGAGAGGGCCG--CAUUAGA---CGGUUCGCCAGGC--AUAA------GCCUACUCG-GCUG URS0000D663F4_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGUUCGCCAGGC--AUAA------GCCUACUCG-GCUG URS0000D6796A_12908/1-52 CAGU-UGAGAGGGCCG--CAUCAGA---CGGUUCGCCAGGC--AUAA------GCCAACUCG-GCUG URS0000D6C24F_12908/1-53 GAGU-UGGGAAAGCUGC-AUUUG----GCGGUCCGUUGGGG--UCAAU-----CCCCACCCG-GCUA URS0000D66EF9_12908/1-51 -GGU-UGGGAGGGCUG--CAUUGU----CGGUCCGCUGGGA--AAAAU-----UCCCACCUG-GCUA URS0000D6A561_12908/1-54 CGGU-UGGGAGGGCUGC-GGCUC----GCGGUCCACUGAGGU-CAAC-----ACCUCACCCG-GCUG URS0000D6965C_12908/1-55 -GGU-UGAGAGGGCUGC-GUUAUC---GCGGUUCGCUGGGAC-GGUCA----GUCCCACUCA-GCUG URS0000D6AD6E_999437/1-52 -GGGUCAAGAGUGCUGC-CUUUAA---GUGGUGCGUCGAG---UUUU-------CUCGCUUGGCCCU URS0000D66317_12908/1-51 GGGU-CAAGAGUGCUCC-CUUUAA---GUGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D6AEA5_12908/1-51 GGGU-CAAGAGUGCUGC-CUUUAA---GUGGUGCGUCGAG---GUUU-------CUCGCUUG-GCUC URS0000D683D1_12908/1-51 GAGU-CAAGAGUGCUGC-CUUUAU---GCGGUGCGUCGAG---GUUU-------CUCGCUUG-GCUC URS0000D6B2A3_12908/1-51 GAGU-CAAGAGUGCUGC-CUUUAA---GCGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D65F16_12908/1-51 AGGU-CAAGAGUGCUGC-CUUUAA---GCGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D65C06_12908/1-51 GGGU-CAAGAGUGCUGC-CUUUAA---GCAGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D671AF_12908/1-51 GGGU-CAAGAGUGCUGC-CUUUAA---GCGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D671AF_1125725/1-51 GGGU-CAAGAGUGCUGC-CUUUAA---GCGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D65ECD_12908/1-51 GGGG-CAAGAGUGCGGC-CUUUAA---GCGGUGCGUCGAG---UUUU-------CUCGCUUG-GCUC URS0000D671AD_12908/1-51 GGGU-CAAGAGUGCUGC-CUUUAU---GCGGUGCGUCGAG---UUAU-------CUCGCUUG-GCUC URS0000D65D86_12908/1-53 GGGU-UGGGAGUGCUGC-CUUUAU---GCGGUGCGUCGGGC--UUUU------GCCCGCCCG-GCUC URS0000D6C815_12908/1-54 GGGU-UGGGAGUGCUGC-CUUUAU---GCGGUGCGUCGGGC--UUUAU-----GCCCGCCUG-GCUC URS0000D6A8DB_12908/1-53 GGGU-UGGGAGCGCUGC-CUUUAU---GCGGUGCGUCGGGU--UUUA------ACCCGCCCG-GCUC URS0000D6CE50_12908/1-54 GGGU-UAGGAGUACUGC-CUUUAU---GCGGUGCGUUGGGC--UUUAU-----GCCCACCUG-ACUC URS0000D6ADAC_1123508/1-49 -GGU-UGGGAGGGCU---GCAUGC---GCGGUCCGCUGGC---GAUAA------GCCGCCCG-GCUG URS0000D6AFD9_12908/1-49 CGGU-UGGGAGGGCU---GCAUUUGC---GGUCCGUUGGC---GCAA-------GCCACCCG-GCUG URS0000D69042_12908/1-55 CAGU-CGGGAGGGCUGC-AUAUCU---GCGGUCCGUCGGGC--AAGAUA----GCCCGCUCG-GCUG URS0000D6999C_12908/1-54 AGGU-CGAGAGUGCUGC-CUAUAA---GCGGUGCGCAGAAC--GAAUG-----GUUCUCUCG-GCUC URS0000D669D1_12908/1-51 CGGU-UGGGAGGGCUGC-CAUU-----GCAGUUCGCCGGAC--UUCG------GUCCGCCCG-GCUG URS0000D6B88A_12908/1-51 CGGU-UGGGAGGGCUGC-CAUU-----GCAGUUCGCCGGAC--UUCG------GUUCGCCCG-GCUG URS0000D6A56B_12908/1-51 CGGU-UGGGAGGGCUGC-CAAC-----GCGGUCCACCGGAC--GCGA------GUCCGCCCG-GCUG URS0000D68872_12908/1-51 CGGU-UGAGAGGGCUGC-UUUG-----GCGGUCCGCCGGAU--GAAA------AUCCGCUCG-GCUG URS0000D6CF67_12908/1-50 CGGU-UGAGAGGGCU---GCAUUGC----GGUCCGUUGAAC--GAAA------GUUCACUCG-GCUG URS0000D6BDD4_12908/1-51 CAGU-UGAGAGGGCUGU-ACGU-----ACGGUCCGCUGAGC--GCAA------GCUCACUCG-GCUG URS0000D66AFD_12908/1-51 CGGU-UGAGAGGGCUGC-AUGU-----GCGGUCCGCUGAAC--GAAA------GUUCACUCG-GCUG URS0000D65C79_12908/1-50 CGGU-UGGGAGGGCUGC-AUU------GCGGUCCGCUGAAC--GAAA------GUUCGCCCG-GCUG URS0000D6A697_12908/1-54 CGGU-UGGGAGAGCUGC-GAAAUC---GCGGUUCGUUGGGU--UAAUA-----GCCCACCCG-GCUG URS0000D6A013_12908/1-54 CGGU-UGGGAGGGCUGC-AAGUCU---GCGGUCCGUUGAGU--GUCUA-----ACUCACCCG-GCUG URS0000D677F7_12908/1-51 CGGU-UGAGAGGGCUGC-CAAU-----GCGGUCCGCUGGGU--GAAU------ACCCACUCG-GCUG URS0000D68391_12908/1-57 CGGU-UGGGAGGGCUGCGUUUG----CGCGGUUCGUUGAGACCCGAG----GGUCUCACUCG-GCUG URS0000D6783B_12908/1-56 CGGU-UGGGAGGGCUGCGGUUU----CGCGGUCCGUUGGGGC-UCUAA----GCCUCACUCA-GCUG URS0000D687F8_12908/1-49 CGGU-UGGGAGGGCUG--CUUCGG----CGGUCCGUUGGG---UUCG-------CCCACCCG-GCUG URS0000D6A31F_12908/1-49 CGGU-UGGGAGGGCUGC-UUCG-----GCGGUCCGUUGGG---UUCA-------CCCACUCG-GCUG URS0000D69264_12908/1-51 -GGU-CGGGAGCGCUGC-CUUU-----GUAGUGCGUUGAACA-UUUG-----UG-UCACCUG-GCUC URS0000D6818A_12908/1-54 CGGU-UAAGAGGGCUGC-CAUUC----GCGGUCCGCGGAGG--UUUACU----CCUCCCUUA-UCCG URS0000D69BCB_12908/1-52 CGAU-UGAGAGGGCUGC-AAUU-----GUGGUCCGUUGCAAC-UAU------GUUGCGCUUG-GUCG URS0000D68730_12908/1-53 CGGC-UGAGAGGGCGAC-AUUCA----GUCGCUCGUUUGGGA-CCU------UCCCAACUCG-GCCU URS0000D6A6DF_12908/1-55 UGGC-UGAGAGGGCGA--CAUUUGGU--UCGCUCGUUUGGG--GUUACA----CCCAUCUCG-GCCU #=GC SS_cons ((((.((((,<<<<<<<._____....>>>>>>>,,<<<<<..____......>>>>>)))).)))) #=GC RF cGGU.UGgGAGgGCuGC.cuUUa....GCgGUcCGuuGGGg..uuua......cCCCaCcCG.GCUg //