# STOCKHOLM 1.0 #=GF ID msiK #=GF AC RF01747 #=GF DE msiK RNA #=GF AU Weinberg Z; 0000-0002-6681-3624 #=GF GA 33.0 #=GF NC 32.9 #=GF TC 34.6 #=GF SE Published; PMID:20230605; #=GF SS Published; PMID:20230605; #=GF TP Cis-reg; #=GF BM cmbuild -F CM SEED #=GF CB cmcalibrate --mpi CM #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 2958934 CM SEQDB #=GF DR SO; 0005836; regulatory_region; #=GF RN [1] #=GF RM 20230605 #=GF RT Comparative genomics reveals 104 candidate structured RNAs from bacteria, #=GF RT archaea and their metagenomes. #=GF RA Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR #=GF RL Genome Biol. 2010;11:R31. #=GF WK MsiK_RNA_motif #=GF ** seedtax: Bacteria; unclassified sequences #=GF SQ 120 BAAY01007686.1/255-195 AAAGAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAAUC AACY023308612.1/1044-986 GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU BX248355.1/160867-160810 CACUUUAU----UUCUUCUACU-CGGAUCGUUCGGCACGUACCUGCCGAUA-AAGAA---UGGAGUU- AACY020556781.1/1408-1350 CGAACA-----UCGCUCUUACUUCGGAUCGUCCGGCACGUUCCUGCCGGUGAGAG-GA--ACCACCA- AACY023290927.1/440-498 GGCCAUCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU AACY023803192.1/795-737 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA AACY023828838.1/892-834 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020296654.1/3720-3776 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023817491.1/7-64 UGUUGGAUG-----CUUUCACCACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023314832.1/131-189 CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAAG----GAGUGCUA AACY022653449.1/402-460 GCGCGGCA-----UCCAUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGA----GAAAAUAA AACY021215036.1/138-80 UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- AM849034.1/2895497-2895439 GCAUCACA-----UCCAUCACCACGGAUCGUCGGGCACGUACCUGCCCGUGAAGGA----GAACACCG AACY020059319.1/116-58 UGGA-----CUUGCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAGA--- CP000667.1/4785498-4785555 CGGCCCGC-----UCUUUCACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAAGG----AAGCACCC AACY022515996.1/291-233 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY023808612.1/943-1001 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA- AE014295.3/1661060-1661118 GAACAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--UAGUAA-- AACY020309138.1/212-270 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020711540.1/892-834 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA AACY020801666.1/396-454 UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU--- AACY023816586.1/1430-1488 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA AE017283.1/439778-439720 GUCACCGA-----UUUUCCACAACGGAUCGUCGGGCACGUACCUGCCCGUGGAAAG----GAACAACG CP001341.1/953078-953020 AAACAUGAA----CCAUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----GAUUGAUA AAMN01000005.1/40921-40863 GGGUUU-----UUCCCUUUACAACGGAUCGUCCGGCACGUUCCUGCCGGUGAAGG-AA--GGCAAUG- AACY020530366.1/1402-1460 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020523976.1/2197-2141 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023442678.1/506-448 CCCA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGGAA--- AACY023841016.1/464-520 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY021171437.1/836-780 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY021496387.1/154-96 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020303265.1/68-126 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020599560.1/709-651 UGGA-----CUUGCUUCAUCCAACGGAUGGUCGGGCACGUACUUGCCCCGAGAAGG-AAGAGAAA--- AACY020064545.1/673-730 AAGAGGC----AC-UCGUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA--- AACY020470988.1/2403-2346 ACGAGGC----ACUC-AUCACGAAGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA--- AACY023319023.1/289-231 GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU AACY023331894.1/236-178 GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU AACY023355258.1/868-926 AAAUCGUU----UCCAUUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAACA- AACY020170145.1/1281-1223 AGGAUGA-----CCUAUCUCCAACGGAUCGUCCGGCACGUACCUGCCGGGAGA-GGG---AGCUAACG AACY023323829.1/260-317 GGCUAACG-----CCUUACCCU-CGGAACGUCGGGCACGUACCUGCCCGGAUAAGG----AAGAAAUA AACY023430589.1/1577-1636 -CCGUGAGA---CCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGA-GAAGG---AGUAAACA AACY020169821.1/1024-1081 UGGUCGCAA-----UACUUCCAAAGGAUCGUCGGGCACGUACCUGCCCGGAAGGA-----GAAAAAAU AACY020177699.1/315-373 UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- AACY020051425.1/729-671 UGGA-----CUUGCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAGA--- AACY023443860.1/741-683 CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGUAAUA AACY020058740.1/867-924 AAGAGGC----AC-UCGUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA--- AACY023834223.1/295-237 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY022769167.1/65-123 GGGA-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAAA--- AACY023291338.1/1308-1251 GCCAUAAC-----CUUCAUCCU-CGGAUCGUCGGGCACGUACCAGCCCGGAUAAGG----AAGUCUUC AP009256.1/2026471-2026413 ACAAAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAA-- AACY023838183.1/673-731 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY023836095.1/167-109 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA AACY021127318.1/81-23 GGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- AACY023352948.1/821-764 AGCGAUCA----C-CUAUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAG---AAACAA-- AACY023256209.1/29-86 ACGAGGC----ACUC-AUCACGAAGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA--- AACY020538448.1/527-469 CUCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY023318012.1/501-443 GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGAAAU AACY022901723.1/625-567 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA AE016822.1/1880494-1880552 CCACAUCA-----UCCAUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGA----GAACACGA AACY023844945.1/1161-1219 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY021052297.1/178-120 GGAGUAAC-----CUCCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAAGGAG----AGCUAGAA AACY021345393.1/154-96 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020554771.1/6628-6686 UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- AACY020176623.1/1738-1796 AAAAAGAC-----CUUCAUCCAACGGAACGUCGGGCACGUACCUGCCCGGAAGAAG----GAGUAAAA AACY023795141.1/1172-1114 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020619186.1/175-233 CUCG-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- ABMI01052056.1/105-49 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023836412.1/551-495 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023792959.1/1429-1476 ---------------UUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023294700.1/958-1016 CAGUA----ACU-CUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AGUAAGUA--- AACY022775623.1/200-141 GCUGGCG-----CCUUUAUCCAACGGAUCGUCGGGCUCGUACCUGCCCGGUUAAGGG---AGUUACUU AACY020468017.1/554-613 -CCGUGAGA---CCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGA-GAAGG---AGUAAACA AACY023982826.1/13-71 GACCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU AACY023340538.1/662-720 GCUCAUCA-----CCUUCACCUACGGAUCGUCGAGCACGUACCUGCUCGGAGAAGG----AGAAAUUC AACY020296024.1/375-317 CGAACA-----UCUCUCUUACUUCGGAUCGUCCGGCACGUUCCUGCCGGUGAGAG-GA--ACCACCU- AACY023434470.1/1454-1512 UGGA-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA--- U12007.1/36-95 -CACCACCA---CCUUCCUACAACGGAUCGUCCGGCACGUUCCUGCCGGUAG-AAGG---GGGCCCUU AACY023331001.1/307-249 UGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGAAAUA BA000030.3/4887082-4887138 UGGACACCA-----CCUUUACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAGG-----GGGCCCCU AACY020525511.1/587-645 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020011956.1/378-436 GGGUGGGU----UCCAUUCACAAAGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAAUC- AAOB01000005.1/162025-162083 GAUCGCUG----UCCAUUCACUAAGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAAAU- AACY020307023.1/1756-1814 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA- AACY023801115.1/426-484 GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA CP000750.2/1372523-1372582 -UGAAGACC---CCAUUCCACAACGGAUCGUCCGGCACGUACCUGCCGGUGGAA-GG---ACACACGA CP000605.1/1702669-1702727 GAACAAAU-----CCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGG----AUUAGUAA AACY023315685.1/655-597 GGUUAGCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAAUUAC CP000850.1/5276815-5276872 CGGUCCGU-----UCUUUCACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAAGG----AAGCACCC AACY023818985.1/972-916 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023293856.1/1006-1063 ACCAGCAC-----CUUCAUCCU-CGGACCGUCGGGCACGUACCUGCCCGGAUAAGG----AAAUGUAA AACY020165622.1/5444-5502 CCAC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGAAA--- AACY023826769.1/1080-1024 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY020533395.1/706-648 GGCUGUCG----UCUCUUCACGACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA- AACY023292971.1/264-205 CAGUGAGA----CCUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGA-GAAGG---AGUAAUUA AP006618.1/5869874-5869931 UGCCGACA-----CCCUGUACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAGGG----AAGUAUCU AACY020524589.1/159-101 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY020296610.1/2203-2147 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY020172986.1/652-594 CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGUAAUA CP000474.1/988504-988446 GAAAAUGAA----CCAUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----GAUUGAUA AACY020174331.1/171-229 GUGUAGGG----CUCUAUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGA-GGAG---AAAAAAU- AACY020176753.1/132-74 UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU--- AACY023806029.1/782-838 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY023822562.1/1011-1067 CCGUCG------UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-GGAGA---GGAAAAA- AACY023799473.1/826-768 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA- AACY022641081.1/812-869 CCACCUUU-----CUUCUUACAACGGAUCGUCCGGCACGUUCCUGCCGGUGA-GAG----GACUUGUC AACY021867778.1/709-766 GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAA-- AAQK01003194.1/85-143 ACAAAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAA-- AY842007.1/445-387 UUCACUG----UUUCUCACACUACGGAUCGUUCGGCACGUACCUGCCGAUG-GAGGAG--AUUCUG-- AACY023826784.1/354-298 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY020467656.1/1124-1066 GGCCAUCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU CP000431.1/4502789-4502731 CGGCACAC----CCCUAACACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGG-AGGG---AUUCAUUU AACY023309530.1/927-871 -GGCCAGCA-----CUUAAUCCUCGGAUCGUCGGGCACGUACCUGCCCGGAUAAG-----GAAAGUGA CP001601.1/1416488-1416546 UUCACUG----UUUCUCACACUACGGAUCGUUCGGCACGUACCUGCCGAUG-GAGGAG--AUUCUG-- AACY021516186.1/700-758 UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU--- AAYI02000004.1/407474-407531 CCACGG------UCACCCCACUACGGAUCGUCCGGCACGUACCUGCCGGUGGGAAGG---AAAACUC- AACY023307698.1/644-701 GCUGUCC-----UCUAUUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAUACAC- AACY020294371.1/1956-2012 GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA AACY022762350.1/772-830 CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGAAAUA AACY023224611.1/1289-1232 GACGAACA----C-CCAUCACAAUGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAG---AAGAUC-- CP000509.1/1122407-1122464 CCGUGCUCA----CC-UUUACGACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----AGUUGUUC #=GC SS_cons ::::::::....:<<<<<<<-----------<<<<<<______>>>>>>>>>>>>>....:::::::: #=GC RF ggcaauca....uCcuuucaCAACGGAUCGUCcGGCACGUACCUGCCgGugaaagG....AgaaAaaa //