raw_data/life/L017/0010-RF01747.stockholm

# 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
//