# STOCKHOLM 1.0
#=GF ID cyano-S1
#=GF AC RF03151
#=GF DE Cyanobacterial ribosomal protein S1 leader
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 39.9
#=GF NC 37.9
#=GF TC 40.3
#=GF SE Published; PMID:17621584;
#=GF SS Published; PMID:17621584;
#=GF TP Cis-reg; leader;
#=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; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 17621584
#=GF RT Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT CMfinder comparative genomics pipeline.
#=GF RA Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL Nucleic Acids Res. 2007;35:4809-4819.
#=GF CC cyano-S1 is a ncRNA recognized in the 5-prime region of genes encoding 30S
#=GF CC ribosomal protein S1 [1], it has been proposed as an cis regulation
#=GF CC element.
#=GF WK Cyano-S1_RNA_motif
#=GF SQ 26

URS0000D6C45B_64471/1-83  UUCUGU-AAAAUU-AAAAAUUACUGACCCUUUGUCGGCGGGCGC-UG-GGUCAAUUUUUAUCGCACUGUCC---UCGGGCAGACCGCCAU
URS0000D694F1_59931/1-83  CUCUGU-AAAGUGAGGGAUUGCCUGGAC-CAGGUCGGCGGGCCU--G-CUCCAGUUUCCUUCGCUCUGCUCA--ACGGGCAGACCGCCAC
URS0000D675B0_221360/1-83 AUCUGACAGAAUGACGGAUUCGAUCGUU-GUGGUCGGCGGGCCA--C-CACGUCAUUCCUUCGCACUGUCU---CCGGGCAGACCGCCAU
URS0000D692FB_74547/1-82  AUCUGU-AGAGUGAUCAAUUAAUUCCGA-AAGGUCGGCGGGCCA--C-UCGGAUUUCCUUGCGCACUGCCA---UAGGGCAGACCGCCAU
URS0000D6C4D8_93059/1-84  AUAUGU-AGAGUG-UUGUAUUAGUUCCUCUAGGUAGGCAGGCCU--A-AGGGAAAUACUUUCGCAUUGCCAUA-ACAGGCAUACUGCUAA
URS0000D6C00F_167539/1-82 AGGUGU-AGAGUGAGUUAUCUGUUCCUU-UAGGUUGGCAGGCCU--A-AAGGGCAAAUGUACGCAUUGCCU---CAAGGCAUACUGCCCG
URS0000D6781A_12908/1-85  AUCAAU-AAAGUAGAAUUUAAUCUCAAU-UUGGUCGGCGGGCCA--U-UUUGUAUUCCUAUCGCACUGUUCUAAAAAGGCAGACCGCCAU
URS0000D6D34B_69042/1-81  AUUUGU-AUGAUC-AUGGAUCGCAUGCG-UCUGUCGGCGGGCAGGCA-CGCGUAU-CCCUUCCUUCUGC-CC--UGA-GCAGACCGCCAG
URS0000D69B47_84588/1-86  AUCUGU-AGGAUU-CAUAGUUCUCCUUGAACCGUCGGCGGGCGG--UUCAAGCGAACCACUCGUACUACCCGCAUGAGGUAGACCGCCAU
URS0000D6CA9C_12908/1-86  AUCUGU-AGGAUU-CAUAAUUCUCCUUGAACCGUCGGCGGGCGG--UUCAUGCGAACCACUCGUACUACCCGCAUGAGGUAGACCGCCAU
URS0000D698AE_110662/1-86 GUCUGU-AAAGUC-AGUAGUUCUCCAUGAAACGUCGGCGGGCGU--UCCAUGCGAUUUUUUCGAACUACCCACCUGAGGUAGACCGCCAG
URS0000D683F8_316279/1-86 AUCUGU-AGAGUC-ACACAUUCUCCGUUCAACGUCGGCGGGCGU--UGGACGUGAAUCCUUCGUACUACCCACCUGAGGUAGACCGCCAA
URS0000D69747_12908/1-78  AUACAU-AUCAAA-AUG-UUUUCUGCUA-UUAGUUUGCAGGCUA--A-UGGCGUU-CCUUUCUAACUACC----GAAGGUAGUCUGCGAU
URS0000D67773_74546/1-78  AUACAU-AACACA-AAU-AUUUUUGCUA-UUGGUUUGCAGGCUA--A-UAGCACU-CCUUUCUAACUACC----UAAGGUAGUCUGCGAU
URS0000D6A90A_12908/1-78  AUACAU-AUCACA-AAC-GUUUUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D67CDB_12908/1-78  AUACAU-AUCACA-AAU-GUUUUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D678F5_12908/1-78  AUACAU-AACACA-ACU-GUUUUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGUU
URS0000D68213_12908/1-79  AUACAU-AUCACA-AAUGUUUUUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAC
URS0000D67B4A_12908/1-79  AUACAU-AUCACA-AAUGUAUUUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAC
URS0000D65EDE_12908/1-79  AUACAU-AUCACA-AAUGUUUUUUGCUA-UUAGUUUGCAGGCUA--A-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D6890A_12908/1-79  AUACAU-AACACA-AAUGUAUAUUGCUA-UUGGUUUGCAGGCUA--G-UAGCAUC-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D6C4EA_12908/1-79  AUACAG-AAUACA-AAUGUUUUUUGCUA-CUAGUUUGCAGGCUA--G-UAACAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D69943_12908/1-79  AUACAU-AGCACA-GAUAUUUUUUGCUA-UUAGUUUGCAGGCUG--A-UAGCAUU-CCUUUCUAACUACC----AUAGGUAGUCUGCGAU
URS0000D6B7BB_12908/1-78  AUAAAU-AACACA-AAU-GUUUUUGCUA-CUAGUUUGCAGGCUG--G-UAGCAUU-CCUUUCUAACUACC----UUAGGUAGUCUGCGAU
URS0000D6BD26_59919/1-80  GAAUAU-AACGUA-CAAAUAAUUUGCUCUUUAGUUUGCAGGCUA--AA-AGCAUU-UCUUUCUAACCAUC----UUAGGUGGUCUGCGUU
URS0000D6CFF3_12908/1-80  GAAUAU-AACUUA-CAAAUAAUUUGCUCUUUAGUUUGCAGGCUA--AA-AGCGUU-CCUUUCUAACCAUC----UUAGGUGGUCUGCGUU
#=GC SS_cons              ::::::.::::::.::::::::::<<<<.<<<<<_AAAAA>>>>..>.>>>>:::::::::::::<<<<<_...___>>>>>:aaaaa::
#=GC RF                   AUaUgU.AaaaUa.aauauUUuUUgcua.uugGUuGGCaGGCca..a.uagcauUucCUUUCgaACUgCCc...UuAGGcAGaCuGCcAu
//
