# STOCKHOLM 1.0
#=GF ID leu-phe_leader
#=GF AC RF01743
#=GF DE leu/phe leader RNA from Lactococcus
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 70.0
#=GF NC 64.6
#=GF TC 74.7
#=GF SE Published; PMID:20230605;
#=GF SS Published; PMID:20230605;
#=GF TP Cis-reg; leader;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 32.99 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF DR GO; 0010468; regulation of gene expression;
#=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 Lactis-leu-phe_leader_RNA_motif
#=GF SQ 9

AE005176.1/1239635-1239796 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCUUU-UGUGGCUAA-AAUAUGUGGGUCCUGUUUGGCGAUA---GUCAUU-UCGAGGACCGAG-AGACGUCCUCAC-GGGCGUCUUUUU
CP000425.1/808768-808614   AAU---AAG-----AAAACGAGGUCCAAAA-AUGACUAAUACACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUU-AGCUA--AAUGUGUGAGUCCUCUUUGGCGUUA---GUCAUUGACGAGGAUGAAG-AGACGUCCUCA--GGACGUCUUUUU
CP000425.1/1233390-1233230 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCU--UUUCGGCUAA-AAUAUGUAGGUCCUAUUUGACAACA---GUCAUU-UCGAGGACCAUG-AGACGUCCUCAG-GGGCGUCUUUUU
AE005176.1/1281659-1281495 AAU---AAUAUUAAAUAUCGAGGUUCCAAAAUGAUUAACAACUUUAAAAAAUUUUAUUUUUUCUUUAUG------AAUGAUCCACAUUAGUU---UUUGGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCCCUG-GGACGUCUUUUU
AM406671.1/1258179-1258019 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCU--UUUCGGCUAA-AAUAUGUAGGUCCUAUUUGACAACA---GUCAUU-UCGAGGACCAUG-AGACGUCCUCAG-GGGCGUCUUUUU
AM406671.1/1728588-1728748 AAU---AA-UUAAAAAAACGAGGUCCAAUAAAUGACUUAUUUACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUUAAGCUA--AAUGUGUGAGUCCUCUUUGACGUUU---GUCAUUAACGAGGACGAAG-AGACGUCCUCA--GGACGUCUUUUU
AM406671.1/1198427-1198591 AUU---AAUAUAAAAUAUUGAGGUUCCAAGAUGAUUAACAACAGUAAAAAAUUUUAUUUUUUCUUUAUA------AAUGAUCCACAUUAGUU---UU-GGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCUCUGGGGACGUCUUUUU
CP000425.1/1276225-1276061 AUU---AAUAUAAAAUAUUGAGGUUCCAAGAUGAUUAACAACAGUAAAAAAUUUUAUUUUUUCUUUAUA------AAUGAUCCACAUUAGUU---UU-GGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCUCUGGGGACGUCUUUUU
AE005176.1/820178-820018   AAU---AA-UUAAAAAAACGAGGUCCAAUAAAUGACUUAUUUACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUUAAGCUA--AAUGUGUGAGUCCUCUUUGACGUUU---GUCAUUAACGAGGACGAAG-AGACGUCCUCA--GGACGUCUUUUU
#=GC SS_cons               :::...::::::::::::::::::::::::((((((,,,,,,<<<<<-<<_____..>>>>>>>,,,,,...,,,,,<<-<<<<<<<<<<<<..____>>>>>-.--->>>>>>>->>,,,,,,,,,,,,...)))))):::<<<<<<<___.___>>>>>>>::.::::::::::::
#=GC RF                    AAU...AAUuuAaAAaAauGAGGuuCuaaAAauGacauauAcacaAgauuuUuuU..aacUuguUguUG...AAGgagGacccACAuUAGcu..UUUuggCUAA.AAuaUGUgggUCcUcUUUGAcGuUa...guCauUaucGaGGAcgAAG.AGAcgUCCuCag.GGaCGUCUUUUU
//
