# STOCKHOLM 1.0
#=GF ID IMES-3
#=GF AC RF02036
#=GF DE IMES-3 RNA motif
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 55.0
#=GF NC 50.6
#=GF TC 127.2
#=GF SE Published; PMID:12376536; Weinberg Z
#=GF SS Published; PMID:12376536; Weinberg Z
#=GF TP Gene;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 28.23 -Z 2958934 CM SEQDB
#=GF DR SO; 0001263; ncRNA_gene;
#=GF RN [1]
#=GF RM 19956260
#=GF RT Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT analysis.
#=GF RA Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL Nature. 2009;462:656-659.
#=GF WK IMES-3_RNA_motif
#=GF SQ 32

AACY020666588.1/528-675   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGGCAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-UGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020184545.1/512-365   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUUGACAAUCUA-AGCGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY022278987.1/242-389   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUUACU-UAGAU---GGUCGUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023906506.1/632-777   AGGAUAAAAACUGGGGGGUAUUAGAAGUCAAGAAAAUAAUAG---AUGC---GUCG----GCAUUUAUAGUUUUCGAACACGGACAAAACCAACUCCAGAUGUAUAGAGUUCAGAUCGUCCACAACCUUUCGGUUGGAUCGGAGCUCGAAGUUGGA
AACY022145704.1/89-236    AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUUGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY020498361.1/1001-854  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCAUU-UAGAU---GGUCAUCGCAAGAUUGACAAUUUG-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020337245.1/1393-1540 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY020257101.1/1740-1593 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACACUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAGCUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023852264.1/707-854   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---CGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY021888837.1/709-563   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY023885650.1/635-781   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUGGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUUGAAGUUGGA
AACY021300597.1/306-453   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCACU-UAGAA---GGUUAUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAACA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCGGU-GAAAGGUGAA
AACY022356298.1/458-605   AGGAUAAAAACUGGGGGGUGCUAGAAGUUAAUCACU-UAAUG---GGUCAUCGCAAGAUCGACAAUGUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAACA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023202785.1/871-726   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAGAUGCAG---AAGC---UUAG----GCGUUUGUAUAUUUCGAAUACGGACAAAACCAAACCCAGAAGUAUAGAGUUCAGAUCGUCCACAACCUUUUGGUUGGAUCGGAACUUGAAGUUGGA
AACY020854413.1/116-263   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-CAGAC---AGUCAUCGCAAGAUUGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUUAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGUAAA
AACY020508546.1/1794-1648 AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY020090496.1/1071-926  AGGAUAAACACUGGGGGGUAUUAGAAGUUAAGAAAAUUGUAG---GCGC---UUUA----GCAUUUACAGUCUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUCAGAUCGUCCACAACCUUACGGUUGGAUCGGAGCUUGAAGUUGGG
AACY020328555.1/1541-1691 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAAACGGGUCGUCGCAAGAUGGACAAUCUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUAAA
AACY020224664.1/2056-1910 AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY021897919.1/485-338   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-CAGAA---GGUCGUCGCAAGAUUGACAAUCUA-GGUGAAAA-ACGGACAAAACCAACUUUGGAUCAAUA-AUCUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAG-UGAAAGGUAAA
AACY020092547.1/380-527   AAGAUAAAGACUGGGGGGUGUUAGAAGUUAAUUGCU-CAGAG---UGUCAUCGCAAGAUAGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY023559001.1/557-704   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGGGAUCGUCCACAACUCUCGAGUUGGAUCGCAGCU-AAAGGCAAA
AACY021990316.1/291-438   AGGAUAAAAACUGGGGGGUAUUAGAAGUUAGUUACU-UAGAG---UGUCAUCGAAAGAUAGAUAAUUUA-AGUAAAAA-AUGGACAAAACCAACUCUGGAUUAAUA-AGCUGAGAUCGUCCACAACUCUCGAGUUGGAUCACAGU-AAAAGGUGAA
AACY020503557.1/1589-1736 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCAUU-UAGAU---GGUCGUCGCAAGACUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020267093.1/346-199   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023713779.1/894-1041  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGCU-AAAGGUGAG
AACY021483546.1/235-90    AGGAUAAAAACUGGGGGGUAUUAGAAGUUAAGGAAAAUAUAG---AAGC---UUCG----GCAUUUAUAGUUUUCGAACACGGACAAAACCAACCCCAGAAGCAUAGAGUUCAGAUCGUCCACAACCUUUCGGUUGGAUCGGAUCUCGAAGUUGGA
AACY023357761.1/718-865   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUUGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY022322085.1/613-759   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY021804107.1/46-192    AGGAUAAAAACUGGGGGGUAUUAGAAGUUUUGAAAUAUAUGA---UAA-GU-UUAG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAAAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAAUUUGAAGUUGGA
AACY020246597.1/967-1114  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCACU-UAGAU---AGUCAUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023888787.1/955-808   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
#=GC SS_cons              ::::::::::<<<<<<<<<-------<<<--<<<<<.<<<<<...-<<<<<<____>>>->>>->>>>>.>>>>>-->.>>------->>>-->>>>>>:::::::.<<<<<-<<<<-----<<<<<____>>>>>>>>>->>>>>::::::::::
#=GC RF                   AGGAUAAAAACcgGgGGGugUUAGAAGuuaagcacu.uagac...uguCguCguaaGacuGacagucua.agugcaAa.aCGGACAAAaCCAACcCcgGAucaAUA.agcugAGauCGUCCACaaCcuUuggGuuGGauCGcagcuuaAAGgUgaA
//
