# STOCKHOLM 1.0
#=GF ID Lacto-rpoB
#=GF AC RF01709
#=GF DE Lacto-rpoB RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 40.0
#=GF NC 39.7
#=GF TC 40.4
#=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 27.00 -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 Lacto-rpoB_RNA_motif
#=GF SQ 31

AE005176.1/1864719-1864661   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
CP000387.1/174628-174686     AUUUGUCG-UGUGCUUUAUUUGAAAUAUUGUCCAAAUAGAAGCUU--ACAGCAGUUAAAUCA
CP000419.1/1720910-1720853   AUUUGUCG-UCUUAUUUGAUUGAAAUAUUGUCCAAUCAAG-AGAU--ACAGCAGUUAAAUCA
CP000017.1/93919-93976       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000056.1/93407-93464       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
AE007317.1/1751875-1751818   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AM406671.1/1970359-1970301   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
CP000407.1/110341-110398     AUUUGUCG-UGUGUCUUGUUUGAAAUAUUGUCCAAACAAG-GCUU--GCAGCAGUUAAAUCA
FM177140.1/2635349-2635292   UUUGGACA-GGCUGUCAGGACGAUCUAUUGUCCGUUCUGG-CUAA--UGAAAAAGCAAAAAC
CP000425.1/1876302-1876244   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
AE009948.1/179028-179085     AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
BA000034.2/88129-88186       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000259.1/93729-93786       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000233.1/234847-234900     AAUUGAUU----GUUUGUUAUGAUAUAUUGUCCAUAGCAG-ACUU---GAUAAAAGCAAAAA
AE004092.1/93363-93420       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
FM211187.1/1927843-1927786   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
CP000408.1/110247-110304     AUUUGUCG-UGUGUCUUGUUUGAAAUAUUGUCCAAACAAG-GCUU--GCAGCAGUUAAAUCA
AE009949.1/94021-94078       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000705.1/1544739-1544681   UGAGUUCA-UUUGAACCUGGUGAUCUAUUGUCCAUCAGAU-UCUGC-AUAAAAGCCAAAGAC
ACHL01000156.1/7622-7564     GAUGAAGA-AAAGGCAGAAACGAAAUAUUGUCCGUUUCGG-CUUUAA-UAUAAGGAAACAAA
CP000918.1/1874948-1874891   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AL766844.1/35933-35990       AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
CP000023.1/1667715-1667658   AUUUGUCG-UCUUAUUUGAUUGAAAUAUUGUCCAAUCAAG-AGAU--ACAGCAGUUAAAUCA
AE016830.1/3112617-3112562   AAGUGACG-A--AGCAGGAGCGAAAUAUUGUCCGUUCCGG-UUUU--UUAUAGGAAAACAAA
CP000114.1/188955-189012     AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
CP000920.1/1824936-1824879   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
CR936503.1/1751463-1751404   GUAGAAAA-AUUUAUUGUGCUGAUCUAUUGUCCAGCACGG-UAUUCAUGAAAAGCAAAAAUA
CP000416.1/1660516-1660460   AACUGAAA-UUGAACGU-GCCGAUAUAUUGUCCGGUGACG-UUUG--UUAUAAGAAGCCAAA
AAPZ02000001.1/635020-634962 UGAGUUCA-UUUGAACCUGGUGAUCUAUUGUCCAUCGGAUUCUGC--AUAAAAGCCAAAGAC
CP000936.1/1942796-1942739   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AP010655.1/195434-195491     AUUUGUCG-UUUGCUUUGGUUGAAAUAUUGUCCAAACAAA-GCUC--ACAGCAGUUAAAUCA
#=GC SS_cons                 :::::::<.<--<<<<<<<<<<__________>>>>>>>>.>>--..>>:::::::::::::
#=GC RF                      AUUUGUCg.uaugaUuugucUGAAAUAUUGUCCAgacaaG.ucUu..acAgaAGuuAAAuCA
//
