# STOCKHOLM 1.0
#=GF ID cow-rumen-3
#=GF AC RF03083
#=GF DE cow-rumen-3 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 86.7
#=GF NC 86.0
#=GF TC 87.1
#=GF SE Weinberg Z
#=GF SS Published; PMID:28977401;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 22.47 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 28977401
#=GF RT Detection of 224 candidate structured RNAs by comparative analysis of
#=GF RT specific subsets of intergenic regions.
#=GF RA Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR,
#=GF RA Sherlock ME, Breaker RR
#=GF RL Nucleic Acids Res. 2017;45:10811-10823.
#=GF CC cow rumen metagenome. Environment (Cow rumen (57))
#=GF WK Cow-rumen_RNA_motif
#=GF SQ 8

URS0000D7223B_12908/1-95  GGGUCGCAGUUAAUGACUACCGCCUCCAGUGUA-------------------------------------------------------------CAAUGGUCUCCAAUAUGAGUAAAAACUAUCAUUUGGACUAGGUGAGAUGCCUUU-GGUCCAUC
URS0000D7223C_12908/1-95  GGUAUGUGCUUAAUGAGUACAUGCUUCGUAUGUA------------------------------------------------------------UAGCGAUCUCCAGUAUGAGGAAAAACUACCGCUUGGAUUGGCUGAGA-GGCCCG-GAUCCAUC
URS0000D7223D_12908/1-142 GGAUCGUGUUUAAUGAGCACCAUCCUCAU-----GAG-UUAGUGC-CA-UCGUC--UUUUC-GGCGAUGAAUACUAGUA--GCAC--CAAACUCCUCUGAUGACCAGUAUGUCUAAAAACUAUCGUUUGGGCUGGGUGCGAUGCCCCUUGGUCCACC
URS0000D72236_12908/1-137 GGAUUGUGCUUAAUGAGUACGAUCUUUAU-----GAG-AAGGUAC-GA-ACCGC--AAAAA-G-GG---AAUACUAGUU--GUAU--CUCUCUCCUCUGGUGACCAGUAUGUCUAAAAACUACCGUUUGGGCUGGGUGAAAUGCCCUU-GGUCCACC
URS0000D72239_12908/1-146 GGCGCGUGCUUAAUGAGUACACGCUUUGU-----AAAAGAAAAUGUAGUUCAGC--GGGAU-GCUGGCUUAUACUAGUUGACAUU--UUCUUUAAUACAAUCUCCAGUAUGAGGAAAAACUACUGUUUGGGCCGCGUGAAAUGCGUCG-GGUCCAUC
URS0000D72237_12908/1-142 GGGUCGUGUUUAAUGAGCACAACCUUCAUA----CGU-UCGGUGC-CG-AGAUC--GUAAU-GGUCUCGAAUACUAGUU--GCGC--UGAAAUGAUAUGGUGACCAGCAAGUCGAAAAACUGCCGUUUGGGCUGCGUGAGAUGCGCCG-GGUCCACC
URS0000D7223A_12908/1-142 GGAUCGUAGCUAAUGACUACCAUCUUCGG-----GGUUAAGAUAC-CA-GCAUC--AAUAU-GGUACUGAAUACUAGUU--GUAU--CUUUUCUGCCGAUUCUCCAGUAUGAGUAAAAACUACCGUUUGGGCUGCGUGAAACGCGCCG-GGUCCACC
URS0000D72238_12908/1-146 GGCACGUGCUUAAUGAGUACAUGCUUCAU-----ACU-GCUGUGC-CA-GCAUCGUUUAAUUGGUGCUGAAUACUAGUU--GCACUAAGCAAGUUAUGAUUCUCCAGUAUGAGUAAAAACUACCGUUUGGGCUGCGUGAGAUGCGCCG-GGUCCACC
#=GC SS_cons              <<<<-<<<<<_____>>>>>->>>>::::.....<<<.<<<<<<<.<<.<<<<<.._____.>>>>>>>----------..>>>>..>>>->>>:::::::<<<______>>>::::::::::::::<<<<<<<<<<_____>>>>--.>>>>>>::
#=GC RF                   gGgucGugcuUAAUGagcaCaacCuUcau.....ggg.gcggugc.cg.gcgcC..auaAu.GgcgccgAAUACUAGUu..gcac..cgcucccuuaugaUcuCCAGUAUGaguAAAAACUAcCGUUUGGgCuGgGuGAgAUgCcCcg.gGuCCAcC
//
