# STOCKHOLM 1.0
#=GF ID cow-rumen-2
#=GF AC RF02947
#=GF DE cow-rumen-2 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 66.0
#=GF NC 37.9
#=GF TC 66.6
#=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 30.00 -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 32

URS0000D68D56_12908/1-107 GAAGGAAAGACAC-CUAGCCCGUGUUUUGCAU--GCC-GCUAUAAGCAUGUAAGUUAGUCAAGCC-CGAGUACAGGAUAGCC-GCUCG-GUCAA-ACUUACA--GUAAGUCUUCUUA
URS0000D6BCE3_12908/1-105 GAAGGAUGAGCGA-GUAGCGACCGCUCAAUAU--GCC-GUCAUGCGUUUU-AUUGAA-UAAAGCC-CAGGUACAGGAUGACC-GCCUG-GUAAGUCAAU-UU--GUAAAAUCGCCUG
URS0000D6AF18_12908/1-107 CGCAGAGGGUUCUGAUAACAAAGAACCUAGAUA-GCC-GC-AUCGGUAUU-AUAGGA-UGUAGUC-GGUGAGCCGGAAUGCCUGCAUC-GUAAGCCUAU-AA--GUAAAUCCCACAG
URS0000D6A6C0_12908/1-108 AAUCGAGUUCUUU-UUAGCAAAUUGGACAUACG-GC--GUCUUGGUUUUC-AUGGGA-UGUAGCU-GCAAUACAGCAAGACCGAUUGC-AUAAGCCCAU-UGAAGUAAAUCCCUAAA
URS0000D6742D_12908/1-107 AUCGAAGCAGAAGAGUAGCGUCUUCUGCACACA-GCC-GCCAUUAGCGCC-UGAAGA-UGUAGCU-GGAAUACAGGAUGACC-GAUCC-AUAAGCUUCA-GG--GUGAGUCUACUCU
URS0000D65FE9_12908/1-106 AACGAAGUUUAAU-CUAGCAAAUUAAACAAAAA-GCC-GUCUUAUGCAGA-ACUAAA-UGUAGCU-GGAAUACAGGAAGACC-GUUCC-AUAAGUUAGU-UC--AUAAGCCAUCUUA
URS0000D68C4B_12908/1-106 GAUAAGCUCAAAA-GUAGCG-UUUUGAGAUAAA-GCCCGUCUAUGGCAUA-ACUAAA-UGUAGCU-GGAAUACAGGUAGACC-GUUCC-AUAAGUUAGU-UA--GUAAGUCCCACAA
URS0000D6BF6D_12908/1-104 UAUCGAGUAUAGC-UUAGCAAACUAUACACUU--GCC-GCCAU-GGCUGA-ACACUA-UGUAGCC-UGAGUACAGGAUGACC-GACCA-GUAAGAGUGU-UC--AUAAGUCCCCCAG
URS0000D662CF_12908/1-104 UGUCGAGCAUAGC-UUAGCAAACUAUGCAUUU--GCC-GCCAU-GGCCUA-ACGCUA-UAUAGCC-GGAGUACAGGAUGACC-GACCC-GUAAGAGCGU-UU--AUAAGUCCCUCAG
URS0000D68430_12908/1-106 AUUGUAGUAUUGA-CCAGCAAUCAGUACGCAUA-GCC-GCCAUAGGCGUU-CCAGGA-UGUAGCC-GGAGUACAGGAUGACC-AACCC-GUAAGCCUGG-AU--GUAAGACCCCACG
URS0000D6A906_12908/1-106 AGCGAAGAGAAAA-GUAGCGAUUUUCUCACAUA-GCC-GUCACGCGCUUU-AUAGAA-UAUAGCC-GGAAUACAGGGUGACC-GCUCC-GUAAGUCUAU-AA--GUAAGCCGCCUUG
URS0000D6C0EC_12908/1-106 AGCGAAGGGAGAA-CUCGCAAUUCUCUCACAAA-GCC-GCCAUUAGCAGC-AGAGGA-UGUAGCC-GGAAUACAGGUUGACC-GCUCC-GUAAGCCUUU-GU--GUAAGUCUACUUG
URS0000D665FE_12908/1-107 AUCGAAGACGGAA-GUAGCGAUUCCGUUAAAAAAGCC-GCCAUUGGCAGU-AUAGGA-UGUAGCU-GGAAUACAGGAUGACC-GAUCC-AUAAGCCUAU-AU--GUAAGACCCGAGA
URS0000D6CD9F_12908/1-107 AUCGACGAUGAGA-AUAGCGAUCUCAUUAGAAAAGCC-GCCAUUGGCAGU-AUAGGA-UGUAGCU-GGAAUACAGGAUGACC-GAUCC-AUAAGCCUAU-AU--GUAAGUCCCGAGA
URS0000D6BB26_12908/1-107 AUCGAAGGUGAUA-GUAGCGAUAUCAUCAUAAAAGCC-GCCAUUGGCGUC-AUGGAA-UGUAGCC-GGAGUACAGGAUGACC-GACCC-GUAAGUCCAU-GA--AUAAGUCCCGAGA
URS0000D6BD6D_12908/1-106 AAUGAAGUUUGAA-GUAACGAUUCAAACAUAUA-GCC-GCCAUUGGUAUC-AUAGAA-UGUAGUC-GGAGUACCGGAUGACC-UUCCC-GUAAGUCUAU-GA--GUAAAUCCCGAAA
URS0000D6A279_12908/1-105 AAUGACGGAAAAC-CUAGCAAGUUUUCCAUGUA-GCC-GCCAU-GGCAUG-UCAAGA-UGUAGCC-GGAGUACCGGAUGACC-AUCCC-GUAAGCUUGA-CA--GUAAGCCCCGAGA
URS0000D66A5F_12908/1-106 ACUGACGUAUUAU-CUAACAAUUAAUACACGAA-GCC-GCCAUUGGCACG-GUAUGA-UACAGUC-GGAGUACAGGAUGACC-AGCCC-GUAAGCAUAU-CG--AUAAGUCCCGAGA
URS0000D6C7E1_12908/1-107 GUCGACGUAUUAUUAUAGCAUAUAAUACUUUAA-GCC-GCCAUUGGUAUC-AGAAGA-UGUAGCU-GGAGUACAGGAUGACC-GACCC-AUAAGCUUCU-GA--AUAAAUCCACUUA
URS0000D68F1B_12908/1-104 AUCGAAGUACGGC-GG-GCGCGCCGUACAUACA-GCC-GCCAU-GGCAUC-UGCGGA-UAUAGCC-GGAAUACAGGAUGACC-GAUCC-GUAAGCCGCA-GA--GUAAGUCCCCCAG
URS0000D67120_12908/1-104 AGCGAAGUACGGC-GG-GCACGCCGUACGUACA-GCC-GCCAU-GGCAGU-AUCGGA-UAUAGCC-GGAGUACAGGAUGACC-GCCCC-GUAAGCCGUU-AC--GUAAGGCCCGUAA
URS0000D65BA2_12908/1-105 AGCGAAGUGCAAA-UUAGCAAUCUGCACGUUUA-GCC-GCCAU-GGUUUU-AACGGA-UAUAGCC-GAAGUACAGGAUGACC-GCCUC-GUAAGCCGUU-AU--GUAAAUCCCGAAA
URS0000D696D6_12908/1-105 AGCGAAGUAAAGA-UUAGCACUCUUUACACAUA-GCC-GCCAU-AGUUUU-AAUGGA-UGUAGCC-GGAAUACAGGAUGACC-GCUCC-GUAAGCCAUU-AU--GUAAAUCUCACAG
URS0000D666D8_12908/1-105 AGCGACGUAUAGA-UUAGCAAUCUAUACAUAUA-GCC-GCCAU-GGCUUG-ACAUGA-UAUAGCC-GAAGUACAGGAUGACC-GCCUC-GUAAGCAUGU-CA--GUAAGUCCCAAGA
URS0000D6C3F0_12908/1-105 AGCGAUGUAUAGG-UCAGCAGCCUAUACGGAUA-GCC-GCCAU-GGCUUG-GCAUGA-UGUAGCC-GAAGUACAGGAUGACC-GCCUC-GUAAGCAUGC-CA--GUAAGCCCCAAGA
URS0000D6CAF3_12908/1-105 AUCGUAGUUAAAU-CUAGCAAGUUUAACACAUA-GCC-GCCUU-GGUUGA-AUAAGA-UGUAGCU-GGAGUACAGGAAGACC-GACCC-AUAAGCUUAU-UC--GUAAAUCCCACAG
URS0000D6B438_12908/1-105 AUCGUAGUUUGGA-UUAGCAACCCAAACAUAUA-GCC-GCUUU-GGUAGA-AUAGAA-UGUAGCU-GGAGUACAGGAAAACC-GACCC-AUAAGUCUAU-UC--GUAAAUCCCACAG
URS0000D6862E_12908/1-106 AUCGAAGUAUUACAUUAGCAAGUAAUACAUAUA-GCC-GCCAU-GGCAUA-GCAAGA-UGUAGCU-GGAGUACAGGAUGACC-GACCC-AUAAGCUUGC-UU--AUAAGUCCCACAG
URS0000D6A67D_12908/1-104 AUCGAAGAAUUAU-CUAGCAAGUAAUUCGUAU--GCC-GCCAU-AGCAUU-UCAUGA-UGUAGCU-GGAGUACAGGAUGACC-GACCC-AUAAGCAUGA-AU--AUAAGUCUCGAAU
URS0000D6A0FB_12908/1-105 AGCGAAGUAUAAU-CUAGCAAAUUAUACAUUUA-GCC-GCCAU-GGUAUG-GUAAUA-UGUAGCC-GAAGUACAGGAUGACC-GCCUC-GUAAGAUUAC-CA--GUAAAGCCCACAG
URS0000D66D84_12908/1-105 AGUGAAGUAUAAU-CUAGCCCAUUAUACAUACA-GCC-GCCAU-GGCAUG-AUAAGA-UGUAGCC-GGAGUACAGGAUGACC-ACCCC-GUAAGCUUAU-CA--AUAAGUCCCACAG
URS0000D699FF_12908/1-107 ACUGAAGUAUUUA--UAGCACUAAAUACAUAUA-GCC-GCCAUCGGUUGU-AUUGAA-UGUAGCUCGGAGUACAGGAUGACC-AGCCCGAUAAGUCAAU-AC--GUAAAUCCUCUUA
#=GC SS_cons              :A::::<<<<<<<._______>>>>>>>:::::.:::.::::<<<<<<<<.<<<<<-.------<.<<<-<---<<____>>.>a>>>.>---->>>>>.>>..--->>->>>>:::
#=GC RF                   aacGaAguguggc.uUAGCaagccacacAuAuA.GCC.GCCAucgGcuuc.acgggA.UgUAGCc.GGagcACAGGAUGACC.gauCC.gUAAGcccgu.ga..GUAaguCcgauaa
//
