# STOCKHOLM 1.0
#=GF ID DUF2815
#=GF AC RF03084
#=GF DE DUF2815 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 41.2
#=GF NC 38.4
#=GF TC 43.8
#=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 26.94 -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 Environmental. Downstream gene
#=GF WK DUF2815_RNA_motif
#=GF SQ 22

URS0000D6638D_12908/1-62 AAGG-UAGAC-GGCUGGCACCUUA-U-AAGUUCAGUCA--AUACAAAGUAAACAAGGAGCCUAGU----AUG
URS0000D65EC2_12908/1-64 GGGU-CAGACGAGCAGAC-ACCCAUUGAAGUUCUGCUC------UACCGUUAAAAGGAAGUAAACCAUCAUG
URS0000D68ACC_12908/1-60 UGGG-UAGACGAAUUGAC-CCCAACUGAAGUUCAAUUC------UAACGUUAAAAGGAGUUUUAU----AUG
URS0000D66D61_12908/1-62 GGGU-UAGAUGAAUCGGC-ACCCAUUGAAGUUCGAUUC------UAUCGUUAAAAGGAAAUAUCAUC--AUG
URS0000D66FFA_12908/1-62 AGGG-UA-ACGAUGCGGC-CCCUA---AAGUCCGCGUCACUUAAAAAGGUAAAAAGGUAAAAAUU----AUG
URS0000D6D0F5_12908/1-65 AGGG-U-GCCGAUUCAGC-UCCU--UUAAGUCUGAGUC-ACUAAAAAUGUAAAAAGGUAAAAAUUAUU-AUG
URS0000D6B5BB_12908/1-64 CGGG-UAGACAGACUAGC-CCCGAUUGAAGUCUAGUC-----UAAAAAGAUACAAGGAUUAAAUUAUU-AUG
URS0000D66AB6_12908/1-61 CGGG-UAGACGAUACGGC-CCCGACUGAAGUCCGUAUC----ACAACGUCAAAAAGGUAGUCUU-----AUG
URS0000D67AEB_12908/1-62 AGGG-UUGUCGAUCUGGC-CCCUACUUAAGUCCAGAUC-----UAAUGCUAAAAAGGUAAUUUAAA---AUG
URS0000D68795_12908/1-59 CGGU--AGAG--AUUGGC-ACCGA-UAAAGUCCAAUCA--AUUUUAAGUUAAAAAGGAAGCAAG-----AUG
URS0000D6762A_12908/1-64 UGGG-UAGACAGACUGGC-CCCAAAUGAAGUCCAGUCU-----UUAUGUUAAAAAGGUAAUAAUCAUC-AUG
URS0000D65A8C_12908/1-64 CGGG-UAGACAGGCCAGC-CCCGAUUGAAGUCUGGUCU-----UUAUGUUAAAAAGGUAAUAAUCAUC-AUG
URS0000D65823_12908/1-64 CGGG-UAGACAGACCAGC-CCCGAUUGAAGUCUGGUCU-----UACAGUUAAAAAGGUAAUAACAAUC-AUG
URS0000D6A0E6_12908/1-63 CGGG-UAGACAGAUUGGC-CCCGACUGAAGACCAAUCU-----UAAUGUUAAAAAGGAAUUAAUAUC--AUG
URS0000D67BCA_12908/1-63 AGGG-AAGACAGGUUGGC-CCCUACUGAAGACCAAUCU-----UAAUGUUAAAAAGGACUUAUCAUC--AUG
URS0000D6A5E9_12908/1-60 CGGG-UAGACGAAUUGGC-CCCGAUUUAAGUCCAGUUC-----UAAAGUAAAUAAGGAAUUAAA-----AUG
URS0000D6BFC1_12908/1-59 AGGU-UAGACGUGCUGGC-ACCUAUUGAAGUCCAGUAC-----UACAGUAAAUAAGGAAUUGU------AUG
URS0000D6B38E_12908/1-61 CGGG-UUGCCGAGUUGGC-CCCGAUUGAAGUCCAACUC----UUUCGUUUAUAAAGGUAAUAUC-----AUG
URS0000D69D95_12908/1-61 CGGG-UAGACGAGCUGGC-CCCGAUUGAAGUCCAGUUC----UAAUGUUUAAAAAGGUAAUAUC-----AUG
URS0000D67FC8_12908/1-60 AGGG-UAGACGAGCUGGC-CCCUAUUGAAGUCCAGUUC----UAACGUUUAAUAAGGUAUAUC------AUG
URS0000D65E99_12908/1-59 AGGG-UAGACGAACUAAC-CCCUAUUGAAGUUUAGUUC--------UUACGUUAAGGAGAAAUAGU---AUG
URS0000D65C64_12908/1-64 ACGGGAAGACGAACCAAC-CCGUACUUAAGUUUGGUUC----UUACGUUAAUAAAGGAAAUACAAA---AUG
#=GC SS_cons             AAAA.:::::<<<<<<<_.aaaa________>>>>>>>.....:::::::::::::::::::::::...:::
#=GC RF                  aGGG.UAGACGaacuGGC.CCCuAUUGAAGUCCaguuC.....uAAaguUAAAAAGGaAaUAauaa...AUG
//
