# STOCKHOLM 1.0
#=GF ID ssNA-helicase
#=GF AC RF03070
#=GF DE ssNA-helicase RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 41.5
#=GF NC 41.3
#=GF TC 42.2
#=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 27.93 -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 Firmicutes, Actinobacteria (1 example). Downstream gene
#=GF WK SsNA-helicase_RNA_motif
#=GF SQ 104

URS0000D6954B_12908/1-48   U-AGCGUAAAAGG-----UAGUAUUA----CCUUUUACGUUA---CAAGCAGCUUGUAGCA
URS0000D67F9C_12908/1-50   U-UGCAG--GGGGG--GUCAGUAUUA---CCCCC--CUGCAA-CUUCUGUAUCUUGUAGCA
URS0000D66AB4_12908/1-48   U-UGCCA-ACAGG-----GAGUAUUA----CCUGU-UGGCAA-AUUAAGUAGCAUGUAGCG
URS0000D65919_12908/1-44   G-GAUGC-AAGG------UAGUAUUA-----CCUU-GCAUCC---UAUGUAGCAAGUAGCA
URS0000D68B44_12908/1-52   UAGGCGG-AAAGGU---UUAGUGUUA---CCCUUU-CCGCCA-CUUCUGUAACUUGUAACA
URS0000D6BDB0_12908/1-46   C-GCCCC-ACGG-----GAAGUAUUA-----CCGU-GGGGCA-GCAAGGUAGCG-GUAGCA
URS0000D6798A_12908/1-46   U-GCCCC-ACGG-----UAAGUAUUA-----CCGU-GGGGCA-GCAAGGUAGCG-GUAGCA
URS0000D6A9FB_12908/1-46   U-UCCCC-ACGG-----UAAGUAUUA-----CCGU-GGGGAA-GCAAGGUAGCG-GUAGCA
URS0000D65AC0_12908/1-46   U-GCCCC-ACGG-----UAAGUAUUA-----CCGU-GGGGAA-GCAAGGGAGCG-GUAGCA
URS0000D66EA6_12908/1-46   U-GCCAG-AGG------CCAGUAUUAC-----CCU-CUGGCA-CUUCUGUCGCAAGUCGCA
URS0000D6BC4A_12908/1-48   U-GCCU--AAGG----UCUAGUAUUAC----CCUU--AGGUAACCUCUGUAUUUUGUAGCA
URS0000D6A863_12908/1-47   U-GCCUA--AGGG----CUAGUAUUA----CCCU--UAGGCA-CAUCUGUAUCUUGUAGCA
URS0000D6C41E_665941/1-49  A-UGCUA-AAGGG-----AAGUAUUA----CCCUU-UAGCAUACAUAUGUAGCACGUAGCA
URS0000D6A993_12908/1-48   U-UUCCA-AAAG-----CCAGUAUUAC----CUUU-UGGAAA-CAUUUGUAUUUUGUAGCA
URS0000D65B1D_12908/1-44   U-CGC---AUAGG----UUAGUAUUA----CCUAU---GCGA-GCGAAGUAGCA-GUAGCA
URS0000D6B6BA_12908/1-50   A-GCCAU-AAGGGU----UAGUAUUAC--ACCCUU-AUGGCU-AAUGUGUAAUA-AUUACA
URS0000D67C6A_12908/1-49   C-CCCGA-AAGGG----UAAGUAUUA----CCCUU-UCGGGG-ACAGUGUAUCAAGUAGCA
URS0000D6B8E7_12908/1-46   G-CGUAA-AAGG------UAGUAUUA-----CCUU-UUACGU-UACAAGUAGCUUGUAGCA
URS0000D67DC8_12908/1-48   U-GUGCA-AGGG-----CAAGUAUUAC----CCCU-UGCACA-CUUCCGUCGCACGUCGCA
URS0000D6B4FB_12908/1-50   -AGCUAU-AAGG----UAUAGUAUUAC----CCUU-AUAGCGUAGCAAGUAGCAUGUAUCA
URS0000D6BD64_12908/1-46   U-GUCCA-AG-G-----CUAGUAUUA-----CCCU-UGGACA-CUUCUGUAUCAUGUAACA
URS0000D6BD64_1263002/1-46 U-GUCCA-AG-G-----CUAGUAUUA-----CCCU-UGGACA-CUUCUGUAUCAUGUAACA
URS0000D69D80_12908/1-46   U-GUCCA-AGG------CUAGUAUUA-----CCCU-UGGACA-CUUCUGUAACAUGUAACA
URS0000D68ADC_12908/1-47   U-CGCCU-AGG------CUAGUAUUAC-----CCU-AGGCGAACAUAGGUAGCGUGUAGCA
URS0000D66109_12908/1-49   U-UCCCU-AAAGG----CUAGUAUUA----CCUUU-AGGGAA-CUUCUGUAACAUGUAACA
URS0000D68867_12908/1-48   U-UCCCU-AGAG-----UUAGUAUUAC----CUCU-AGGGAA-CUUCUGUAACGUGUCGCA
URS0000D67359_12908/1-48   U-UCCCU-AGAG-----UCAGUAUUAC----CUCU-AGGGAA-CUUCUGUAACGUGUCGCA
URS0000D6D0B8_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUA----CCCCU-AGGCAA-CUUUUGUCGCAUGUCGCA
URS0000D69B7E_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUCUGUAUAAUGUAUAA
URS0000D6AD2E_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUCUGUAAAAUGUAAAA
URS0000D6A81A_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUCUGUAAAGUGUAAAA
URS0000D6A1B2_12908/1-48   U-UGCCU-AGGG-----CCAGUAUUAC----CCCU-AGGCAA-CUUCUGUGACAUGUGACA
URS0000D68361_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUA----CCCCU-AGGCAA-CUUUUGUAACGUGUAACA
URS0000D67ED3_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUUUGUAUCGUGUAUCA
URS0000D6A0DE_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUUUGUGACAUGUGACA
URS0000D67898_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUUUGUGUCAUGUGUCA
URS0000D6C734_12908/1-48   U-UGCCU-AGGG-----UUAGUAUUAC----CCCU-AGGCAA-CUUCUGUGUCAUGUGUCA
URS0000D6CFD7_12908/1-48   U-UGCCU-AAAG-----CUAGUAUUAC----CUUU-AGGCUA-CUUUUGUAGCGUGUAGCA
URS0000D66274_12908/1-46   U-AGCCU-AAG------CCAGUAUUAC-----CUU-AGGCUA-CUUCUGUAGCGUUUAGCA
URS0000D6A0FD_12908/1-49   U-UGCCU-AAGGG----CUAGUAUUA----CCCUU-AGGCAA-CUUCGAUAGCGUGUCGCA
URS0000D679E0_1428454/1-46 U-CGCCU-AAG------CUAGUAUUAC-----CUU-AGGCGA-CUUCUGUAACGUGUCACA
URS0000D6A0B8_12908/1-49   U-UGCCU-AAGG----GCUAGUUUUA-----CCUU-AGGCAAACCUCUGUCUCUUGUAGCA
URS0000D67BD6_12908/1-47   U-GUCCU-AAGG-----CUAGUAUUA-----CCUU-AGGACA-CUUCUGUCGCAUGUCGCA
URS0000D663A6_12908/1-47   U-UCGCU-AAGG-----CUAGUAUUA-----CCUU-AGCGAA-CAUCUGUCGCUUGUCGCA
URS0000D69904_12908/1-51   G-UUCCAUAAGGG----UUAGUAUUA----CCCUUAUGGAAC-AGUAUGUAGCAAGUAGCA
URS0000D67F75_12908/1-50   U-UUGCU-AAGG----UCAAGUAUUAC----CCUU-AGCAAUACAUAAGUAGCAUGUAGCA
URS0000D68757_12908/1-51   U-AUGCU-AAGGGG---GAAGUAUUA---CCCCUU-AGCAUA-UAUAUGUAGCAUGUAGCA
URS0000D68044_12908/1-49   U-AUGGA-AAGGG----UUAGUAUUA----CCCUU-UCCAUA-CAAAUGUAGCAUGUAGCA
URS0000D68843_12908/1-48   U-UCCCA-AAGGG----UAAGUAUUA----CCCUU-UGGGAA-C-CAUGUAGCAGGCAGCA
URS0000D6C99A_12908/1-56   U-CCUAU-AAGGGUUGG-GAGUAUUACCAACCCUU-AUAGGG-AACAUGUAGCAAGUAUCA
URS0000D68691_12908/1-50   U-CGCGA-AAGGGG----CAGUAUUA---CCCCUU-UCGCGU-AUCAUGUAGCAUGUAGCA
URS0000D6BE67_12908/1-48   U-ACGAU-AGGGG----UUAGUAUUA----CCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D68456_12908/1-47   U-GCGAU-AGGGG-----UAGUAUUA----CCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D6915A_12908/1-48   U-GCGAU-AGGGG-----UAGUAUUAC---CCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D68456_657321/1-47  U-GCGAU-AGGGG-----UAGUAUUA----CCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D6C154_12908/1-47   U-GCGAU-AGGGG-----GAGUAUUA----CCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D6BB6E_12908/1-48   U-GCGAU-AGGGGG-----AGUAUUA---CCCCCU-AUCGUA-GCAAUGUAGCA-GUAGCA
URS0000D68BE7_12908/1-48   C-AGCAU-AAGGC-----UAGUAUUA----CCCUU-AUGCUA-UGUAUGUAGCAUGUAGCA
URS0000D67F51_12908/1-50   U-ACUAU-AAAGGG----GAGUAUUA---CCCUUU-AUAGUA-GCAAUGUAUCGUGUAGCA
URS0000D663D0_12908/1-49   U-ACUAU-AAAGGG----GAGUAUUA---CCCUUU-AUAGUA-GCAACGUAGCA-GUAGCA
URS0000D668C1_12908/1-48   A-UCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGAU-GA-UAGUAGCAUGUAGCA
URS0000D6B68F_12908/1-48   G-UCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGAU-G-AUAGUAGCAUGUAGCA
URS0000D66298_12908/1-49   G-UCCAU-AAGGG----UAAGUAUUA----CCCUU-AUGGAC-AUCAAGUAGCAUGUAUCA
URS0000D6BED2_12908/1-50   C-UCCAU-AAGGGG----AAGUAUUA---CCCCUU-AUGGAA-AUCGUGUAGCGUGUAGCA
URS0000D66C56_12908/1-50   C-UCCAU-AAGGGG----AAGUAUUA---CCCCUU-AUGGAA-AUCGUGUAGCAUGUAGCA
URS0000D6B1C9_12908/1-48   U-UCCAU-AAAGG----AUAGUAUUA----CCUUU-AUGGAA-GCAAUGUAGCA-GUAGCA
URS0000D6ABAB_12908/1-49   U-GCCAU-AAGGG----AUAGUAUUA----CCCUU-AUGGCUACACAGGUAGCA-GUAGCA
URS0000D65749_12908/1-50   U-GCCCU-AAAGG---UUAAGUAUUA----CCUUU-AGGGCA-ACCAUGUAGCAUGUAGCA
URS0000D68C53_12908/1-49   C-GCCAU-AAGGG----AUAGUAUUA----CCCUU-AUGGCG-ACAAUGUAGCAUGCAGCA
URS0000D68DE1_12908/1-49   -AGCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-UAUGUGUAGCAUGUAGCG
URS0000D6BFD8_12908/1-56   U-GCCAU-AAGGGUUU-AUAGUAUUACAAACCCUU-AUGGCA-ACCAUGUAGCAUGAAGCA
URS0000D6C30A_12908/1-49   U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-ACCAUGUAGCACGUAGCA
URS0000D6BC94_12908/1-49   U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-ACCAUGUAUCAUGUAGCA
URS0000D67D87_12908/1-49   U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-ACCAUGUAGCAUGUAGCA
URS0000D6BB13_12908/1-48   U-GCCAU-AAGGG-----UAGUAUUA----CCCUU-AUGGCA-ACCAUGUAGCAUGUAGCA
URS0000D6CD8F_12908/1-49   G-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-AACAUGUAGCAUGUAGCA
URS0000D6CC2B_12908/1-50   U-CCCAU-AAGGG---GGCAGUAUUA----CCCUU-AUGGCA-AAUAUGUAGCAAGUAGCA
URS0000D6A05C_12908/1-49   U-GCCAU-AAGGG----UCAGUAUUA----CCCUU-AUGGCA-AAUAUGUAGCAAGUAGCA
URS0000D67CA1_12908/1-49   U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-AAUAUGUAGCAAGUAGCA
URS0000D67CA1_1263003/1-49 U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCA-AAUAUGUAGCAAGUAGCA
URS0000D67921_12908/1-47   U-GCCAU-AAGG-----UUAGUAUUA-----CCUU-AUGGCA-UAUAUGUAGCAUGUAGCA
URS0000D6CC60_12908/1-48   U-GCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGCU--AUAUGUAGCAUGUAGCG
URS0000D68D2F_12908/1-50   U-CCCAU-AAGGG----UCAGUAUUAC---CCCUU-AUGGGA-AACUUGUAGCAUGUAGCA
URS0000D6AE9F_12908/1-54   U-CCCAUAAAGGGG---UUAGUAUUA---CCCCUUAAUGGGAAACUUUGUAGCAUGUAGCA
URS0000D6CCD6_12908/1-51   U-CCCAU-AAGGGG---GCAGUAUUA---CCCCUU-AUGGGA-AACAUGUAGCAUGUAGCA
URS0000D6986E_12908/1-51   U-CCCAU-AAGGGG---GCAGUAUUA---CCCCUU-AUGGGA-AACUUGUAGCAUGUAGCA
URS0000D6986E_649724/1-51  U-CCCAU-AAGGGG---GCAGUAUUA---CCCCUU-AUGGGA-AACUUGUAGCAUGUAGCA
URS0000D68175_12908/1-51   U-CCCAU-AAGGGG---UUAGUAUUA---CCCCUU-AUGGGA-AACUUGUAGCAUGUAGCA
URS0000D68175_658087/1-51  U-CCCAU-AAGGGG---UUAGUAUUA---CCCCUU-AUGGGA-AACUUGUAGCAUGUAGCA
URS0000D6C207_12908/1-49   G-UCCAU-AAGGG----UUAGUAUUA----CCCUU-AUGGAAGCACAUGUAGCA-GUAGCA
URS0000D6752F_12908/1-48   U-UCCAU-AAGGA-----UAGUAUUA----CCCUU-AUGGAAGCACAUGUAGCA-GUAGCA
URS0000D69A34_12908/1-49   U-UCCAU-AAGGG----AUAGUAUUA----CCCUU-AUGGAAGCACAUGUAGCA-GUAGCA
URS0000D6AF12_12908/1-48   U-UCCAU-AAGG-----AUAGUAUUAC----CCUU-AUGGAAGCACGUGUAGCA-GUAGCA
URS0000D6ADB1_12908/1-49   U-UCCAU-AAGG----CGUAGUAUUAC----CCUU-AUGGAAGCACGUGUAGCA-GUAGCA
URS0000D69F32_12908/1-49   U-UCCAU-AAGGG----CAAGUAUUA----CCCUU-AUGAAAGCAUAAGUAGCA-GUAGCA
URS0000D67400_12908/1-49   U-UCCAU-AAGGG----CAAGUAUUA----CCCUU-AUGGAAGCAUAAGUAGCA-GUAGCA
URS0000D67962_12908/1-49   U-GCCAU-AAGG-----UCAGUAUUACC---CCUU-AUGGCA-UGAAUGUCGCAUGUCGCA
URS0000D6CA8A_12908/1-49   U-GCCAU-AAGGG----CUAGUUUUA----CCCUU-AUGGCA-UGAAUGUCGCAUGUCGCA
URS0000D659B9_12908/1-46   U-UGCAU-AAGG-----CAAGUAUUA-----CCUU-AUGCAAG--GGUGUAGCAAGUAGCA
URS0000D6A10B_12908/1-44   U-CGCAU--AGG-----UGAGUAUUA-----CCU--AUGCGA-GCGAAGUAGCA-GUAGCA
URS0000D6628E_12908/1-44   U-CGCAU--AGG-----UUAGUAUUA-----CCU--AUGCGA-GCGAGGUAGCG-GUAGCA
URS0000D6A611_12908/1-51   U-GCCAU-AAGGGG---GGACUAUUA---CCCCUU-AUGGCA-CAUACGUCGCACGUCGCA
URS0000D6B4B7_502558/1-45  C-CGCCA-AAG------CAAGUAUUA-----CCUU-UGGCGG-UUCGUGUAGCA-GUAGCA
URS0000D6779F_12908/1-50   C-CAUAU-AAGGG----CUAGUAUUAC---CCCUU-AUAUGU-AGCAUGUAGCAUGUAGCA
#=GC SS_cons               <.<<<<<.<<<<<...._________....>>>>>.>>>>>>.::::::::::::::::::
#=GC RF                    u.ucCaU.AAGGG....uUAGUAUUA....CCCUU.AuGgaa.cuuaUGUAGCAUGUAGCA
//
