# STOCKHOLM 1.0
#=GF ID porB
#=GF AC RF03042
#=GF DE porB RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 35.1
#=GF NC 34.9
#=GF TC 35.6
#=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 29.40 -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 Neisseria (Betaproteobacteria). Downstream gene
#=GF WK PorB_RNA_motif
#=GF SQ 85

URS0000D69A42_1030841/1-60 CAUUUAUAUUAGCAGUCAUGGAAUCGCCG-UUAA--UGGCGGUGAAUUCAA-AACUUAGACGAA
URS0000D66E3B_12908/1-58   CAAUUAUAGUGACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AAGUA--AGCCUAAGUAGA
URS0000D66D10_12908/1-59   CAAUUAUAGUGAGAGUAAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D692BD_12908/1-59   CAAUUAUAGUAAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D692BD_933266/1-59  CAAUUAUAGUAAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6ABFE_12908/1-59   CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGUGGA
URS0000D6ABFE_546266/1-59  CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGUGGA
URS0000D6D0FA_933267/1-59  CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6D0FA_12908/1-59   CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6D0FA_665946/1-59  CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6D0FA_547045/1-59  CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6D0FA_1095748/1-59 CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D6D0FA_997348/1-59  CAAUUAUAGUGAGAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUAA-AGCCUAAGCGGA
URS0000D699CE_12908/1-58   CAAUUAUAGUAACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUA--AGCCUAAGCGGA
URS0000D699CE_546268/1-58  CAAUUAUAGUAACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUA--AGCCUAAGCGGA
URS0000D699CE_435832/1-58  CAAUUAUAGUAACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AUGUA--AGCCUAAGCGGA
URS0000D68499_12908/1-58   CAAUUAUAGUAACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AAGUA--AGCCUAAGCGGA
URS0000D67845_12908/1-58   CAAUUAUAGUGACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AAGUA--AGCCUAAGCGGA
URS0000D67845_546264/1-58  CAAUUAUAGUGACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AAGUA--AGCCUAAGCGGA
URS0000D67845_596320/1-58  CAAUUAUAGUGACAGUCAUGGAAUCGCUG-AUUC--CAGCGAUA-AAGUA--AGCCUAAGCGGA
URS0000D67776_12908/1-58   CAAUUAUAGUGACAGUCAUGGAAUCGCUG-AUUC--UAGCGAUA-AAGUA--AGCCUAAGCGGA
URS0000D6A24E_528359/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528351/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528347/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_521006/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_242231/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528345/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528358/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528360/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528348/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528352/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_940296/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6A24E_528346/1-62  CAUCUAUAGUUUCAGACAUGUAACCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D658AD_935588/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69815_1069614/1-62 CAUCUAUAGUUUCAGACAUGUAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69815_1069616/1-62 CAUCUAUAGUUUCAGACAUGUAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69815_528355/1-62  CAUCUAUAGUUUCAGACAUGUAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69815_122587/1-62  CAUCUAUAGUUUCAGACAUGUAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69815_935595/1-62  CAUCUAUAGUUUCAGACAUGUAAUCGCCGAGCCCCUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6598E_489653/1-62  CAUUUAUAGUUUCAAACAAGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6598E_546265/1-62  CAUUUAUAGUUUCAAACAAGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6598E_933280/1-62  CAUUUAUAGUUUCAAACAAGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6598E_869214/1-62  CAUUUAUAGUUUCAAACAAGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D69CB5_546267/1-62  CAUUUAUAAUUUCAAACAAGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6C1AB_935590/1-62  CAUUUAUAGUUUCAGACAUGAAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6BB3C_630588/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AAC-UAAGCGGC
URS0000D6D2AD_935592/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGAAA-AGC-UAAGCGGC
URS0000D6890F_662598/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_935599/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_909420/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_562020/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069608/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069617/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069620/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1095699/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_272831/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_374833/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_942513/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_935593/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_933290/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_935597/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069609/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069618/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1069622/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_1095671/1-62 CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D6890F_862513/1-62  CAUCUAUAGUUUCAGACAUGGAAUCGCCGAAAACGUCGGCGGUAAAUGCAA-AGC-UAAGCGGC
URS0000D667C8_12908/1-60   CAUUUAUAGUUUCAGACAUGGAAUCGCCG-AUAU--CGGCGGUAGACGUAA-AGCCUAAGCGGA
URS0000D6A6F5_1077282/1-60 CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGAAGUAA-AGCCUAAGCGGA
URS0000D6A6F5_1053687/1-60 CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGAAGUAA-AGCCUAAGCGGA
URS0000D6A6F5_1069619/1-60 CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGAAGUAA-AGCCUAAGCGGA
URS0000D6A6F5_1190578/1-60 CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGAAGUAA-AGCCUAAGCGGA
URS0000D6A026_12908/1-60   CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGACGUAA-AGCCUAAGCGGA
URS0000D6A026_546262/1-60  CAUUUAUAGUUUCAGACAUGGAAUCGCCG-ACAU--CGGCGGUAGACGUAA-AGCCUAAGCGGA
URS0000D6C787_604162/1-63  CAUUUAUAGUUUCAGACAUGAAAUCGCCGAACCCCUCGGCGGUAGGUGUAA-AGCCUAAGCGGA
URS0000D6C787_1145159/1-63 CAUUUAUAGUUUCAGACAUGAAAUCGCCGAACCCCUCGGCGGUAGGUGUAA-AGCCUAAGCGGA
URS0000D676CC_12908/1-60   CAUUUAUAUUAACAGCCAUGUAAUCGCUG-GCAA--CAGCGAUAAACGCAACAGCUUAAUCGG-
URS0000D6C236_12908/1-61   CAUUUAUAUUAAUAGCCAUGUAAUCGCUG-GCAA--CGGCGAUAAACGCAACAGCUUAAUCGGA
URS0000D6C236_546263/1-61  CAUUUAUAUUAAUAGCCAUGUAAUCGCUG-GCAA--CGGCGAUAAACGCAACAGCUUAAUCGGA
URS0000D67203_12908/1-61   CAUUUAUAUUAACAGUCAUGUAAUCGCUG-GCAA--CGGCGAUAAACGCAACAGCUUAAUCGGA
URS0000D661D9_12908/1-61   CAUUUAUAUUAACAGCCAUGUAAUCGCUG-GCAA--CGGCGAUAAACGCAACAGCUUAAUCGGA
URS0000D66E52_12908/1-62   CAUUUAUAUUUACACCCAUGCAAUCGCCC-GAAUA-GGGCGGACAACGCAACAGCUUAAUCGGA
URS0000D6BA34_888742/1-62  CAUUUAUAUUUACGCCCAUGCAAUCGCCC-GAAUA-GGGCGGACAACGCAACAGCUUAAUCGGA
URS0000D6BA34_12908/1-62   CAUUUAUAUUUACGCCCAUGCAAUCGCCC-GAAUA-GGGCGGACAACGCAACAGCUUAAUCGGA
URS0000D6B0D0_1127694/1-61 CAUUUAUAUUAGCAGUCAUGUAAUCACCC-GAGC--GGGUGGUCGACGCAACAGCUUAAUCGGA
URS0000D69CE7_12908/1-62   CAUUUAUAUUAGCAGUCAUGUAAUCACCC-GAUUC-GGGUGGUCGACGCAACAGCUUAAUCGGA
#=GC SS_cons               ::::::::::::::::::::::<<<<<<<._____.>>>>>>>::::::::.::::::::::::
#=GC RF                    CAUUUAUAGUuuCAGaCAUGgAAuCGCCG.aaaCg.CGGCGgUAAAUGcAA.AGCcUAAGCGGa
//
