# STOCKHOLM 1.0
#=GF ID RT-17
#=GF AC RF03020
#=GF DE RT-17 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 40.4
#=GF NC 40.1
#=GF TC 40.6
#=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 26.65 -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 Bacteroidales (Bacteroidetes), Clostridiales (Firmicutes). Nearby to self-
#=GF CC splicing intron genes
#=GF WK RT_RNA_motifs
#=GF SQ 63

URS0000D68146_12908/1-87   AGCCUUACCUCUU-GGUAAAA----AAUA-AAUUU--UC-AAAAAGGG-AU-UGGUAG--G-U-----UAAA---------A--UCCGAAG-AUC-C--UGAUAUGAAGUAAAGGCG-AUGA---
URS0000D6B6DE_12908/1-98   GGCCUUGCCUCUU-GGCAAAAA----ACA-UAACG--UC-AGAAAGGA-GC-UGGUAGGAACGCCCGUUGU-----AUGGGC-UACCGAAC-GCC-C--CGAAUAAGAAAAGCAAAG-CA-----
URS0000D6C2C7_12908/1-97   GACCUUGCCUCUU-GGCAAAACA--CAAA-GCAGA--GC-CUCAUUUG-GUUUGGUAG--UCCCGA--UAUA------UCGG-GAUCGAAGAACCAG-AGGCGACAUAAGCAAAAAG--------
URS0000D668D1_12908/1-99   GACCUUGCCUCUU-GGCAAAACA--CAAA-GCAGA--GCCUCUUUUGG-UU-UGGUAG--GUCUGGU-GAUU-----ACCGG-AGUCGAAG-AAUCAGAGGCGACAUAAGCAAAAAG--------
URS0000D65A2F_12908/1-96   AGCCAUGCCCCUU-GGCAAAACA--CAAAGCAAUG--CC-UCAUUCGU-GU-UGGUAG--UCCCGU--UUUUU-----UCGG-GGUCGAAU-ACU-C--GGAGGUGA----AAUAAG-CAAAA--
URS0000D6C340_12908/1-94   AGCCGCACCUCAA-GGUGAAA----GAAA-AACGU--UG-GAUGUAGU-GU-UGGUAA--UCGUGC--AAGG------GCAC-GGCUGAAG-ACA-G--AGAGAAAC----AAAAAG-CAGACAA
URS0000D6C565_12908/1-96   AGCCACACCCAAUAGGUGAAA----AAUC-AACUU--UU-GAUGUAGU-GU-UGGUAA--UCGUGC--AUUUG-----GCAC-GGCUGAAG-ACA-G--AGAAAAAG----UAAAAG-CAGACAA
URS0000D6C11A_12908/1-95   AGCCACACCCAAU-GGUGAAA----AAUC-AACUU--UU-GAUGUAGU-GU-UGGUAA--UCGUGC--AUUUG-----GCAC-GGCUGAAG-ACA-G--AGAAAAAG----UAAAAG-CAGACAA
URS0000D6BB23_12908/1-94   AACCGCACCCCAC-GGUGAAA----AAUA-CACUG--AU-AAAGAAGU-GC-UGGUAG--ACAUAC--ACAC------GUAU-GGCCGAAG-GCA-G--GGACUUAG----GAAAAG-CAGACAA
URS0000D69F35_12908/1-93   AACCGCACCCCAC-GGUGAAAA---AUAC-ACUGA--UU-AAAGAAGU-GC-UGGUAG--ACAUA---CACG-------UAU-GGCCGAAG-GCA-G--GGACUUAG----GAAAAG-CAGACAA
URS0000D6D162_12908/1-97   AACCGCACCUCAA-GGUGAAA----GAUA-AAGAU--GA-CAGGAAGU-GC-CGGUAG--GUUUGGC-AUAC-----GCCAU-UCUCGACA-GCA-G--GGACUACAG---GAAAAG-CAGACAA
URS0000D6D2C5_12908/1-94   GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GCUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D6A2F7_709991/1-94  GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D6A2F7_12908/1-94   GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D6A2F7_457424/1-94  GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D6A2F7_817/1-94     GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D6A2F7_1121098/1-94 GACCUUGCCACUU-GGCAAAAGA--UGAC-GAACG--CU-CAAAAGGACGC-UGGUAG--GCCG----GUAA--------CG-GUUCGAAC-GCU-U--CCGAGUAAG---GCAAAG-CAGACAC
URS0000D69EC1_12908/1-88   GACCUUGCCGCAU-GGCAAAA----AAUA-AAUAG--CG-UAACGGAU-GC-UGGUAG--G-UU----GAAA--------GA--UUCGACG-GUU-U--CCAAUUAA----GCAAAG-CAGACCC
URS0000D6AD7F_12908/1-91   AGCCUUGCCGCUU-GGCAAAAA---AUAA-CAAGC--AG-UAACGGGU-GU-CGGUAG--GCCG----GUAA--------CG-GUUCGAAG-GCU-C--CCAAUUAA----GCAAAG-CAGACCC
URS0000D6B63C_12908/1-101  GACCCCGCCUCAC-GGCGAAAA---AUAA-ACUAA--AA-ACGGAGGU-GU-CAGUAG--ACCGGGU-ACAUA----AUCCG-GGCCGACC-GCA-A--CGACGUUCAAG-AAAAAG-CAGACAA
URS0000D66E1D_997885/1-100 GACCUCGCCUCAC-GGCGAAAA---AUAA-ACUAA--AA-ACGGAGGU-GU-CAGUAG--ACCGGGU-AAAU-----AUCCG-GGCCGACC-ACA-A--CGACGUUAAAG-AAAAAG-CAGACAA
URS0000D657A6_12908/1-96   AACCUCGCCUCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGCAU-------CG-GGCCGAAG-GUA-A--CGAGGUCAGAAGAAAAAG-CAGACAA
URS0000D6C609_12908/1-96   AACCUCGCCCCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGAAU-------CG-GGCCGAAC-GUA-A--CGAGGUCAGAAGAAAAAG-CAGACAA
URS0000D68EE7_12908/1-95   AACCUCGCCCCUU-GGCGAAAA---AUAA-ACUAA--AG-GCUAAGGU-AC-UGGUAG--ACCG----UGAAU-------CG-GGCCGAAC-GUA-A--CGAAGUCAGAA-GAAAAG-CAGACAA
URS0000D670B9_1235787/1-98 GGCCUCACCCCAC-GGUGAAAAA--CAAA-CGACA--GG-CGGGCAGU-GC-CGGUAG--ACGGG---UUUAU------CCC-GGCCGACA-GCA-A--CGAAGCCGGAA-GAAUUG-CAGACCA
URS0000D6AF49_12908/1-103  GGCCUCACCUCAU-GGUGAAAAA--CAAA-CGAAA--UG-CGGGCAGU-GC-CGGUAG--ACGGGA--CCGAUAA---UCCC-GGCCGACG-GUA-A--CGAAGCAAGAGAAAAUUG-CAGACAC
URS0000D69A0E_12908/1-95   GGCCUCGCCCGAC-GGCGGAA----AAUA-AACUA--AA-CGAAAGAU-GC-UGGUAG--AUCGUA--AAUUG-----UACG-AGCCGAAC-GCG-U--GAUAAGUA----AAAAAG-CAGACAA
URS0000D68416_12908/1-95   GGCCUCGCCCGAC-GGCGGAA----AAUA-AACUA--AA-CGAAAGAU-GU-UAGUAG--AUCGUA--GAUUG-----UACG-AGCCGAAC-GCG-U--GAUAAGUA----AAAAAG-CAGACAA
URS0000D671ED_12908/1-102  GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--UAGGAUAAA---AAAUAG-CAGACAA
URS0000D681A0_12908/1-102  GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UAGGGUAAA---AAAUAG-CAGACAA
URS0000D69E01_12908/1-102  GACCUCGCCCCAU-GGCGAAA----CAUA-CACAU--AG-UUCAUCUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--UAGGGUAAA---AAAUAG-CAGACAA
URS0000D66F62_12908/1-102  GUCCUCGCCCCAU-GGCGAUA----CAUA-CACAC--AC-CAAGAUUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UGAACAUUA---AAAAAG-CAGACAA
URS0000D6CB38_12908/1-102  GUCCUCGCCCCAU-GGCGAUA----CAUA-CACAC--AC-CAAGAUUA-GC-UGGUAG--AUGAUGACAAUAAG--GUCAUCCGGUCGAAG-GUU-A--UGAACAUUA---AAAAAG-CAGACAC
URS0000D671D5_12908/1-99   GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA-----GAAAG-CAGACAA
URS0000D696A2_12908/1-103  GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAAAGUU-A--GGACAUUUA---GAAAAGCCAGACAA
URS0000D6B9EC_12908/1-100  GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-AAGUAG--AUGAUGGCAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA----GAAAAG-CAGACAA
URS0000D6686D_12908/1-100  GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUUA----UAAAAG-CAGACAA
URS0000D6CAC1_12908/1-100  GGCCUUGCCUCAU-GGCAAAA----CAUA-CACUU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUCA----UAAAAG-CAGACAA
URS0000D67BDF_12908/1-100  GGCCUUGCCUCAU-GGCAAAA----CAUA-CACAU--UA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAUGG---GUCAUCCGGUCGAAA-GUU-A--GGACAUCA----UAAAAG-CAGACAA
URS0000D6838E_12908/1-102  GACCUUGCCCCAA-GGCAGAA----AAUU-CACUU--AU-CUAGAUUA-GC-UGGUAG--AUGAUGACAAUAGG--GUCAUCCGGUCGAAG-GUU-A--GGACUCUUA---AUUAAG-CAGACAA
URS0000D6A207_12908/1-102  GGCCUUGCCCCAA-GGCAGAA----AAUA-CACUU--GU-UAAGAUUA-GC-UGGUAG--AUGAUGACAGUAGG--GUCAUCCGGUCGAAA-GUU-A--GGAUUUUAG---AAAAAG-CAGACAA
URS0000D694D4_12908/1-100  AGCCUUGCCUCAU-GGCAGA-----ACAU-ACACU--AA-GCAGAAUA-GC-UAGUAG--AUGAUGACAAAAGG--GUCAUCCAGUCGAAU-GUU-A--GGACAUAA----AAAAAG-CAGACAA
URS0000D6C873_12908/1-86   UGCCUUGGCUCAU-GCCAAAACA--UAAC-AAACU--UC-AACGCUGU-AU-UAGUAG--ACGC----CGAG--------GC-GGUUGAAA-AUU-C--AGCA----------AAAA-CAAACAU
URS0000D6ABFC_12908/1-95   CGCCCUGCCACUU-GGCAAAAUA--UAAA-AAUAC--AA-UGAACUAU-AU-UAGUAA--AUUUGA--GAAA------UCAAAAGGUGAAA-GUU-U--AGUUUG------UAAAUG-CAUACAA
URS0000D66DAF_12908/1-92   UGCCCUGCCACUU-GGCAAAAUA--UAAA-AAUUA--UU-UGAACUGU-UU-UGGUAA--AUCCU---GCAA-------AGGAAGUUGAAG-AAU-C--AGUUU-------GAAGUG-CAUACAA
URS0000D68438_12908/1-95   UACCUUGCCACAU-GGCAAAAC---ACAA-AAAUU--UA-UUAACUGU-AU-UAGUAG--ACUUGAACAAU-----GUUCAA-GGUUGAAG-AUU-C--GGUUA-------UAUUAG-CAUACAC
URS0000D6B951_12908/1-99   UACCUUGCCUCUA-GGCAAAAC---AUAU-CAAUU--CU-GAAGCUGU-AU-UAGUAG--ACUUUGAAAGCAAAAUUUCAAA-GGUUGAAA-AUU-C--GGCA--------AACGAG-CAUACAA
URS0000D6CB95_12908/1-95   UACCGUGCCACUU-GGCAAAACA--UCAA-AAACACCAA-AGAACCGU-AU-UAGUAG--ACCCGGC-AUCU-----GCCGG-GGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAA
URS0000D6B51A_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D6B51A_742740/1-90  UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D6B51A_657313/1-90  UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACUGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D677C6_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGCC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D69C0A_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-AUU-C--GGU---------UCAGUG-CAUACAG
URS0000D6A1E3_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUUA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D69754_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUA--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUUGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D6C89F_12908/1-90   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUG--CA-UGGGCUGU-AU-UAGUAG--ACCGUC--ACCU------GACG-GGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D695C3_12908/1-94   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--CA-UGGACUGU-AU-UAGUAG--GUUGCACUCAUU----UGUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D65A8A_12908/1-94   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--CA-UGGACUGU-AU-UAGUAG--GUUGCACCCAUU----UGUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D6BAA7_12908/1-94   UACCGUGCCACUU-GGCAAAAC---AUCA-AAAUU--UA-UGGACUGU-AU-UAGUAG--GUUGUAC-UCAUUC---GUGCA-AGUCGAAA-GUU-C--GGU---------UCAGUG-CAUACAG
URS0000D67C59_12908/1-96   CACCGUGCCACUU-GGCAAAACAUUCAAA-AAUUC--AA-UAGGCUGU-UU-UGGUAA--ACUGCC--CAAACA----GGCA-GGUUGAAG-AAU-C--GGCU--------UUAGUG-CAUACAA
URS0000D6B22E_12908/1-99   UGCCUUGCCACAU-GGCAAAACA--UAAC-AAUUC--AA-UAUCCUGU-GU-UAGUAG--ACUUUGAAAGUUAAGAUUCAAA-GGUUGAAC-GCU-U--GGGG---------GAUUG-CAUACAC
URS0000D65DE4_12908/1-101  GACAGCCCCCGAAAGGGGGAAGU--UAAA-AAUAA--AA-UUUGUCGU-AU-UGGUAG--ACUUUGAAAGUUAAUUUUCAAA-GGUUGAAG-AUU-C--GGCU--------GAUGUG-CAUACAA
URS0000D68472_12908/1-101  GACAGCCCCCGAAAGGGGGAAGU--UAAA-AAUAA--AU-UUGGUCGU-GU-UGGUAA--ACUUUGAAAAUUAACUUUCAAA-GGUUGAAG-AUU-C--GGCU--------GAUGUG-CAUACAA
#=GC SS_cons               :::::<<<<____.>>>>::::...::::.:::::..::.:::::::<.<<.-----<..--<<<<..____......>>>>.--->----.>>>.:..::::::::....::::::.:::::::
#=GC RF                    gaCCuuGCCuCaU.GGCaAAAc...aaaA.aAauu..aa.uaagauGu.gc.UGGUAG..ACcgug..aaua......cacg.GGUCGAAa.gca.a..gGaaauaa....aAAAAG.CAgACAa
//
