raw_data/life/L020/0002-RF02452.stockholm

# STOCKHOLM 1.0
#=GF ID ncr1575
#=GF AC RF02452
#=GF DE Bacillus sRNA ncr1575
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 60.0
#=GF NC 59.2
#=GF TC 60.0
#=GF SE Eberhardt R
#=GF SS Published; PMID:20525796
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 35.30 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 20525796
#=GF RT Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK Bacterial_small_RNA
#=GF SQ 29

AEFY01000060.1/10854-11054 UUAAUAACAUGAGAAGGGA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AACGUUUGAAAU-U-G-AU--AUUU--CAAAU--CAU--ACAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUAU-------ACGUAAGC------GCUAUUUCUGAA-----------------------------GAAUAG
CP000560.1/574422-574226   UAA--CAAAUACGAAGGGA-UGAUGGGUGGACAAUGAUUAACUAAUCU-UAUUUUG-ACCGUUUGAAAU-C-AAAU--AUUU--CAAAU--CAG--AAAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUACGA----UACGAAA--------GCUAUGUA---A-----------------------------AAAUAG
AAOX01000024.1/57078-56873 CAACUAAGUGCGAAAGGAA-UGAUGGGUGGACGAUGGAUAACUGAUCU-UAUUUUUUCUUGAUUGAAAU-AGC-AU--AUUU--CAAUU--CACACAAAAA-AUA-GGAUUAGUCUGCCCAUU-UUUCACUU-A----UACAUCAUUC----AGCCAUUA-UG-A-----------------------------UAAUGG
CP000227.1/2437378-2437587 UAUUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUC-A-AUACAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGCAAUAG
ACMD01000088.1/8944-9153   UACUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUC-A-AUAAAUUU--CAAUU--U-A-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCUUAC-A-----ACGGUAUU------GCUAUUUAUU-AUG-------------------------CGUAAUAG
CP001176.1/2494406-2494615 UAUUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAUA-UUG-------------------------CGCAAUAG
ACLT01000056.1/51155-51364 UAUUAAUGACAGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAG-A-----ACGGUAUU------GCUAUUUAU--GUU------------------------ACGUAAUAG
ACMY01000063.1/95493-95702 UACUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUGA-A-AUAAAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAUA-UUG-------------------------CGCGAUAG
ACNK01000052.1/72455-72664 UACUAAUGAGGGGAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCGAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGUAAUAG
ACMF01000050.1/21045-21254 UAUUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-AAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGCAAUAG
ACNC01000090.1/185-394     UACUAACGAUGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUUUU------GCUAUUU-----GAUU---------------------UGCGUAAUAG
ACMU01000051.1/2518-2309   UACUUAUGACGGAAAGGAU-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUA-A-AUAAAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU--GUU------------------------GUACAAUAG
ACMJ01000045.1/2590-2799   UACUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUA-A-AUAAAUUU--CAAUUUGUA----AAAA-AUA-GGAUUAGUCUGCCCAA--UUCCAUUC-A-----ACGGUAUU------GCUAUUU-----GAUU---------------------UGCGUAAUAG
ACLS01000064.1/23579-23787 UACUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUGA-A-AUAAAUUU--CAAUUUAUA----AAAA-AUA-GGAUUAGUCUGCCCAA--UUCCAAAC-A-----ACGGUUUU------GCUAUUU-----GAUU---------------------UGCGUAAUAG
AGIP01000011.1/90019-90227 GAACAUAAUGAUGAGAGGACUGAUGGAUGGACAAUGGUUAACUAAUCU--AUAUUU-U-UAUUUGAGUU-G-A-AU--AACUUCCAAAU-ACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UCUAUAA-A----UCAGU----------G-UACAUG-------UCAUGAAUUUAAUGGCAAACU-----ACAAAC
CP000817.1/2916920-2917132 -UAUACAAUUAUGAGAGGACUGAUGGAUGAACAAUGAUGAACUAAUCU--AUAUUU-UAAG-UUGAAAU-C-A-AU-UACUU--CAAACUACA----AAAU-AUA-GGAUUAGUCUGUCCAUU--UUUAUUC-A----UCAGUUUAU------ACUUUAU-------UUGUCAUUU------UCCUAUGGCA--AAAAGG
AL009126.3/606606-606407   UAAUCAAAACAAGAAGGGA-UGAUGGGUGGACAAUGAUUAACUAAUCU-UAUUUUU-ACCGUUUGAAAU-C-A-AU--AUUU--CAAAU--CA----AAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUAU-A----UACGACACU------GCUAUUUAUAAA-----------------------------AAAUAG
AFRV01000003.1/54844-55060 AAAUACAAUUAUGAGAGGACUGAUGGAUGGACAAUGAUUAACUAAUCU--AUAUUU-U-UAUUUGAAAU-G-A-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-A----UCAG--UUU------ACACUUUAU---UUGUCAUGAUU-------CCAAUGGCAAAAAAGAG
AJ293027.1/6225-6003       UACUAUUAAUCGAAAGGAG-AGAUGGGUGGACAAUGAAGAACUAAUCU-AAUUUUU-AACAAAUGAAAU-AGU-AU--AUUU--CAGUU--UA----AAAA-CUUAGGAUUAGUCUGCCCAUUUUUCCAUAU-AC---UAAAUAAAU------GUAAGACUG---AAUAGCUAAA--------AAGGCUAAAUAGUUUUA
AAXV01000013.1/57287-57073 AUAUACAAUUAUGAGAGGACUGAUGGAUGAACAAUGAUGAACUAAACU--AUAUUU-UAAG-UUGAAAU-C-A-AU-UACUU--CAAACUACA----AAAU-AUA-GGAUUAGUCUGUCCAUU--UUUAUCA-A----UCAGUUUAU------ACUUUUUUC---GUCAUUUU------------CCUAUGGCAAAAAAG
ACMV01000132.1/9772-9988   AAAUAGAAUUAUGAGAGGACUGAUGGAUGAAUAAUGAUUAACUAAUCU--AUAUUU-UAA-UUUGAAAU-U-A-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-A-----UCA-----------GUUCAUACU---UUAUUUGUCAUGA---UUCCAAUGAUUAAUAAGAA
ADJR01000035.1/12266-12474 AAAGACAAUUAUGAGAGGACUGAUGAAUGGACAAUGAAGAACUAAACU--AUAUUU-U-UAUUUGAAUU-G-A-AU-GAUUU--CAAAC-ACA----AAAU-AUA-GGGUUAGUUUAUCCAUU--UUUAACA-A-----UCAGUU-U------GCAUUGUAU---UUGUC------------------AUGACACAAAUG
ACMZ01000088.1/41335-41548 AAUAGAAUUAUGAAAGGAA-UGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU-UUUAAAAU-U-----CAGUUCAU------ACUUUAUUU----GUCAUGAU----------UCAAAUGAUUAAUAAG
ACLW01000071.1/41842-42052 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-UU---CAUUUCAUA-----CUUUAUUUAU---CAUG---------------------AUUCAAAUGA
CP002508.1/3357927-3358143 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-------UUCAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUA
ABCZ02000041.1/1982-2197   AAAUAGAAAUAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAA-UUUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-U----U--CAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUA
CP000001.1/2406369-2406154 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUG-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-U----U--CAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUA
HQ128580.1/8169-7952       UCUUCAAAUAUGAAUGGAC-UACUGGGUGGAAGAUAAUUAACUAAUCUGUAUUCUU-CUAAUUUGAAAU-G-A-AUAAGUUU--CAAAG--UAC--UAAGAUAUA-GGAUUAGUC-AUCCAUU-UUUUUUAA-A----UCAGUUUAACUAGAUGUUUUGU-U------UGUCG-------------AAUGA-C-AAAAAA
AJ579365.1/3731-3942       AAAUAAAUAGACGAAAGGACUGACUGUAUAAUAAUGAUUUACUAAUUC----AACU-U--AUUUGAAAU-A-A-AU--AUUU--CAAACUCUA----AGUU-AUA-GGAUUAGUCUGAUCAUU--UUUAUAA-GUCGGUUUGUGACA------CCUAUUGCG---U--CAAAUG-----------CUGUUGGUACAAUAG
#=GC SS_cons               :::::::::::::::<<<<.---<<<<--<<<----------<<<<<<.<<<<<<<.---<<<<<<<<<._._.__._>>>>..>>>>>----....>>>>.>>>.>>>>>>>>>-->>>>--.>>>>::::.:....::<<<----......<<<<<<<__..._____..................______>>>>>>
#=GC RF                    uAaUAaaaauaugAAggaa.UGAUGGgUGGAcaAUGAUUAACUAAuCU.uAUuuUU.uAaguUuGAAaU.u.a.AU.AAuUU..CaAacUauA....AAaa.AUa.GGaUUAgUCUgcCCAUU.uuccAUAa.A....Uacguuauu......gcuauuuaU...uuuua..................uauauaaaauag

AEFY01000060.1/10854-11054 C-UUAUUUGAUCAUGGCAAA--G--GC--A-CGGCUAAUCCUUCCA-A--AA-CA--UUUGGGAGGAUUUUUUG
CP000560.1/574422-574226   C-UUAUUUGAUCAUG-CACA--G--GU--A-CGGCUAAUCCUUCCA-A--AU-CA--AUUGGGAGGAUUUUUUU
AAOX01000024.1/57078-56873 U-UUAUUUGCUGAUG-CAAA--G--GU--A-CGGCUAAUCCUUCCA-A--UU-CA--AUUGGGAGGAUUUUUUU
CP000227.1/2437378-2437587 C-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMD01000088.1/8944-9153   C-UUAUUUGGGUAUA-AAUA--U--GUUAA-CGACUAAUCCUGCCA-A--AUUAA--UUUGGGAGGAUUUUUUU
CP001176.1/2494406-2494615 C-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACLT01000056.1/51155-51364 C-UUAUUUGGGUGUG-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMY01000063.1/95493-95702 C-UUAUUUGGGUAUA-AAUA--UUUUU--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACNK01000052.1/72455-72664 C-UUAUUUGGGUGUA-AAUAUUU--UA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMF01000050.1/21045-21254 U-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUA
ACNC01000090.1/185-394     C-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUA
ACMU01000051.1/2518-2309   C-UUAUUUGGGUAUA-AAUA--UUUUA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMJ01000045.1/2590-2799   C-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A--AA-UUACUUUGGGAGGAUUUUUUU
ACLS01000064.1/23579-23787 C-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
AGIP01000011.1/90019-90227 U----UAUUU--AUG-AAAA--U--UA--A-CGGCUAAUCCUUCCAUA--UC-CA--UUUGGGAGGAUUUUUUA
CP000817.1/2916920-2917132 UCCUUUAUUAUU----ACCU--G--UA--ACCGACUAAUCCUUCCA-A--UG-AA--AUUGGGGGGAUUUUUUU
AL009126.3/606606-606407   C-UUAUUUGAUCAUG-CACA--G--GC--A-CGGCUAAUCCUUCCA-A--CA-CA--UUUGGGAGGAUUUUUUU
AFRV01000003.1/54844-55060 C-UUAU-UUACUAU---AAG--U--GA--A-AGACUAAUCCUUCCA-A-UUACAA--AUUGGGAGGAUUUUUUA
AJ293027.1/6225-6003       U-UUGAGUCCUUAAA-AAGU--G--AC--A-UGACUAAUCCUUCCA-A-CAU-UA--UUUGGGAGGAUUUUUUA
AAXV01000013.1/57287-57073 U-CCUUAAU-CAAUA-CCUG--U--AA--C-CGACUAAUCCUUCCA-A-UGA-CA--AUUGGGGGGAUUUUUUU
ACMV01000132.1/9772-9988   C-UUAU-UAAGUAUA-AG----U--GA--G-AUACUAAUCCUUCCG-A-UUACAA--AUUGGGAGGAUUUUUUU
ADJR01000035.1/12266-12474 G-CAAAUCGUAUUUA-UUUA--G-UGA--A-AGACUAAUCCUUCCA-AUGCA-CA--AGUGGAGGGAUUUUUUC
ACMZ01000088.1/41335-41548 U-ACUUAUUAA-GUA-UAGA--C--GA--A-AGACUAAUCCUUCCG-A-UUA-CA--AUUGGG-GGAUUUUUUU
ACLW01000071.1/41842-42052 U-UAAUAAGUACUUA-CUUA--AGCGA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUCGGGGGAUUUUUUU
CP002508.1/3357927-3358143 C-UUACUUAAGUAUA-AGC------GA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUUGGGGGAUUUUUUU
ABCZ02000041.1/1982-2197   C-UUAUU-AAGU--A-UAAG--A--GA--C-AGACUAAUCCUUCCG-AUUAA-UA--AUUGGG-GGAUUUUUUU
CP000001.1/2406369-2406154 C-UUAU---UAAGUA-UAAA--A--GA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUUGGGGGAUUUUUUU
HQ128580.1/8169-7952       C-UCUUA-UUUAGUA-UAAA--U--GA--A-UAGAUAAUCCUUCCA-A-UAA-UA--AUUGGGAGGAUUUUUUA
AJ579365.1/3731-3942       GGACUUUUAAAUAUG-A-----G--AC--C-AGAUUAAUCCUUCCA-A--AU-UC--UUUGGAAGGAUUUUUAU
#=GC SS_cons               >.---->>>::::::.::::..:..::..:.:::::<<<<<<<<<<.<.___.__.._>>>>>>>>>>>:::::
#=GC RF                    c.UuaUacgauuAUA.aAuA..u..ga..A.aGACUAAUCCuuCCA.a.uuu.uA..uuUGGgaGGAUUUUUUu
//