# STOCKHOLM 1.0
#=GF ID P11
#=GF AC RF00625
#=GF DE Pseudomonas sRNA P11
#=GF AU Daub J; 0000-0001-6022-563X
#=GF GA 70.0
#=GF NC 69.7
#=GF TC 70.4
#=GF SE INFERNAL
#=GF SS Predicted; RNAalifold
#=GF TP Gene;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.20 -Z 2958934 CM SEQDB
#=GF DR SO; 0001263; ncRNA_gene;
#=GF RN [1]
#=GF RM 16870723
#=GF RT Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT sRNAPredict2.
#=GF RA Livny J, Brencic A, Lory S, Waldor MK
#=GF RL Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC by northern blot analysis [1]. P11 is located between a putative threonine
#=GF CC protein kinase and putative nitrate reductase and appears to be conserved
#=GF CC in several Pseudomonas species. P11 has a predicted Rho independent
#=GF CC terminator at the 3'end but the function of P11 is unknown [1].
#=GF WK Pseudomonas_sRNA_P11
#=GF ** seedtax: Bacteria; unclassified sequences
#=GF SQ 15

CP000075.1/2450746-2450611 AGAU--GCGAGUUGGCACAAGCACUGCAUGG--UC-UCUUGCAGAUAAUUCAUAACACGCAGCCCUCAACGAUGAAGGCUGCGUC-UCCCGAGAGAACGGGACC-G-GACAAAGGCGUCCUCGUCAGGCCACUGACGGGACGCC
AE016853.1/2548871-2548734 GUGAACACGAGUUGGCACAAGCGCUGCAUAG--UC-CCUUUCAGAUCAUUCAUAACGCGCAGCCUUCAACGAUGAAGGCUGCGCC-UCCCGAGAGAACGGGACC-G-GACAAAGGCGUCCCCGUCAGGCAACUGGCGGGACGCC
AF112870.1/4018-4154       AAUAGCGCAAGUUGGCACGGCGCCUGCUUGGGUUC-UCCCGACAAUCGACAACAAAGCGCCUGCCUCAACGACGA-GGCGGCGUU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP000058.1/2429276-2429141 GAAUGCG--AGUUGGCACAGGCGCUGCAUUG--UC-UUGUGCAGAUCAUUCAUAACGCGUAGCCCUCAACGAUGAAGGCUGCGCC-UCCCGAUAGAACGGGACC-G-GACAAAGGCGUCCCCGUCAGGCAACUGGCGGGACGCC
CP000744.1/3650435-3650571 AAUAUCGCAAGUUGGCACGGCGCCUGCUUGGACUU-UCCCGACAAUCGACAACACAGCGCCGACCUCAACGACGA-GGCUGCGCU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP000680.1/2325584-2325446 CUUCGAGAAAGUUGGCACAGGCACUGCAUUG--UU-ACUGGCAGCAAACACAUAAAGCGCGACCUUCAACGAAGAAGGCUGCACU-UCCCGAUAGAACGGGACCUG-GACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
AACY021569628.1/361-230    ------G--AGUUGGCACAAGGGCUGCAUUC--ACAACUACCACAAACCACAUAAAGCGCGACCUUCAACGACGAAGGCUGCACU-UCCCGAUAGAACGGGACC-UGGACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
CP000304.1/2631424-2631562 GUAUUUCAGAAUUGGCACAGGCUCUGCAAAG--CA-AACGUCGAAGAUGACAUACGACCUGACCCUCAACGUGGAGCGGCAGGUU-UCCCGACUGAGCGGGACACG-GACAAAGGCGUCCUCACCGGAGAACCGGUGGGACGCC
CP001157.1/2336638-2336501 CAUCCGUGAAACUGGCACAGCCCCUGCAUCG-AGA-AAACCGACAGAUCACAUAA-GCAUUGCCUUCAACGUGGAGGGCAGUGUU-UCCCGACAGAACGGGAAU-G-GACAAAGGCGUCCUCGCUGGGUAACCGGCGGGACGCC
CP000094.2/1982387-1982251 CCCGCCGCGACUUGGCACAACCACUGCAU----UA-ACGUUUUCAACUGACAUAAAGCCCGACCUUCAACGACGAAGGCCAGGCU-UCCCGAGAGAACGGGACAAG-GACAAAGGCGUCCUCGCUAGGUAACUGGCGGGACGCC
AE004091.2/1928802-1928666 AACAGCGCAAGUUGGCACGGCGCCUGCUUGGGUUC-UCCCGACAAUCGACAACAAAGCGCCUGCCUCAACGACGA-GGCGGCGUU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP002727.1/3606931-3607057 UUUGAUGCUGAUUGGCACACUCCCUGCUCAU--GU-AUCCGCA-----GACAUCGAGCCUGUCGG----CACA---CGGCAGGCUCCCCGAAACGAAUCGGGACCG-GACAAAGGCGUCCUUGCACU-CACGGUGCAGGACGCC
CP002620.1/2870847-2870985 UUCCGAGAAAGUUGGCACAAGCGCUGCAUUG--UU-ACUGGCAGCAAACACAUAAAGCGCGACCUUCAACGAAGAAGGCUGCACU-UCCCGAUAGAACGGGCUCUG-GACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
CP002585.1/2059414-2059278 CUUCGCGCCAGUUGGCACAACCACUGCAUAA-----UCCCUUUCAACAGACAUAAGGCAACGCCUCCAACGAUGAAGGCGGUGCU-UCCCGAGAGAACGGGACCAG-GACAAAGGCGUCCUCGCUAGCUUGCUAGCGGGACGCC
CP002881.1/2488319-2488457 GCAUUUCAAAAUUGGCACAGGCUCUGCAAAG--CA-AACGUCGAAGAUGACAUACGACCUGACCCUCAACGUGGAGCGGCAGGUU-UCCCGACUGAGCGGGACACG-GACAAAGGCGUCCUCACCGGAGAACCGGUGGGACGCC
#=GC SS_cons               :::::::::::(((<<<_______>>>,,,,..,,.,,,,,,,,,,,,,,,,,,,,<<<<<-<<-<<______>>->>->>>>>,.<<<<<______>>>>>,,,,.,,))):<<<<<<<-<<<<<<____>>>>>>>>>>>>>
#=GC RF                    auuuuugcaAgUUGGCACAagcaCUGCauag..uu.acuuucaaAuaauacAUAaagCgcgaCcuuCAACGauGaagGccgcGcU.uCCcGAuaGAACgGGaccuG.GACAAAGGCGUCCUCGCcggguaAccgGCGGGACGCC
//
