# STOCKHOLM 1.0
#=GF ID Cis90_sRNA
#=GF AC RF02648
#=GF DE Ruegeria cis90 sRNA
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 50.0
#=GF NC 49.4
#=GF TC 50.2
#=GF SE Argasinska J
#=GF SS Predicted; RNAfold;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF DR GO; 0010468; regulation of gene expression;
#=GF RN [1]
#=GF RM 27065955
#=GF RT Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL Front Microbiol. 2016;7:380.
#=GF CC Cis-encoded. Targets ABC transporter. Functions in transport. Higher sRNA
#=GF CC expression during C-limited growth.
#=GF WK Ruegeria
#=GF SQ 2

CP000031.1/3999629-3999858 AGGUCGAGGCGACCAGCGGUUCCUUGAAAUUGGCCUGUUGCAUCGGAUCGAAGUAGCCGCCCGGGUUGCCCGCCAUCCAGGUAUAGGUACGGGUCGAGCUGAGCCAUUGCAGGAACAGAUAGACCGCCUCGGGAUGCUGCGACUGCGACGAGAUCCAGGCCGU---GAUGUGGUAAUACAGAACCGACCGGCG-GUUCAG
CP002623.1/4382961-4383194 AGGUUUCCUCCACGAAGGGUUCCGAGAAGUUUGCCUUCUGGAAGGGAUCGAAAUACCCGGCGGGGUUGCCCGCCAUCCAUGAAUAGGUCCGCGUGGAACUGAGCCACUGCAGGAAAAGGUAUGCGGCCUCCGG--GUUGGCGCUGCGC-GAGCUGACGGUACCGGUGAUGUUGUAAUAGAUCACCGACCGGCGCACGAGG
#=GC SS_cons               :[[<<<<<<-<<<<___>>>>>>>>>>,,((((-((-(((((-------(--(((((--(((((((<<<<-<<<_____>>>--->>>>,,<<<<---<<<--<<______>>-->>>--->>>>)))-))))--)))))--))))))--))--))))<<<<<------<<<<<------<<<<<<_____>>->>>>--
#=GC RF                    AGGucgcggCgaCcAaggGucccgcgaAauuggCCuuuuGcaagGGAUCGAAguagCCGcCgGGGuugCCCgCcAUCCAgGcAUAGGuaCGgGucGAaCugAGCCAuUGCAGGAAcaGaUAgaCcgCCUCcGgAUGcugcgaCugCgacGaGaUccagGccgcGGUGAUGugguAAUAgAgcgcCGACCGGCGcgcgcaG

CP000031.1/3999629-3999858 CUGAUCACCAAAGCGGCGCCCCACC-GGCA--GGUGG
CP002623.1/4382961-4383194 CCGUCGUCAUGCUGCACACCCGGCGGGGCAUGGGCCG
#=GC SS_cons               --->>>>>---->>>>>,]]<<<<<_______>>>>>
#=GC RF                    CuGaccaCaaaagcggCaCCCggCcGGGCAUGgGccG
//
