# STOCKHOLM 1.0
#=GF ID Rp_sR47
#=GF AC RF02800
#=GF DE Rickettsia sRNA47
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 60.0
#=GF NC 59.7
#=GF TC 60.9
#=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 RN [1]
#=GF RM 27375581
#=GF RT Identification and Characterization of Novel Small RNAs in Rickettsia
#=GF RT prowazekii.
#=GF RA Schroeder CL, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R,
#=GF RA Fofanov Y, Sahni SK
#=GF RL Front Microbiol. 2016;7:859.
#=GF CC Expressed in human microvascular endothelial cells (HMEC) infected with
#=GF CC Rickettsia.
#=GF WK Rickettsia
#=GF SQ 2

AJ235269.1/287678-287363 UUAGUUUUACAGCAGCCCUAGAAUUAAUUUGUGUUAAAGCCUGAACUGAUCCUUUACCAAAAGAUUUAGUACCAAGUAUUAUUGCUCUUUUAUGAUCUUGCAAAGCUCCAGCAACUAUUUCUGAAGCAGAUGCAGAAUUACCGUUUAUUAAAACAAUCAUAGGUACUUUUGGGGCUUUUAACGAAAACUCAUUCGCUUUA
CP003334.1/398228-397913 UCAGUUUUACGGCAGCCCUAGAAUUGAUUUGCGUUAAAGCCUGAACUGAUCCUUUACCGAAAGACUUAGUGCCAAGUAUUAUUGCUCUUUUAUGAUCUUGCAAAGCUCCGGCAACUAUUUCCGAGGCAGAGGCAGAAUUACCGUUUAUUAAAACUAUCAUAGGUACUUUGGGAGCUUUUAAUGAAAACUCAUUUGCUUUA
#=GC SS_cons             :::[[--[[--[[((((((((((---(((((((,,,,,,,,,,,<<<<<--<<<<____>>>>-->>>>>,,,,<<<<____>>>>,,,,,,<<<<-<<<<<--<<<-<<<_________>>>->>>--->>>>>->>>>,,<<<<____>>>>,,,)))))))--)))))))))),,,,,<<<<______>>>>,,,<<
#=GC RF                  UuAGuUUuaCaGCaGCcCuagaaUUaauuugcGUUAAAGCCUGAaCugaUCCuuuACCaaaaGAuuuaGuaCCAaGuaUUAUugCuCUUUUAugauCuuGCaAAGCuCCgGCAACUAUUUCcGAaGCAGAuGCagAauuaCCGuuuAUUAaaaCaAUCguagguACuuuugGgGCuUUUAAcgaaAACUCAuucgCUUua

AJ235269.1/287678-287363 GUUUCGCUAUUACUUGAUGUAGUUCUACCUUUUGUUGUAACAAUGACACCAGAAUCAAUAAAAUAAUCACUAACAGCAAUAGCUUGAUCAAGUAUACCACCAGCAUUAUUACGUAA
CP003334.1/398228-397913 GUUUCACUAUUACUUAAUGUAGUUCUACCUUUUGUUGUUACAAUUACACCGGAAUCAAUAAAAUAAUCACUAACAGCAAUAGCUUGAUCGAGUAUACCUCCGGCAUUAUUACGUAA
#=GC SS_cons             <<___>>>>,((((((((,<<<<------<<<<<<<<------<<____>>---->>>>>>>>----->>>>,,<<<____>>>,,)))))))),,,,,,,,]]--]]--]]::::
#=GC RF                  GuUUCaCuaUuaCuugauGuaGuUCUACCuuuuguuGUaACAAugACACcaGAAUCaauaaaaUAAUCaCuaACaGCAAUAGCuUGaucaaGuaUACCaCCaGCAUuaUUaCGUAA
//
