# STOCKHOLM 1.0
#=GF ID rliE
#=GF AC RF01459
#=GF DE Listeria sRNA rliE
#=GF AU Osuch I
#=GF GA 90.0
#=GF NC 65.9
#=GF TC 210.3
#=GF SE INFERNAL
#=GF SS Predicted; WAR
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 29.48 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 17259222
#=GF RT Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT prediction of mRNA targets.
#=GF RA Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL Nucleic Acids Res. 2007;35:962-974.
#=GF WK Listeria_monocytogenes_non-coding_RNA
#=GF SQ 4

AL596169.1/38059-38283     UGAAUAAAAGAAAUAAAAAUAGAACUAUAGAUUAUUAGUAAAAAGUAAACCAUCCGCCACCUCCUAGUUGUUACAAACAGAAUAGCAAAGAAGAUUUAUUUUUGCACAUUGAUAAAAUGAUGUUUUCACUGGGUAGA-CUAACUAAAAAACACCUAUUUUCUACUAAGAGAAAAUAGGUGUUUUU-AUUUACUUUUAGCA
AL591979.1/174586-174808   UGAAUGAAAGACAUAAAUACCGCACUAUAAAUAGCUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUGUUAAAAACAGAAUAGCAGAGACGAAAUUUUUUUGCACAUAGCUAAAAUCACUUUUCCAUCUUCUAUUGCAUA-ACAAAAACACCUAUUUUCAUUAGUG-GAAAACAGGUGUUUUU-A-UAUAUUUUAUCU
AE017262.2/1564293-1564515 UGAAUGAACGACAUAAAUACUGCACUAUAAAUAGCUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUGUUAAAAACAGAAUAGCAGAGACGAAAUCUUUUUGCACAUAGCUAAAAUCACUUUUCCACCUUCUAUUGCAUA-ACAAAAACACCUAUUUUCAUUAGUG-GAAAACAGGUGUUUUU-A-UAUAUUUUAUCU
AARN04000022.1/18360-18579 UGAAUAAAAGACAUAAAUAUUACACUAUAAAUUAUUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUG-UAAAAAUAGAAUAGCAGAGUUAAAUUAUUUUUGCACAUAGCUAAAAUCGUUUUUUCACACUCUAGA-CAUA-GCAAAAA-CCCUAUUUUCCAUCUAA-GAAAAUAGG-GUUUUUUA-UAUAUUUUAGCC
#=GC SS_cons               ::::::::::::::::::::::::::[[[[[[[[[[[--[[[[[[,,,,,<<-<<<________>>>->>,,,,,,,((((,,,<<<<<<<_______>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,.,,<<<<<<<<<<-<<<<<_______.>>>>>->>>>>>>>>>.,.,,,,,,,,,,,,
#=GC RF                    UGAAUaAAaGAcAUAAAuAuugcACUauaaauagcuaaUaaaaaGUAAAuCaUCuguCACCUCCuaGUuGUUAaAAAcagaAUAGCagagaugAauUauuuuuGCACAUaGcUAAAAUcAuuUUUuCAcuuucUAua.CauA.acaaaaaCaCCuAuuuuCaauaaag.GaaaauaGGuGuuuuu.A.UauaUUUUAuCu

AL596169.1/38059-38283     UACGAAAA-UACUAUUUUAGUAGUUUGC
AL591979.1/174586-174808   UCUGAAAA-UCCUUUUUUAGCUAUUUGU
AE017262.2/1564293-1564515 UCUGAAAA-UCCUUUUUUAGCUAUUUGU
AARN04000022.1/18360-18579 UCUGAAAAU-CCUUUUUUAGCUAUUUGU
#=GC SS_cons               )))),,,,.,,]]]]]]]]]]]]]]]]]
#=GC RF                    ucugAAAA.UcCuuuuuuagcuauuugu
//
