# STOCKHOLM 1.0
#=GF ID rli54
#=GF AC RF01491
#=GF DE Listeria sRNA rli54
#=GF AU Osuch I
#=GF GA 80.0
#=GF NC 59.5
#=GF TC 86.0
#=GF SE INFERNAL
#=GF SS Predicted;RNAalifold
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 21.52 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 19448609
#=GF RT The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA Johansson J, Cossart P
#=GF RL Nature. 2009;459:950-956.
#=GF WK Listeria_monocytogenes_non-coding_RNA
#=GF SQ 5

AL591977.1/188584-189111   GUAUUAAUAAAAUUCUUGUUUUCGAGUAAAACAGAAAUAACAUUUUAAAUAAAAGGAAAGUUCCUGUUUUUUUAUGAAACAUUGUGAAAGAAUGAAAGUUUUUUCACAUACUCUCUUAAAACCCAUGUUUUCAAUGAGGAAUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUAGUUAAUAGGAAUUUAGAAAAAAGCUU
AM263198.1/1043902-1044428 GUAUUAAUGAAAUUCUUGUUUUUUAGUAAAACAGAAUUAAC-UUUUAUUAAAAAGGAAAGUUCCUACAUUUUUAUGAAACAUUGUGAAAGAAUGAAAGUUUUUUCACAAUCUCUCUUAAAACCCAUGUUUUCAAUAAGGAUUUUGUGGUAAUAACUGGAGAGGCUGUGCAAUAAGUUGAUGGGAAUUUAGAAAAAAGCUU
AE017262.2/1079194-1079721 GUAUUAAUAAAAUUCUUGUUUUUAAGUAAAACAGAAAUAAC-UUUUAACUAAAAGGAAAGUUCCUGAUUUUUUAUGAAACAUUGUGAAAGAAUGAAUAUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUGGUUAAUAGGAAUUUAGAAAAAAGCUU
AADR01000017.1/24753-25280 GUAUUAAUAAAAUUCUUGUUUUUAAGUAAAACAGAAAUAAC-UUUUAACUAAAAGGAAAGUUCCUGAUUUUUUAUGAAACAUUGUGAAAGAAUGAAUAUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUGGUUAAUAGGAAUUUAGAAAAAAGCUU
AL596167.1/96029-96557     GUAUUAAUAAAAUUCUUGUUUUUGAGUAAAACAGAAUUAACAUUUUAAAUAAAAGGAAAGUUCCUGUUUUUUUAUGAAACAUUGUGAAGGAAUGAAUGUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUGCGUAAUUAGUUGAUAGGAAUUUAGAAAAAAGCUU
#=GC SS_cons               {{{{{{{{,,,,<<<<-<<<<<_____>>>>>>>>>,,,,,.,,,,,,,,[[[[[[[[[[[[-[[[,,(((((((--(((,<<<<<<<<<<<<____>>>>>>>>>>>>,<<<<<<------<<<<<--<<<_____>>>--->>>>>-------->>>>>>,,,,,,,,,,,,)))-))))))),,<<<<<<-<<<<__
#=GC RF                    GuauuaauaAAAuuCuUGuuuuuaAGUaaaaCaGaaaUAAC.UUUUAaauaaaaGgaaaGuuCCuguuuuuuuauGAaaCAuuGuGaaagaacGAAuguuuuuuCaCaaaCuCuCuUAAAACCCaugUUuuCAAUgAGgauUUuguGGUAAUAACUgGaGaGGCUacGuAAUuaGuuaauaggaaUUuaGaaaAaaGCUU

AL591977.1/188584-189111   CCGGAAUCUGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAAAACCAU-CUAGUAAGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCU
AM263198.1/1043902-1044428 CCGGAAUUCGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAGAUGAAUCAUUUUAGGAUGGUAAAUGACCGGACGAGCGUUACAUGAAACGCGUACCUGACUAAUGAAGAAUUU-AAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCU
AE017262.2/1079194-1079721 CCGGAAUCUGCUUCUUUCUAUAGAAAGACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCU
AADR01000017.1/24753-25280 CCGGAAUCUGCUUCUUUCUAUAGAAUGACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCU
AL596167.1/96029-96557     CCGGAAUCUGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCU
#=GC SS_cons               _________>>>>->>>>>>]]]---]]]]]]]]]]]],,,,,,,,,,,,,,,}}}}}}}}::::[[[[[-[[(((((((((((,,,<<<<<<____>>>>>>,,,,,,,,<<----<<<<<______>>>>>--->>,,,,,,,,,,,,,,))))))))))),,,<<<<--------------------<<<<<<<<<<
#=GC RF                    CCGGAAUcuGCuuCuuuCuacaGAAuaaCuuuuCuuuuUACUACGCUAUUAUAauuaauaCACAAuCaggAuGgCaGuuucaaaagAacCcauuUAGaugGguAAAUGACCGGACGAGCGuuACAUaAaaCGCaUACCUaACUAAUGAAGAAuuugaaaCuGuACAauGuGAAUGACGAAAGGGUGGAUACGaaaugGCu

AL591977.1/188584-189111   UCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUGGUUCAAAUUUUGAAUGAAAAAGGAGAAAUUGUUAAUCCAGAUUUAAUGCCGGAUUUAACA
AM263198.1/1043902-1044428 UCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUGGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUAAAUCCAGAUUUAAUGCCAGAUUUAACU
AE017262.2/1079194-1079721 UCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUUAAUCCAGAUUUAAUGCCGGAUUUAACU
AADR01000017.1/24753-25280 UCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUUAAUCCAGAUUUAAUGCCGGAUUUAACU
AL596167.1/96029-96557     UCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUCUAAAUGAAAAAGGAGAAAUCGUAAAUCCAGAUUUAAUGCCGGAUUUAACU
#=GC SS_cons               <<<_______>>>>->>>>>>->>>>>>>,,,,,,,]]-]]]]](((,,<<<<<--<-<<<<<<<<____>>>>>>>>->-->>>>>,,,<<<___________>>>,,,,,,,,,)))::::::::::
#=GC RF                    uCuAAAACAAaGaaGGCuauuAuCGaCguAAAGAAACaAuuuGaGGCUGuuCauAAaCaauuuGaaUUaGuuCaaauuuugAauGaaAAAGGaGAAAUcGUuAAuCCAGAUUUAAUGCCgGAUUUAACu
//
