# STOCKHOLM 1.0
#=GF ID rli38
#=GF AC RF01470
#=GF DE Listeria sRNA rli38
#=GF AU Osuch I
#=GF GA 49.0
#=GF NC 48.6
#=GF TC 49.0
#=GF SE INFERNAL
#=GF SS Predicted; RNAalifold
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=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 20

AL591977.1/262768-262917     ACAGAGUGGGAAUAGAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUGUUU
AADR01000004.1/105341-105192 GCUGAGUGGGAGUAAAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUGCCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACGGGGAUUUAUUU
AE017262.2/1132593-1132739   ACAGUAU---UAUAUUAAUU-UAGCUGUUAAAGUAUG-G-AAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUC--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAA-AUG-AUG-CUUGACAGGGAUUUGUUC
AARM02000208.1/1543-1692     UCCGAAUGGGAAUAAAAAAC-UAACAUACUAAAAAUU-G-GAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUUUUU
FM242711.1/1125921-1126070   GUUGAGUGGGAGUAAAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUGCCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACGGGGAUUUAUUU
AARI02001017.1/655-768       GUUGAGUGGGAAUAGAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUACC------------------------------------------ACAA
ACHK01000120.1/48426-48568   GUGGAGUGGGAAUAAAGAGC-CAACAUAAUAUGAAUG-GGGAA-UGCCGACAAAUCAAC-GUUUUUCA-ACU--------UUUGAAA-UGCU-UGUUUG--UCAUUGAAAAUG--AUAUGGUUCC--CUACCA---U-UUUCCCUACCAAA-A-------UUUGGUAGGGG--UCUUU
AAAK03000042.1/10371-10239   GUGGAGUGGGAAUAAGACGU-AAAUAUAAUAUGGAUG-GGGAA-UGCCGAUAAAUCAAC-GUUUUUCA-ACU--------UUUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUCC--CUACCA---UUUUU-----------CCU-ACC---------AAAAAAGGGC
ACIX01000266.1/4908-4755     ACAGGUA-GGAAUAAAGAGC-CAACAUGAUAUGAAUG-A-GAG-UGCCGUUAAAUCAAC-GUUUUUCA-ACU--------UACAAAA-UGCU-UGAAUU--UCAUUAAAAAUG--AUAUGGAUCCCCCUACCAAAAUAAAACCCUGCUGAG-AUG-AUA-CUUGGCAGGGAAUUUUUU
AARL02000856.1/384-530       GUUGAGUGGGAAUAGUAAGC-UAACAUAGUAAGUAUG-GAGAA-UGCAGAUAAAUCAAC-GUUUUUC-------------AACUAAA-UGCU-UGGUUA--UCAUUAAAUAUG--AUAUGCUUCC--CUACCA---UUUU-CCUUACCAAA-GUG-AAAUCUUGCUAAGAUGAAGCUA
ACNB01000009.1/7203-7351     AUUGAGUGGGAAUAAGACAU-UAAAUUAAUAAUAUUU-G-UGA-AGCCUAUCUUAAAGC-GUUUUUCA-ACU--------UGUUAAA-UGUU-UUAAAU--GCUUGAUUUAUG--AUAGUAUUCA--CCACCA---AAAGACCCCCCCAAGAUAU-AUUUCUUGGGGGG---UUAAUU
ACLO01000034.1/26824-26974   GUAGAGUGGGAAUAAAAUAU-AAACCUAAUUUAAA---G-UGA-CUUGAUUGAUUUAACAGCAUUUUG-AAUU-----GUUUUAAAA-CGCU-AAAAUC--UAAUUAAUUAU---AUUUGGUUCC--CCACCA---AAUA-CCCCACCAGA-AUUUCUU-UCUGGUGGGGAUUUUUUA
AAJM01000261.1/5712-5863     AUUGAGUGGGAAUAAAGAUA-UAACAUUGUUUAAAGU-G-AAAUUACUGUUCUAACAAC-GUUUUAGC-UAU--------UAUGUAA-UGGC-UGAAAA--CAAUUAAAUAUU--AACUUGUUUA--CCACCA---AAAACCCCACCAAUACAAC-AAG-UAUUGGUGGGGUUUUUAG
ABYO01000191.1/18041-17909   AUUGAAUGGGAAUAAAUAUA-UAAAAUGAUUUGAAUG-G-GAA-ACUCUAAAUUUCAAC--GUUUUUA-AAU--------GAUGAAAGUCAA-UGAAAU---CAAAUGAAUUGAUAUAUAGAUCC--CUGCCA---AAAUCC-----------UG-CCA---------AGGAUUUAUA
CP000056.1/799047-799191     CUUAAAUAAGAAGCAGAUAG-CAAUUUGAG----AGC-G-AAA-UCCCGAUUUAUCAGU-CUUUUAGA-GCUUAUAGCGAUUUGAAG-AAAC-UGAUAA--------AAU--G--AUUUGGUUUU--UUGCCA---AAAA-UCCUGCCAAA-AAA-AUC-UUUGGCAGGAUUUUUAUU
CP001348.1/2574349-2574222   AUUGAGUGGGAAUAAAAGUG-UAAGUUAAAUUGAUUG-GGGAA-AGCCUAUUUUGAA-G-GUUUUCCCCAUU--------UUUGUAA-GGUA-AUAAAA--UGGUUAGAAAU---AAAUAGUUCC--CCACCA---AAAACC---------------CA----------GAAUUGAGC
CP000407.1/961832-961683     GUUACUCUUAAAUAAGAGUCACAUCAUAAUUAGAUUGCG-GAA-UCCCUAUUUACCAG---UCUUUGA-GAG--------CGAUAAG-CGAU-UGAUAGAAACUGAUAAAUUG--AUUUGGUUUC--CUGCCA---AAAA-UCCUGCCAAA-AAU--UC-UUUGGCAGGAUUUUUGUU
CP001015.1/1258926-1258786   AAUAAGAGGCA-UA--------UACCAAUUAGAAUUC-G-GAA-UACUAUAGUAUCAGC-CUUUUAGA-AUCGUGAACACAUUUUAG-AAAC-UGAUAA--------AUU--A--AUUUAGUUUC--CUACCA---AAAA-CCCUACCAAA-AAU-UAA-UUUGGCAGGGUUUUUCUU
ACDZ02000009.1/22044-22191   AUUGAAUGGGAAUAGAUUAC-AAAUAUAAUUUGAAUG-G-AGA-AUCC--UAAUUUAACUGCGUUUCU-AGUU------GUUAUAAA-UGUUGUAAAUC--UAUUUAAUUCA---AUUAGGUUCC--CCACCA---AAAA-CCCCACCAAA-AUA---C-UUCGGUGGAGUCUUUUUA
AARN04000033.1/25262-25411   AUAGAGUGGGAACAAAAAGC-CAACAUAAUAAGUAUG-G-AAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUC--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUGUUU
#=GC SS_cons                 :::::::(((((,,,,,,,,.,,,,,,,,,,,,,,,,.,.,,,.,,,,,,,<<<<<<<-.<<-<<<<<.___........__>>>>>.->>>.>>>>>>..<<<<_____>>>..>,,,,,))))..):::::...:<<<<<<<<<<<<<<.___.___.>>>>>>>>>>>>>>::::
#=GC RF                      aUuGAgUGGgAAUAAaAaac.uAAcaUAAUauGAAUg.G.gAA.UaCCaAUaaauCAaC.guUUUuca.AcU........UaugaAA.Ugcu.UGauuu..uCauUAAAaauG..aUaUgGUUcC..CUACCA...aAaacCCCugcCAag.Auu.Aua.cuUGgcaGGGguuUuuUu
//
