# STOCKHOLM 1.0
#=GF ID cspA
#=GF AC RF01766
#=GF DE cspA thermoregulator
#=GF AU Moore B; 0000-0002-4074-1933
#=GF GA 78.0
#=GF NC 77.9
#=GF TC 78.0
#=GF SE Published; PMID:20129052
#=GF SS Published; PMID:20129052
#=GF TP Cis-reg; thermoregulator;
#=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; 0002168; RNA_thermometer;
#=GF DR GO; 0009266; response to temperature stimulus;
#=GF DR GO; 0006417; regulation of translation;
#=GF RN [1]
#=GF RM 20129052
#=GF RT The cspA mRNA is a thermosensor that modulates translation of the
#=GF RT cold-shock protein CspA.
#=GF RA Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P,
#=GF RA Gualerzi CO, Pon CL
#=GF RL Mol Cell. 2010;37:21-33.
#=GF WK CspA_mRNA_5'_UTR
#=GF SQ 15

CP000946.1/174765-174338     AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA-
CP000822.1/4602942-4603373   AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAGGCAGUC--C---CC--U-UCAA-GAG-UUAUCC-GUU-GAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUA-AAAAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA-
L23115.1/459-834             AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCGAGU--C---CC--U--CAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CGUCUUC-A-AAAU----CUGUA--------AAGUC---AUGCUC--CA---UA--U-C-GCC----GA-AA-
ABEH02000004.1/260631-260204 AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-CCAUUAGAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUA-AAAAAU----CUGUA--------AAG-C---ACG--C--CA---UA--A-C-GCC----GA-AA-
AF017276.1/479-855           AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAUGCAAGU--C---CG--U-CCAAUGAG-UUAU-CCAUUAGAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--A-CGGCC----GA-AA-
CP000647.1/4296745-4297166   GCAGGUUUG-A-UGUACAGACC-A-C--AGAG-CAGUC-G------AA-U-AGAGCAGU--C----C--U-UCUA-AGG-UUAUCC-AAA-GAUA-CCCC-CGUA-GUGAACUUUCCCU-U--UA--UC-GCUU-U-AAAU----CUGUA--------GUC-C---AGA--C--CC---CU--A-C-GCC----GC-AA-
CP000653.1/190938-191361     GUCGGUUUG-U--UCACAGACC----U-AAAG-CAGUU-U------AG-UUAAGC-AGU--C---C----A-GAU-GAG-UUAU-C-UUA-GAUA-CCCUUCGUA-GUGACCCUUCCUC-U--AU--CG-CUUA-A-AAAU----CUGUA--------ACA-C---AUU--C--CAUCAUC--G-C-GCC----GG-AA-
ABXW01000053.1/281917-281471 AUCGGUUUG-AAAGUACAGACC-U-AUUUAUGAAAGCA-A------GU-UUUGAAAAGUUCC---CC--A-UCAA-GUGUUAUC-C-AUU-GAUAUCCACUCGUA-GUGAAUUCCUCCU-A--AU--UAGUUCC-AUAAGU----AUAAA--------GAAGUAUCAAA--C--CU---AU--A-U-GCC----GU-GU-
ABJD02000101.1/494629-495045 UACUGAGU-----UUGUGUUCU-A-AA-GAAGAAAGUU-A------UC-CCAGAUAG--------CC--U-U------U-GAC--C-GU--GACG-CU--UCAUC-UUGGUUUUUUCCU-GAUUA--AA-UAGU-U-GACU----CUGGC--------CCA-U-----------------A--UAU-GCC----GAAAA-
AAOS02000014.1/93711-93269   CUCGGCCUG-U-GGUACAGACCUA-UU-UAUG-CACGA-CAUCUUGAG-UAAAGUGGUU--CAUA-U--U-UAAA-GCG-UUAU-C-GUU-GAUAGCUCUUCACU-GACGAAUUUCCUU-C--AU--AG-UGCC-U-CCAU----AAGUAACGACUGAUAA-C---CGG--C--UA---UAACA-C-GCC----CA-UGG
M30139.1/461-888             AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA-
ACCI02000028.1/45583-45145   ACUGGUUUGGA-AGUACAGGCC-UAUU-UAUGUUAGUC-A------GUUUUAAGAUGUU--C--ACC--A-UUAA-GCG-UUAU-C-UCA-GAUA-CCACU-UCA-UUGCGAAUUCCUUCU--AAUUAA-UUCC-C-AUAAGUACCACAA--------GAA-C---AAA--CCGCA---AC--A-U-GCC----UU-AU-
AALD02000025.1/10362-9916    CCCGGUUGA-C-AGUAACAUUU-A-UG-CAAG-CAGUUUU------AG-UAAAGCAGUU--C---CCCGU-AUUA-GCG-UUAU-CAGACAGAUA-CCUCUUCUCCGC-GAAAUUCCUU-C--UA--AG-UGCCCC-AUAA----GUUGU--------GCC-C---AAG--C--CU---AU--U-C-GCUCGCCUA-UGG
ABWL02000023.1/204545-204970 AACGGUUUG-A-CGUACAGACC-A-UU-ACAG-CAGUU-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGAGCAUUUCCU-U--UA-CUG-UUAA-A-AAAU----CUGUA--------GAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA-
ABWM02000027.1/244578-245001 GUCGGUUUG-U-UACACAGACC----U-AAAG-CAGUU-U------AG-UUAAGC-AGU--C---C------AGA-UUG-UUAUCC-AUA-GAUA-CCCUUCGUA-GUGACCCUUCCUU-C--AU--CG-CUUA-A-AAAU----CUGUA--------ACG-C---AA---C--CA---UC--G-C-GCC----GG-AA-
#=GC SS_cons                 :::<<<<<<._.____>>>>>>.:.::.::[[.-[[[[.-......--.---[[--[[[..[...[[..[.[---.--[.[[[-.[.[[[.[[-[.[[,,,((((.(((------((((.(..((..,<.<<<_._.____...._____........>>>.>...,,,..,..,,...,,..,.,.<<<....__.__.
#=GC RF                      aaCgGucug.a.agUAcagaCc.A.uu.aAaG.cAGug.u......ag.UaAggcaagu..C...CC..u.ucaA.Gag.uuaU.C.guu.GAUA.CCccUCgua.guGaacaUUcCuU.u..aa..ag.cucc.a.AaAU....cUguA........gag.c...Aag..C..Ca...ua..u.c.GCC....ga.aa.

CP000946.1/174765-174338     -GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGU
CP000822.1/4602942-4603373   -GGCACACU------UA-UUUU---UUAAAA-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCCAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGACGGUUACAAAUCCCUGGAUGAAGGUCAGAAAGUUU
L23115.1/459-834             -GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGU
ABEH02000004.1/260631-260204 -GGCACACU------UA-UUUU---UUAAAA-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUUAUUACUCCUGAUGACGGUUCUAAAGACGUGUUCGUACACUUCUCCGCUAUUCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUU
AF017276.1/479-855           -GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUUAUUACUCCUGAUGACGGUUCUAAAGACGUGUUCGUACACUUCUCCGCUAUUCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUU
CP000647.1/4296745-4297166   -GGCUCACU------UA-UUUU--UUUAA-A-GGUAAUU--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGCUACAAAUCCCUGGACGAAGGUCAGAAAGUAU
CP000653.1/190938-191361     -GGCAAAAC------AA-AUAU---UUAA-AAGGUAAAA--U-CUAUGUCUGGUAAAAUGACUGGUCUGGUAAAAUGGUUCAACGCUGAUAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUAUUCGUACACUUCUCUGCUAUCCAGAACGAAGGCUACAAAUCUUUGGACGAAGGCCAGAAAGUUU
ABXW01000053.1/281917-281471 -GGCAACAA------UU-AAAA---UUUA-A-AGGAAUU--CAAUAUGUCUAAUACAAUGACUGGUUUAGUAAAAUGGUUUAACGAAUCUAAAG-GCUUUGGCUUUAUUUCUCCUGCUGAUGGCAGCAAAGAUGUGUUCGUACACUUCUCUGCAAUUCAAAGCGACAGCUUCAAAACGCUGAACGAAGGACAAAAAGUUA
ABJD02000101.1/494629-495045 -GGCAAGUUUUUUUGAU-GUUA---UAUA-G-GAAAAGU--CAA-AUGUCCGACAAAAUGAAAGGUCAAGUUAAGUGGUUCAACGAGUCUAAAG-GCUUCGGUUUCAUCACUCCUGCUGAUGGUAGCAAAGACGUUUUCGUUCACUUCUCUGCCAUUCAGGGCGCUGGUUUCAAAACUCUGGCAGAAGGCCAGCAAGUUG
AAOS02000014.1/93711-93269   CGGCAAAAU------UU-UUUA---AUAA-A-GGAAAUA--CACA-UGUCUAACAUGAUGAAAGGUCAAGUAAAGUGGUUCAACGA-GUCUAAAGGCUUCGGUUUCAUCACUCCAGCUGAUGGCAGCAAAGACGUGUUCGUUCACUUCUCUGCUAUCCAAGAUCAAGGCUUCAAGACCCUGGCUGAAGGCCAGAAUGUAC
M30139.1/461-888             -GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGU
ACCI02000028.1/45583-45145   -GGCAAUUU------UA-AAAA--AUUAA-A-GGAAAUU--CUAUG--UCUAAUACAAUGACUGGUACAGUAAAAUGGUUUAACGAUGAUAAAG-GUUUUGGUUUUAUCACUCCUGCAGACGGCAGCAAAGAUGUAUUUGUUCACUUUUCUGCAAUUCAAAGUGAUAACUUCAAAUCAUUAGCAGAAGGCCAACAAGUUU
AALD02000025.1/10362-9916    CGGCAAUCA------AAAAUAA---UUGA-A-GGAAGUAUC-UCUAUGUCUAAUAAAAUGACUGGUUUAGUAAAAUGGUUUAACGCUGACAAAG-GUUUUGGUUUCAUCUCUCCUGCUGACGGCAGCAAAGACGUGUUCGUUCACUUCUCUGCCAUCCAGAGCAAUGAUUUCAAAACUUUAGAAGAAGGCCAGAAUGUUG
ABWL02000023.1/204545-204970 -GGCACACU------UA-UUUU--UUAAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUU
ABWM02000027.1/244578-245001 -GGCACAAC------AA-AUUUUUAAU-A-A-GGUAAUU---UCUAUGUCUGGUAAAAUGACUGGUCUGGUAAAAUGGUUCAACGCUGAUAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAAGGCUACAAAUCUCUGGACGAAGGUCAGAAAGUGU
#=GC SS_cons                 .>>>,,,,,......,,.,,,,...)))).).))-----..))))))),<<<<<______>>>>>,,,,,,,,,,,]]]]]]]]]-]]]]-]]].]----]]]]]]--]]]]-]]::((((((,,,,,,,<<_____>>,,<<<<<<-<<<<<<-<<<<<<--<<<________>>>>>>>>>---->>->>>>>>>>>>
#=GC RF                      .GGCAaacu......ua.aUua...uuaA.a.GguAAUa..CacuauGUCcgguAaAAUGaccgGUauaGUAAAAUGGUUCaacGcugacAaaG.GcUUcGgcuucAUcaCUCCuGacGAugGCucuAAAGAcGUgUUCGUacACuUCuCUGCcAucCAgaaCGauGGuUaCAAauCucUGgacGAAgGuCAGaAaGUgu

CP000946.1/174765-174338     CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---C-UGCU--UAA--A--AGCAC--A---GA--A--UCUAA----GAUCCCUGCCAUUU-GGCGGGGAUUUUUUU
CP000822.1/4602942-4603373   CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---U-AGCU-UUAU--A--AGCUC--A---GA--A--UUGAA----GAUCCCUGCCAAUC-GGCGGGGAUUUUUUU
L23115.1/459-834             CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCAGCUAACGUAACCUCC-CUGUA---A-------------------------------------------------------------------------------
ABEH02000004.1/260631-260204 CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AGCU---U-------AAA--A--AGCUC--A---GA--A--UUUUG----AAUCCCUGCCUGAU-GGCGGGGAUUUUUUU
AF017276.1/479-855           CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---A-------------------------------------------------------------------------------
CP000647.1/4296745-4297166   CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGCAACGUAACUUCU-CUGUA---AGUU---CAAGC-----------CGCUA--A---GA--A--UCGAG----AAUCCCUGCCUGAU-GGCGGGGAUUUUUUU
CP000653.1/190938-191361     CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCAGCAGCUGGUAACGUUGUAAGC-CUGUA---AGCUU-CC-AACU--CAG--C--AGCAA--A---GA--A--UUUAA----AAACCCGCC--UCU--GGCGGGUUUUUUUC
ABXW01000053.1/281917-281471 GCUUCUCAGUAGAGAAUGGUGCAAAAGGUCCAGCGGCUGUAAACGUC-GUAGC-UCUUUAAGAUAC---C-CGCU--UAA--UACAGCGC--U---UA--AAAUUUCA----AACCCCUGCCAAUU-GGCGGGGGUUUUUCG
ABJD02000101.1/494629-495045 AAUUCACCAUUGAAAAUGGUGCGAAAGGCCCAGCAGCUGCUAACGUAA------CUGCA---AUCU---A-AGCU--UAA--U--UGCUU--AACUGA--UUUUCUAA----AGCCCGUCAUUUUUAAUGACGGGCUUUUUC
AAOS02000014.1/93711-93269   AGUUCUCUAUCGAGAACGGUGCUAAAGGUCCGUCUGCAGCAAACGUA-ACUG--CAAUC---UAAU---U-GGCC--UUU-----GGCUG--A---UU--A--UA-AA----AAAACCCGCUAA---GGCGGGUUUUUUACU
M30139.1/461-888             CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---C-UGCU--UAA--A--AGCAC--A---GA--A--UCUAA----GAUCCCUGCCAUUU-GGCGGGGAUUUUUUU
ACCI02000028.1/45583-45145   CAUUCACCAUUGAAAAUGGUGCUAAAGGCCCAGCAGCAGCUAACGUUAUC--G-C--UA---AAUA---A-CGAU--AAACGA--AUCGC--U---AAGCA--UUCAA----AAACCUCGCUAAAU--GCGAGGUUUUUUCG
AALD02000025.1/10362-9916    AGUUCUCUAUCGAGAAUGGCGCUAAAGGCCCGGCAGCGGCGAAUGU-UGUUGCUCUGUA---AGAGUGAA-UA--ACUGA--ACC--UAAUAC---CC--A--ACUCA----UUGGAGUUACAGCU-GUAACUUCAAGGACG
ABWL02000023.1/204545-204970 CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGCAACGUAACCAGC-CUGUA------------AGCU--UAA-CA--AGCUC--A---AA--A--UUCUG----AAUCCCUGCCAAAC-GGCGGGGAUUUUUUU
ABWM02000027.1/244578-245001 CCUUCACCAUCGAAAGCGGCGCUAAAGGCCCAGCAGCUGGUAACGUUGUAAGC-CUGUA---AGCU---U-C-----CAA--C--UCAGC--A---GC--A--AAGAAUUCUAAAACCCGCCUUCU-GGCGGGUUUUUUCGU
#=GC SS_cons                 ,,,,,,))))))::::<<<-<<<___>>>>>><<<<<<<<<______>>>>>-.>>>>:...:<<<...-.<<<<..___.._..>>>>-..>...>>..:..:::<<....<<<<<<<<<<____.>>>>>>>>>>>>:::
#=GC RF                      ccUUCaCcaUCgAAAacGGcGCcAAAgGCCCggcaGCugcuAACGUaagcaGc.CuguA...Aucu...u.cGcu..uAa..a..agCgc..a...ga..A..Uuuaa....aacccccgccaauU.ggcggggguuuuuuu
//
