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RNA Secondary Structure Atlas - PDB - 3J2C_M



RNA: 3J2C_M
Rfam family: -

GCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCU
Reference structure (std) [ sec struct ] (.((...(..((((...((((((..(.......((........))...........((((.(..(....((.(((..(.(((((....))))).)....(....)...))).).).).((.(((....((.((.......(((((((......))...(((......)))...)))))........((.((((..(...((..((.......))))....)..))))..(....(.(.....).).......)..)).........).).)...)..)))))....).)))).....)...)))))).(...(.(((((.....(((..((...((......))...))....))).....))))).)......(....((((.((........)).))))....)..)...)))).....(((((((.........)))))))......).....)).)..
Reference structure (ext) [ sec struct ] ((((((aaa)(((((.((((((((.d.(...)(((........))....c.....cccc(<<<{[.<..<<<<<<<<<<<<<<<<.)>>>>>>>>>.(((>...))).>>>>>>.}]>cc.cccf.b(F(((((..().((((gg(.(....))..).eeee...)EEEE...GG..)).....((((.((((((().(((..((((..).))))))....)))))).h(.(.(((((...))))).).H..)..))))......)).)))B)..).CCCCC..>.>>.CCCC(..D(.)))))))))((..(.(((((((.(.(((..)((((((((..))))))))......))).).)))))).)..)().((.((((((((((C..)..)))))))))).))..)..)))))(..((((((((((.(...).)))))))))))..AAA...)))))..
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CentroidFold (ext) [ FASTA input ] [ sec struct ] ((((((....))))..........((((...((((........)))).))))..(((((.((((.....((......(((((((....))))))).........))......)))))))))........((((....))))(((..............(((......)))....)))............(((((((.......(((.....)))......)))))))..((((((((.....))))))))........((((((.....)))))).(((((((.......)))))))..............((((((((.....(((.......(((....))).........))).....))))))))...(((((..(((((((........))))))).....)))))..........(((((((.........)))))))..............))..
CentroidFold [ FASTA input ] [ sec struct ] ((((((....))))...((((((((((((..((((........)))))))))..(((((.((((.....(.......(((((((....)))))))..........)......))))))))).........(((....)))(((((.............(((......)))...)))))...........(((((((.......(((.....)))......)))))))..((.(((((.....))))).))........((((((.....)))))).(((((((.......)))))))...)))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))..........(((((((.........)))))))..............))..
CentroidHomfold‑LAST [ FASTA input ] [ sec struct ] ...............................................................................................................................................................((......))...............................................................(((((.....)))))..............................((((((.......))))))................(((((((.....(((..((...(((....)))...))....))).....)))))))...........(((((((........)))))))....................(((((((.........)))))))..................
ContextFold [ FASTA input ] [ sec struct ] (((((.((..((((((.((((((((((....((((........))))........(((((((......(((((((..(((((((....))))))).(.((....)).)))))).))..((.((((..((((((.((...(((((((((....)))..((((......))))..)))))).....((((.(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).)).....))))....)).).)))...))))))))....)))))))...)).)))))))).)...(((((((.....(((..((...(((....)))...))....))).....)))))))......(....(((((((........)))))))....).....))))).....(((((((.........)))))))......))...)))))..
Contrafold [ FASTA input ] [ sec struct ] ((((((....))))...((((((((((((..((((........))))))))).((((((.(((((...(((.(((..(((((((....)))))))......))))))....)))))))))))........(((....)))(((((..(((........(((......)))))))))))......(((..(((((((...((..((((...))))))....)))))))..((.(((((.....))))).)).)))....((((((.....)))))).(((((((.......)))))))...)))))))((.(((((((((.....(((..((...(((....)))...))....))).....))))))))).))((((..(((((((........))))))).....))))((.((......(((((((.........))))))).....)))).....))..
Fold [ FASTA input ] [ sec struct ] (((((((((.((......)).))))((((..((((........)))))))).(((((((((.((...((((((((.......((((((((((..(((((.(((((((.......((((...((.(((((((((....)))).))))).))....))))........)))))....)))))))...))))).))))).(((.((((((((((((((...(((....))).)))(((((.....)))))...........((((((.....)))))).(((((((.......)))))))....((.(((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))).))...(((((((........)))))))....))))).)))))).))).))))))))...)).)))).))))).........)))))..
HotKnots [ FASTA input ] [ sec struct ] (((((.((.((((((..((((((((((((..((((........)))))))))...(((((((......(((((((..(((((((....)))))))...((....))..))))).)).(((.(((..(((((((.((((.((((((.........(((.(((.....))).)))))))))....((((..(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).)).....))))..)))).).))))))...))))))...))))))).......)))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))))))))).)).(((((((.........)))))))...........)))))..
IPknot [ FASTA input ] [ sec struct ] (((((....(((((...(((((((((((...((((........)))).)))...(((({{(((.......(((((..(((((((....)))))))...((....))..)))))))).))))......((((...(((((.((...[[[[[[.......(((......)))......))]]]]]].....(((((((...((..(((.....)))))....))))))).....(((((.....)))))...........<<)))))....))))>>..((((((.....}}))))))...))))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))).)))))....(((((((.........)))))))...........)))))..
MaxExpect [ FASTA input ] [ sec struct ] (((((.((.(((((.(.((((((((.(((((((((((((((((((........(((((.(((((.(..(((.((((.(((((((....))))))).....)))))))....))))))))))).......((((....)))).)))))))).....)))))))))))...(.(.................(((((((((.((.((......)).)).))..)))))))..((.(((((.....)))))))....).)..((((((.....)))))).(((((((.......)))))))..)))))))).).(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))).))))).)).(((((((.........)))))))...........)))))..
McQFold [ FASTA input ] [ sec struct ] ..((((....))))...(((((((((((((((((((((((((((((.......(((((((((..)))...(((((..(((((((....))))))).............)))))...)))))).......((((....))))))))))))).....))))))))))))(((((............(((..(((((((........[[[[[(.{{{{{{{{.))))))).....(((((.....))))))))...)))))((((((.....)))))).(((((((.......)))))))..))))))))...(((((((((..........((((..)))).........)]]]]].......)))))))))..(((((..(((((((........))))))).....)))))..........(((((((.........)))))))......}}}}}}}}....
PknotsRG [ FASTA input ] [ sec struct ] (((((.((.((((((..((((((((((((..((((........)))))))))...(((((((........(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))((((((...(((((.................(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).))...)))))((((((.....)))))).))))))....))))))).......)))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))))))))).)).(((((((....[[[[[))))))).....]]]]].)))))..
ProbKnot [ FASTA input ] [ sec struct ] (((((....((((((..((((((((.(((((((((((((((((((........(((((.(((((.((.(((.((((.(((((((....))))))).....)))))))...)))))))))))).......((((....)))).)))))))).....))))))))))).(((...............(((.(((((((........................)))))))..((.(((((.....)))))).))))..)))((((((.....)))))).(((((((.......)))))))..))))))))...(((((((((.....(((.......(((....))).........))).....)))))))))..(((((.((((((((.(.....))))))))....))))))))))))....(((((((((....)).)))))))(((....))).)))))..
RNASLOpt [ FASTA input ] [ sec struct ] (((((....((((((..((((((((...........(((((((((........(((((.((((((.......((((.(((((((....))))))).....)))).......)))))))))))......(((((....)))))))))))))).....((((((((..((((((.................(((((((.......((((...))))......))))))).....(((((.....)))))......)))))).)))).)))).......(((((((.......)))))))..))))))))...(((((((((................((((........))))..........)))))))))..(((((..(((((((........))))))).....)))))))))))....(((((((.........)))))))...........)))))..
RNAfold [ FASTA input ] [ sec struct ] (((((....((((((..((((((((((((..((((........)))))))))...(((((((........(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))((((((...(((((.................(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).))...)))))((((((.....)))))).))))))....))))))).......)))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))))))))).((((((((((.........)))))))...))).....)))))..
RNAshapes [ FASTA input ] [ sec struct ] .((...((.((((((..((((((((......((((........))))........(((((((........(((((..(((((((....)))))))...((....))..))))).((((..(((.(((((((((....)))).))))).)))...))))((((((...(((((.................(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).))...)))))((((((.....)))))).))))))....)))))))......))))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))...((((..(((((((........))))))).....)))).)))))).))....((((.........)))))).(((....)))........
RNAsubopt [ FASTA input ] [ sec struct ] (((((.((.(((((((.((((((((.((((((((((((((((((((((.(((......)))))((((...(((((..(((((((....)))))))...((....))..))))).(((((.(.......).)))))))))..))))))))).....))))))))))).(((((.....)).....((((.(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).)))))).)))((((((.....)))))).(((((((.......)))))))..)))))))).).(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))))))))).)).(((((((.........)))))))...........)))))..
RNAwolf [ FASTA input ] [ sec struct ] (((((.(((.((......)).)))(((((((...(((((((.........((......))..))).))))(((((...((((((....)))))).....((...))..))))).(((((...((....)))))))..((((..............))))..))))).)).((.(((.(((((...(((.(.((((((((((((...(((....(((..)))...)))..)))(((.((.((((((((...((((...(((((((.....)))))))....))))....))))))...(((..))).)))).))).))).)))))).))))....(((((....)))))..............)))))))).)).(....(((((((........)))))))....)..((((.((.((.....(((((..((...))))))).....)))))))))))))..
RNAwolf (ext) [ FASTA input ] [ sec struct ] (((((.(((.((((..)))).)))(((((((...((((((((...)..((((......))))))).))))(((((((.(((((((..))))))).....((...)))))))))((((((...((....)))))))).((((((........).).))))..))))).)).((.(((.(((((((((((.(.((((((((((((.(.((((((.(((..))))))))).))))((((((.(((((((((.(((((...((((((((...))))))))....))))).).))))))...(((..))).)))))))).))).)))))).))))..(.((((((..))))))(..).).....))))))))))).)).((((((((((((........))))))))))))..((((.((.((..((.(((((..((...))))))).))..)))))))))))))..
Sfold [ FASTA input ] [ sec struct ] (((((....((((((..((((((((((....((((........))))..))....(((((((......(((((((..(((((((....)))))))...((....))..))))).))..((.(((..(((((((.(((((((((((..........(..(((.....)))..).))))))....((((..(((((((...((..(((.....)))))....)))))))..(..(((((.....)))))..).....)))).))))).).))))))...)))))....)))))))......))))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))))))))....(((((((.........)))))))...........)))))..
UNAFold [ FASTA input ] [ sec struct ] (((((.((.((((((..((((((((((((..((((........)))))))))...(((((((......(((((((..(((((((....)))))))...((....))..))))).)).(((.(((..(((((((.(((((.(((..((((((...(((((((.......)).)))))..))))))((((.(((((((...((..(((.....)))))....)))))))..((.(((((.....))))))).))))..))).))))).).))))))...))))))...))))))).......)))))))...(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....))))))))))).)).(((((((.........)))))))...........)))))..



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