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RNA Secondary Structure Atlas - PDB - 3ZEX_B



RNA: 3ZEX_B
Rfam family: -

UCCCAACUGCAGACCGUACUCAUCACCGCAUCAGGUCCCCAAGCAUCGAAUGCUCUGGUAACAUAGAGAAAGGUACACUCAGGGAAGUCGGCAAAAUAGAUGCGUAAGUUCGCAAGAAGCAUUGGCUCUGAGGGCAAAGUGGGGGUCCACAGGAGGGCCAGUGUCCUUUGAAGGCUACCCUCCCGAGCCGUAUCUACUAACCUCCUUCUGGUGUGUUGUUUUUACGUCUCACUCCCGCGCAGGUGUUUUCGCUUCCUUUUUUUGGUUGCGCACCUACAAAUUGCCAACUCAGAACUGCUUACGGCGGGGAAUCCAACUGUAUAAUUAAAACAUAGGUUUGUGAUGCAUCCAAGUGGUGUAUGUCGCAAACUGAUUUCUGCCCAGUGCUCUGAAUGUCAACGUGAGAGAUUCACCGACGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCUUCCAAUUAGAGACGCGCAUGAAUGGAUUAAUGAGAUUCCCUCUGUCCCGAGUUACUAUCUAGCGAAACGACAGUCAAGGGAACGGACUUGAAGGGCUAAGCGGGGAAAGAAGACCCUGUUGAGUUUGACUCCAGUCUGGCUCUGUGCGGCGACUUUGGAGGUGUAGUAUAGGUGGAAGCGCAAGCUCAAAUGAAAUACCACCACUCGGAACGUUGCUUCACUUAUCGAAUGAAGAGACCAAUGGUUGUUUUGCGCAGUCUUCGGGCUGUGCGCCGUCUAGGCUGGGCAUAAUUGUGGUGUUUCUUUCACCGCCACGGGAGGGGUGUUGGUUUUUUAUCCUCCUCUCCGUUUCUCCUUUUCUCUCUUUCUCCCUUUUUUUGGGCGUUUGAGGGUUGGUGACCCGUGGGCGCCCACGCGUGCGGAACUACUGCGCCAACGGGGUGGGAACUUUUCGUUUCUUCUCCGGAGUCUUGUUUCGAGACAUCUGCCAGAUGGGGAGUUUGGCUGGGGCGGCAUAUCUGUUACACGACAACGCAGGUGUCCUAAGGCGAGCUCAGUGGGAACAGAAAUCUCACGUGGAACACAAGCGUAAAUGCUUGCUUGAUUAACGAUUUCCAGUACGAAUCGAGACUGCGAAAGCAAGGCCAGCGAUCCUUUGCGAAGAACAGGAAAUAUGAACAAAUCAUACCAGAGGUGUCAGAAUAAUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAACCUAGCGCCGCAGAAGACGCUAAGGGUUGGAUUGUUCACCCACUGACAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUGGUUUUACCCUACUUGGCUGGAGAUUGCGAGUAAAAGAUUAUCCGCGCAAAGCGGAGGCAGUCCGUUUUUUUCUGGGUCUGCCGUUCGGUGGCAUGUGCUUGGCGCUGCCAUCUC
Reference structure (std) [ sec struct ] .........................((......))......((((.....)))).........((((....((((..(((.((..(....(.......(((((....(....).....)))))((.(((((((((...((((((........((((....(((.((((..)))).)))))))..(((.((((...(.((.................)).)..)))).)))..))))))...((((....(((..((.......))..)))))).).......)))..)))))).))(.).......((((((((....((.........))...(..((((....((((.....))))......))))..)...(((.(((...((.((.....((....(((.......)))....))..)).)..).)))(((((.........)))))........((..........(((((.......)))))..)..)....))).....).))))))).)..))).))).)))).)))).........(..[[[[[......).]]]]]....(((((..(((.(........(((..((((...(((((.(((((((...((..(((.((.((.((........(...aaaa..((....))..........).AAAA...))).)..)).)))..))....((((.....((......(...((...((((((((....))))))))...).))..((.((((........((((.......))))..((((((..((......((.....))..)).((.((...((((.....(.(((...............))).)...))))...)).))))))))...))))....))...................((((.((((((.....)))))).)))).....))...))))........)))))))..)))))..(((.......)).)((((((...........))))))((.{...{{{{{{{.(.((((((.......))))))...).{{)(..((}}....}}}}}}}....(....(((<....(..>)))...)..((......)).}))..)......((((...............(((.......)))..)))).....)).....)))..).)))........(..(.(.((((((...((.......))...))))))...))...).......((((..((((((...((((((.(......).))))..))..(((.(.....).))).....)))))..)....)).))....(((((((....))).)))).....)..))).)))))........................(((((.....)))))(((((((((........)))).)))))....((((((..((((...)))).))))))..
Reference structure (ext) [ sec struct ] .()...............g..(..G((......))).....((((.....)))).........(((((...((((.((((.((((.....(.......((((((..((f(.F))...))))))((((((((((((((.(((((((..).(..((((e...(.(.((((..)))).)E))))).)(((.(((((..((((((...(...)..)..).)))).))))).)))..))))))().((((....)((((((.(...).))))))..)).).....)))))..)))))))))(.).......(((((((((((.(((m..(.M).)).)((((((((((..((((.....)))))..)..))))))))).(((.((({.(.((((..(..((((.((((i..(..I))))).))).)))))..}))))(((((.......())))))(...).(.o(.....(.)..(((((d..(..D)))))..).(O)...)))..).)).))))))).)).))).)))))))))))))...(....((..rrrrr(....)))RRRRR....cccccc.ccc.((...l(((((((aaaaaa(.)((((((((((((...(((((((.(((((.((.....j<.(.J((((((((.....).)....>....)))))))..))).)).)).)))))))(.(.((((..)..(((..b(((...(((..((((((((....))))))))..))).)).B(.((((........((((((...)))))).(((((((..(((...(.((.....)))))).((.((.(.((((.....(.(((...............))).)...)))).).)).)))))))))..)))))....)..(...............(((((.((((((.....)))))).)))).).))))....))).))..(.))))))))).))))...((q......(Q).)((((((.().......)))))))((([.[)kkkkkkkk((((((((...(..))))))))..).k.)(.(((K...K.KKKKKKK](](n(..(((((h...(.H)))))..N))((((..))))).))).)..(..((((((..............(((......)))).)))))))...)).)..AAAA..AA))))...)L..(.((.(((((((((.(((p..(..P))).)))))))..))))..)....)..((sss.ssssss..((((((((().....))))))..))).ss)ss.)...SS.SS(...)SSSSS..S...SSS..)..)((((()(((..)))..)))).)..)).)CCCCCCCCC......(.....)...........(((((.....)))))(((((((((........)))).)))))...(((((((..((((...)))).))))))).
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     (                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         )                                                                                                                                                                                                                                                                                         
                                                                    (                                                                                                                                                                                                                                                                                                                                                                                                                                                                              )                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
Afold [ FASTA input ] [ sec struct ] (...(((.(((((((...........(((.....((..((((((((...))))).)))..))....(((..((((.((((.((((.((((..........((((......))))..(((((..(..(((((((((((.(((((((......((((((..(((.((....))..))).)))))).(((.((((...((.((((.((....)).).)))))...)))).))).)))))))..(((((....(((..((.......))..)))))))).....)))))..)))))).)))))).)))).(((((((((...............(((((((((((((((((((.....)))))..)))))))))..(((((((((...(((.(((..((((...(((((...))))).))))..))))))...)))))))))..)))))...............(((.((((..((((((.......)))))).))))...))).....)).)))))))....)))))))))))).))).)))......(((..(((((((((((((....(((((.(((((((........))))))).)))))..((((((((.((((((.(((((((..((((((((((.((((..(((((..((....))((....))....)))))...((...)).)))).))))).))))).((((((....(((..(((((.((((((((....))))))))(((((((((((..(..((..((((((((.((((..((((...((((((((((.(.(((....))).))))))).))))...((((.((((.................(((((((..(.(((((...))))).)..)))))))((((...(((....(((.(((..(((((.((((((.....)))))).))))).(((((((.((((...((((.....))))..(((((((.((((((((.(.....((((....)))).....).)))))).)).))))))).((((((.......)))))).(((((..((((((....)))))).(((.....))).)))))...)))).)))))))((....))..))))))...)))..)))).)))).))))..(((((.....))))).....))))..))))....))))))))..))..)..))))).)))))).)))))..)))..((((((((.............)))))))).)))))).........)))))))..))).))).(((((..((((....(((((((.((.(....))).)).)))))...(((((((....))).))))))))..)))))....))))))))..................(((((.....)))))...))))))))))))))))))))))).))).(((((((.((((...))))))))))).)
CentroidFold [ FASTA input ] [ sec struct ] ....(((..................(((((...........((((.....))))...........(((((((........................((((((((......).............((((.......................(((((((....))))))..............).)))).))))))).............................(((.....(((((((.((((.....((..((.......))..))...................(((((.........(((((.(((((.....(...........)...((((((((((((((.(....)))))..))))))))))))))))))))......)))))..................))))...))))))).....)))((((((.......)))))).............((((..((((((.......)))))).))))................(((((((((((....((((.....)))).....)))))...))))))((((((.((.(((((.(((((((........))))))).)))))...)).))))))......................................(((....))).....((((((((((..........(((.(((((.........))))).))).............((((((((....))))))))......................))))))))))...........(.(((((((.................))))))))...............)))))))........((((((((((.((((.....)))).))))))))))....)))))..............(((((.((((((.....)))))).)))))..((((((...)))))).....(((((.......)))))............(((((((.((((((..........................((((((.......))))))........((((((....)))))).........(((((.........)))))...............((((((..(((((..................(((.......)))...........................)))))..))))))....................((((....))))........................(.(((((((((((.(......).)))))..))))))).........................................)))))).)))))))..........................................(((((.....)))))(((((.((...........)).)))))))).(((((((.((((...)))))))))))..
CentroidFold (ext) [ FASTA input ] [ sec struct ] ....(((((((((((..........................((((.....))))...............................................(((......)))......................................(((((((....)))))..............))..................................................(((((((.((((.....((..((.......))..)).).................(((((.........(((((.(((((.....................(((((((((((((((.....)))))..))))))))))))))))))))......)))))...................)))...)))))))........((((((.......)))))).............((((..((((((.......)))))).))))................(((((((((((......................)))))...))))))...........((((.(((((((........))))))).))))....((((((((((.........................................................................((.(((((.........))))).))..............((((((((....)))))))).....)))))))))).........((((.......))))...(((.((((((.................))))))))).............................((((((((((((((((...))))))))))))))))......(.........)......((((((((((((.....))))))))))))..((((((...))))))..................................((((((((((((((.......................(((((((((.......))))))........(((((......))))).........(((((.........)))))...............((((((((((((((........................................................))))))))))))))......................((((((((.............)))))))).......(((((((((((((......)))))))..)))))).............)))..........................))))))))))))))..........................................(((((.....)))))...................))))))))))).(((((((.((((...)))))))))))..
ContextFold [ FASTA input ] [ sec struct ] .(((.......(((((...............).)))).(((.(((.....)))..))).......................))).............(((((.((.(((......((((((((((((((....(..((((((((.......((((((.....((((......((((((((((((..(((((...................(((.(............).))).(((((((((((((.......................))))))............................((((.(((((.....................((((((((((.((((.....))))...))))))))))...............(((.............))).))))).))).))))))))...)))))))))).......((...))....)))))))......(.((((((.......)))))).).......))))..........))))))((.((((((((((((...............(((((........)))).)(((((.(((((((........))))))).)))))..((((((..(.(((......))).)..))))))..))))))..(((((..((....))............))))))))))).))....))))))))..)......)))).))))))....))))((((((((....)))))..))).......(((((((((......((((.......))))(((((((((((((.(............)))))))))...(....((((((((.(..(((((.......((((((((((.(((.......))).))))))))))((((...........(.((((..(((((.((((((.....)))))).)))))..((((.......)))).((.(((((((.....))))))).))...((((..(((((...........)))))))))....)))).).((((((((............((((.........)))).((((((((............((((.(((..........)))..))))(((((.((((..(((((..................((((.....)))).......(((.............))).)))))..))))))))...)...))))))))...((((((((((.............)))))))).))....((((((.((((..........))))...))))))........)))))))).......))))((((((((...(((((((....))).))))((......)).)))))))))))))..).))).)))))...)(((((.....)))))(((((.((..(.......))).))))).....)))))..))))))))))))))))))).
Contrafold [ FASTA input ] [ sec struct ] ....(((....((((..................)))).((((((((...))))).))).......(((((((((((((....(((((..((.....((((((((......)............(((((.((((((.........)))(...(((((((....)))))))...)(....))))..))))))))))))....))..))))).)))))..(......)(((.....(((((((.((((.((((((..((.......))..))(((.........)))((..(((((((((.....(((((.(((((....(((.........)))..(((((((((((((((.....)))))..))))))))))))))))))))))))..))))).)).........))))..))))...))))))).....)))((((((.......)))))).........((..((((..((((((.......)))))).))))....))..........(((((((((((....((((.....)))).....)))))...))))))((((((.((.(((((.(((((((........))))))).)))))...)).))))))................................((((..(((....))).....((((((((((..........(((.(((((.........))))).))).........((.(((((((((....))))))))(((.....))).....).))..))))))))))...))))...((.(((((((....((........)).))))))))).............))))))))........((((((((((.(((((...))))).))))))))))...((((((.....))))))...(((((.((((((.....)))))).)))))((((((((...)))))).)).(((((((.....)))))))..(((......(((((((.((((((......((...(..............((((((.......))))))........((((((....)))))).........((((((.......))))))(...(((....)))(((((((..((((((................(((((.....))))).....((..............))..))))))..)))))))...................(((((())))))..........)......((((((.(.(((((((((((.(......).)))))..)))))))..(((..(((.......))))))..)))))).)......)))))))).)))))))........)))...............................(((((.....)))))(((((.(((.......)..)).)))))))).(((((((.((((...)))))))))))..
Fold [ FASTA input ] [ sec struct ] ....(((.((((((((((((..(((((......)))..((((((((...))))).))).........))..)))))...((((((.(((((..........(((......))).(((.(((((((.(((((((((((.((((((((.....((((((..(((.((....))..))).)))))).(((.((((...((..(((.......)))..))......)))).)))))))))))..(((((....(((..((.......))..)))))))).....)))))..))))))......(((((..((....))..))))).............(((((((((((((((.....)))))..)))))))))).........))))))))))((((.((.......)).)))).)))))((((((((((..(((((((((.......))))(((((...((((((.((((..((((((.......)))))).))))...))).))).))))).((((((((((....((((.....)))).....)))))...))))).((((((.((.(((((.(((((((........))))))).)))))...)).)))))).....(((.(((((((((.(((..((.((((..((...(((....)))...))...)))).))..))).))).)))))).))).....(((.((.((.((((.((((((...(((.((((((...(((.....)))....)))))).))))))))))))).)))).))).)))))((((((((((.((.........)).)))))).)))).....((((((((....(((((.......((((((((((.(((((...))))).))))))))))...((((((.....))))))...(((((.((((((.....)))))).)))))((((((((...)))))).)).(((((.(((((((((((.(((((((.....((((((...........))))))))))).)).))))))).((((((.......))))))(((((((.(((((......)))))(((((((.((........))...)))))))..(((....))).((((((..((((((.(.........((...(((((.....)))))))...((((..........)))).)))))))..))))))(((((((......)).))))).((((((((.............)))))))).......(((((((((((..........))))..))))))).......(((((((.((.......)).)).)))))...(((((((....))).)))).))))))))))).))))).)))))....))).))))).)))))))))).(((((((.....))))))).))))))))))))).))).(((((((.((((...)))))))))))..
IPknot [ FASTA input ] [ sec struct ] ...........((............................((((.....))))...............................................(((....aa)))...AA..((((...........................[[[[[[[))))]]]]]]]...(((((((......................................................(((((((.((((....(((..((.......)){{)))...........((..}}.(((((.........((((((.((((.....((.........))...(((((((((((((((.....)))))..))))))))))))))))))))......)))))....))............))))...)))))))...............................)))))))..((((..((((((.......)))))).))))................(((((((((((....(((.......))).....)))))...)))))).(((((....(((((.(((((((........))))))).)))))......))))).......................................(((....))).............................(((((.........))))).................((((((((....)))))))).......................(((((.......))))).....(((((((....((........)).)))))))...............................((((((((((.((((.....)))).)))))))))).....(((.......))).....(((((.((((((.....)))))).)))))..(((((.....)))))..................................((((((...........)))))).................((((((.......))))))........(((((......))))).................................((....))..........................................................................................((.................<<<<<<)).............>>>>>>.......((.((((.((((..........))))...))))))...............................((((...(((((((....))).))))......))))...............................(((((.....)))))bbbb..((...........))))BBBB....(((((((.((((...)))))))))))..
MaxExpect [ FASTA input ] [ sec struct ] ....(((.((((((((((((....(((......)))..((((((((...))))).))).............)))))...((((((.(((((.........((((......)))).(.((((((((((((((((((((.((((((((.....((((((..((...(........))).)))))).(((.((((...((..(((.......))).....))...)))).)))))))))))..(((((....(((..((.......))..)))))))).....)))))..))))))......(((((..((....))..))))).............(((((((((((((((.....)))))..)))))))))).......).))))))))).((((.((.......)).)))).)))))((((((((((.....((((((.......))))))....((((......)))).((((((.......)))))).(((((((.((((((..((((((...((((((((......((((((.((.............(((((.((((((.((.(((((.(((((((........))))))).)))))...)).)))))).....(((.(((((((((.(((..((.((((...(...(((....)))...)....)))).))..))).))).)))))).)))...............(((...))).....(((.((((((...(((.....)))....)))))).))).....((((((.......)))))).((((((((((...............)))))).))))...................))))).....((((((((((.(((((...))))).))))))))))...((((((.....))))))...(((((.((((((.....)))))).)))))..((((((...))))))....)).)))))).(((((((.(((((((.....((((((...........))))))))))).)).)))))))...)))).))))))))))..........(((((......)))))(((((((.((........))...)))))))..(((....))).((((((..((((((...........((...(((((.....)))))))...((((..........))))..))))))..))))))...((((((...((.......))...))))))...))))))))).)))).(((((.(((.(((((((((..........))))..)))))))).(((((.((........))))))).)))))((((...(((((((....))).))))......))))(((((..(........).))))).....)))))))))).(((((((.....))))))).))))))))))))).))).(((((((.((((...)))))))))))..
McQFold [ FASTA input ] [ sec struct ] ........(((((((..........((((((..(((((((.....((((((((((.........(((((((((((((((....((((((((((.......))).((((((((.......((((((((((.........(((((..)))))...))))))))))((((((((.(((((((((((((..((((..................((((((.......)))))).....(((((((.(((((((((((.........(((({{{{{{............)))).(((((((((.....((((((((........................(((((((((((((((.....)))))))..))))))))..))))))))))))..)))))........)))))))...))))...)))))))...))))))))))..................)))))))..((((..((((((.......)))))).))))....(((..........)))..(((((......................))))))))))))).)))))))).((((((((((((((........)))))))......((((..)))))))))))......)))))))...)))))).....(((((((}}}}}}........((((((((((..(((((..((((((((((.........)))))....))))).......((((((((((..)))))))))).........))))).......))))))))))))))))).....((((((((...............))))))))........)))))))))................))))))))))))).....))))((((((..)))))).))))))..((((((((((..(((((.((((((.....)))))).)))))..............(((((((((((((((.........((((...)))).))))))............)))))))))....))))....))))))...((((((.....((((((...(((((((..)))))))((((.....((((((((((......(((((.........((((((.........))))))(((((........(((((((.....(((((...)))))...........(((((((.........)))))))..[[[[[[[))))))).((((((((.............))))))))..)))))(((((((((((..........)))))..))))))...((((((...............)))))).((((..((((((.............)))))).))))..)))))))))))))))))))..........)))))).((((((((.....))))))))))))))))))))).....(((((((...]]]]]]]..)))))))..
PknotsRG [ FASTA input ] [ sec struct ] ....(((.(((((((...........(((.....((..((((((((...))))).)))..)).((((....((((.((((.((((.((((..........((((......))))..((((...((.(((((((((((.(((((((......((((((..(((.((....))..))).)))))).(((.((((...((..((..((....)).))...))...)))).))).)))))))..(((((....(((..((.......))..)))))))).....)))))..)))))).)))))).)))).(((((((((...............(((((((((((((((((((.....)))))..)))))))))..(((((((((...(((.(((..((((...(((((...))))).))))..))))))...)))))))))..)))))...............(((.((((..((((((.......)))))).))))...))).....)).)))))))....)))))))))))).)))))))......(((..(((((((((((((....(((((.(((((((........))))))).)))))..((((((((.((((((.(((((((..((((((((((.((((..(((((..((....))((....))....)))))...((...)).)))).))))).))))).((((((....(((..(((((.((((((((....))))))))((((((((((((((..((..((((((((.((((..((((......(((((((....((........)).))))))).....((((.((((.................(((((((((..(((((...)))))..)))))))))((((...(((....(((.(((..(((((..(((((.....)))))..))))).(((((((.((((...((((.....))))..(((((((.(((((((.....((((((...........))))))))))).)).))))))).((((((.......)))))).(((((..((((((....)))))).(((.....))).)))))...)))).)))))))((....))..))))))...)))..)))).)))).))))..(((((.....))))).....))))..))))....))))))))..))..)))))))).)))))).)))))..)))..((((((((.............)))))))).)))))).........)))))))..))).))).(((((..((((....(((((((.((.......)).)).)))))...(((((((....))).))))))))..)))))....))))))))..................(((((.....)))))...))))))))))))))))))))))).))).(((((((.((((...)))))))))))..
ProbKnot [ FASTA input ] [ sec struct ] ....(((.((((((((((((....(((......)))..((((((((...))))).))).............)))))...((((((((((((.........((((......)))).(.((((((((((((((((((((.((((((((.....((((((.......(((....)))...)))))).(((.((((...((.((((.......)))....)))...)))).)))))))))))..(((((....(((...............)))))))).....)))))..))))))......(((((....aaaa....))))).............(((((((((((((((.....)))))..)))))))))).AAAA..).)))))))))(((((.............))))))))))((((((((((.....((((((.......))))))...(((((......)))))((((((.......)))))).(((((((.(((((((.((((((...((((.(((......((((((.(((...........((((((.((((((....(((((.(((((((........))))))).)))))......)))))).....(((.(((((((((.(((.....((((.....(.(((....)))).......)))).....))).))).)))))).)))..........((((((((...))))(((.(((.((((((..................)))))).))).))).((((((..bbb..)))))).((((((((((...............)))))).))))......<<<....))))..))))))....((((((((((.(((((...))))).))))))))))...((((((.....))))))...(((((.((((((.....)))))).)))))((((((((...)))))).))))).)))))).(((((((.(((((((.....((((((..{{{......))))))))))).)).)))))))...)))..))))))))))..........((((((....))))))(((((((......[[[.......)))))))..(((]]].)))(((((((..((((((.(..............(((((.....))))).....((((..BBB.....)))).)))))))..)))))))..((((((.................))))))..)))))))))).)))).(((((.(((.(((((((((..........))))..)))))))).(((((.((........))))))).)))))((((...(((((((}}}.))).))))......))))(((((.((........)))))))>>>..)))))))))).(((((((.....))))))))))))))))))))).))).(((((((.((((...)))))))))))..
RNAfold [ 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 ] ....(((.(((((((...........(((.....((..((((((((...))))).)))..))....(((..((((.((((.((((.((((..........((((......))))..(((((...(.(((((((((((.(((((((......((((((..(((.((....))..))).)))))).(((.((((...((.(((..((....))...)))))...)))).))).)))))))..(((((....(((..((.......))..)))))))).....)))))..)))))).)))))).)))).(((((((((...............(((((((((((((((((((.....)))))..)))))))))..(((((((((...(((.(((..((((...(((((...))))).))))..))))))...)))))))))..)))))...............(((.((((..((((((.......)))))).))))...))).....)).)))))))....)))))))))))).))).)))......(((..((..(((((((((....(..((.(((((((........))))))).))..)..((((((((.((((((.(((((((..((((((((((.((((..(((((.(((....)))...........)))))...((...)).)))).))))).))))).((((((....(((..(((((.((((((((....))))))))(((((((((((..(..((..((((((((.((((..((((...((((((((((..(.........)..)))))).))))...((((.((((.................((((((..(..(((((...)))))..)..))))))((((...(((....(((.(((..(((((..(((((.....)))))..))))).(((((((.((((...((((.....))))..(((((((.(((((((.....((((((...........))))))))))).)).))))))).((((((.......)))))).(((((..((((((....)))))).(((.....))).)))))...)))).)))))))((....))..))))))...)))..)))).)))).))))..(((((.....))))).....))))..))))....))))))))..))..)..))))).)))))).)))))..)))..((((((((.............)))))))).)))))).........)))))))..))).))).(((((..(((.....(((((((.((.......)).)).)))))...(((((((....))).)))).)))..)))))....))))))))..................(((((.....)))))...)))))))))..)))))))))))).))).(((((((.((((...)))))))))))..