RNA Secondary Structure Atlas - RNASTRAND - Hammerhead_1

RNA: RFA_00658

			AUCCAGCUGACGAGUCCCAAACAGGACGAAACGCGCGUCAAACUGCAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((())))....))))))
Afold	[ FASTA input ]	[ sec struct ]	((.(((.(((((.((((......))))........)))))..))).))
Alterna	[ FASTA input ]	[ sec struct ]	((.(((.(((((.((((......))))........)))))..))).))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........)))).........
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........)))).........
CRWrnafold	[ FASTA input ]	[ sec struct ]	...(((..((((.((((......))))........))))...)))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.......(((((.((((......))))........)))))........
Carnac(20)	[ FASTA input ]	[ sec struct ]	................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..((....((........))...........))...))))))
CentroidAlifold(20)	[ 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 ]	...(((.(((((.((((......))))........)))))..)))...
Cylofold	[ FASTA input ]	[ sec struct ]	.......(((((.((((......))))........)))))........
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)...))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..((....(((.........................))).....))..
DotKnot	[ FASTA input ]	[ sec struct ]	.......(((((.((((......)))).....[[[)))))...]]]..
Fold	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
HotKnots	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
IPknot	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((..((((....))))(((...))))))).))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........)))))...)))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........)))))...)))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((....(((..(((........))).........))).....))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.((((......))))........))))....)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
McQFold	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
Multilign(seed)	[ FASTA input ]	[ sec struct ]	................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	................................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((...((..........))..........))....))...
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))...).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....))....))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	........((.(....)....................)).........
PPfold(seed)	[ FASTA input ]	[ sec struct ]	........(....((..........))...........).........
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)...............................
Pknots	[ FASTA input ]	[ sec struct ]	.......(((((.((((......)))).....[[[)))))...]]]..
PknotsRG	[ FASTA input ]	[ sec struct ]	.......(((((.((((......)))).....[[[)))))...]]]..
ProbKnot	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
RDfolder	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
RNASLOpt	[ FASTA input ]	[ sec struct ]	.......(((((.((((......))))........)))))........
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.......(((((.......................)))))........
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAfold	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
RNAshapes	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
RNAsubopt	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	..(((((((((((((((......))))).......)))))).))).).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((.((...((((.((((......))))........))))....)).))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((.(((..((((.((((......))))........))))...))).))
Sfold	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
TurboFold(20)	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
UNAFold	[ FASTA input ]	[ sec struct ]	...(((.(((((.((((......))))........)))))..)))...
Vsfold4	[ FASTA input ]	[ sec struct ]	.......(((((.((((......))))........)))))........
Vsfold5	[ FASTA input ]	[ sec struct ]	.......(((((.((((......))))........)))))........

---

RNA: RFA_00659

			AUCCAACUGACGAGUGCCCAAUAGGAGGAAACGCGCGUCAAACUGCAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((())))....))))))
Afold	[ FASTA input ]	[ sec struct ]	((.((..(((((.(((.((.......))...))).)))))...)).))
Alterna	[ FASTA input ]	[ sec struct ]	((.((..(((((.(((((........))...))).)))))...)).))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((..(.(......).).........)))).........
CMfinder(20)	[ FASTA input ]	[ sec struct ]	................................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	...((..((((..((((...............))))))))...))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............((((...............))))............
Carnac(20)	[ FASTA input ]	[ sec struct ]	................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((....................................))))))
CentroidAlifold(20)	[ 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 ]	.......(((((.(((.((.......))...))).)))))........
Cylofold	[ FASTA input ]	[ sec struct ]	.(((...{{{{(.{{{{......))).........)}}}}....}}}}
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)...))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	................................................
DotKnot	[ FASTA input ]	[ sec struct ]	.(((...[[[[[.[[[.......))).....]]].]]]]]........
Fold	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
HotKnots	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
IPknot	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((((((..)))).(((((..)))))))))))).)))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((.((.....))))........)))))...)))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	................................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((....(((....((......))...........))).....))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	................................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
McQFold	[ FASTA input ]	[ sec struct ]	.......(((((.......................)))))........
Multilign(seed)	[ FASTA input ]	[ sec struct ]	................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	................................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........))....)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	................................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....))....))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	................................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	................................................
Pknots	[ FASTA input ]	[ sec struct ]	.......((((..((((((....)).(....)))))))))........
PknotsRG	[ FASTA input ]	[ sec struct ]	.......(((((.....((....)).......[[[)))))...]]]..
ProbKnot	[ FASTA input ]	[ sec struct ]	.......(((((.(((...............))).)))))........
RDfolder	[ FASTA input ]	[ sec struct ]	.......(((((.(((...............))).)))))........
RNASLOpt	[ FASTA input ]	[ sec struct ]	.......(((((.......................)))))........
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAfold	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
RNAshapes	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
RNAsubopt	[ FASTA input ]	[ sec struct ]	.......((((..((((((....)).(....)))))))))........
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	..(((((((((((((((((.......)).).))))))))).)))).).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((.((...((((..(.(.........).)......))))....)).))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	................................................
Sfold	[ FASTA input ]	[ sec struct ]	.......(((((.(((...............))).)))))........
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	................................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	................................................
UNAFold	[ FASTA input ]	[ sec struct ]	.......(((((.(((.((.......))...))).)))))........
Vsfold4	[ FASTA input ]	[ sec struct ]	.......((((..((((...............))))))))........
Vsfold5	[ FASTA input ]	[ sec struct ]	.......(((((.......................)))))........

---

RNA: RFA_00664

			CCCUGGCUGACGAGUCCCAAACAGGACGAAACGCGCGUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(...((((....)))).....(((((((.......)))))))..)
Alterna	[ FASTA input ]	[ sec struct ]	.............((((.....((((((.......))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................(((((.......))))).....
CRWrnafold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	....((((....)))).....(((((((.......)))))))...
Cylofold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..............(((......)))...................
DotKnot	[ FASTA input ]	[ sec struct ]	...(((.......[[[)))..(((((((.......)))))))]]]
Fold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
HotKnots	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
IPknot	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
MCFold (ext)	[ FASTA input ]	[ sec struct ]	...(((..(((..))))))((((((((((.....))))))))).)
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	...(.....................................)...
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.((((......))))........)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
McQFold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	....((((..[[)))).....(((((((.....]])))))))...
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((...........))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	........(....((..........))...........)......
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
PknotsRG	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
ProbKnot	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
RDfolder	[ FASTA input ]	[ sec struct ]	...(((..........)))..(((((((.......)))))))...
RNASLOpt	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
RNAshapes	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
RNAsubopt	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.(.(((..(((..)))))))(((((((((....).))))))))..
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	..(((...((((.((((......))))........)))).)))..
RSpredict(20)	[ FASTA input ]	[ sec struct ]	..((((..((((.((((......))))........))))))))..
Sfold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.....(((....)))......(((((((.......)))))))...
UNAFold	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
Vsfold4	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...
Vsfold5	[ FASTA input ]	[ sec struct ]	....((((....)))).....(((((((.......)))))))...

---

RNA: RFA_00667

			AUCUUUCUGACGAGUUUCAAAUAGGACGAAACGCGUGUCAUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((.....(((.(((((.........))))).))).....))))
Alterna	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........))))......
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((...((((..(((((.........)))))....)))).))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............(((((.........))))).............
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	((((...(((((.(((((.........))))).))..))).))))
Cylofold	[ FASTA input ]	[ sec struct ]	.......(((((.(((((.........)))))...))))).....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................
DotKnot	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
Fold	[ FASTA input ]	[ sec struct ]	((((.....(((.(((((.........))))).))).....))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((.....(((.(((((.........))))).))).....))))
IPknot	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((((((((((((((...)))))))))))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	........................((...........))......
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.(((........)))........)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((.....(((.(((((.........))))).))).....))).
McQFold	[ FASTA input ]	[ sec struct ]	.......(((((.(((((.........)))))...))))).....
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	....((((((((.(((((.........)))))...))))).))).
PknotsRG	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((.....(((.(((((.........))))).))).....))))
RDfolder	[ FASTA input ]	[ sec struct ]	.........(((.(((((.........))))).))).........
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............((((......))))..................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.......(((((.......................))))).....
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((...(((((.(((((.........)))))...))))).))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((..((((((((((((.........)))))..)))))))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((((....((((.((((......))))........))))..))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((((....((((.((((......))))........))))..))))
Sfold	[ FASTA input ]	[ sec struct ]	.(((...(((((.(((((.........))))).)..)))).))).
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((...(((((.((.................)).))))).))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((.....(((.(((((.........))))).))).....))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((...(((((.(((((.........)))))...))))).))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((((((....[[[[[...))))).]]]]].........))).

---

RNA: RFA_00668

			AUCCAGCUGACGAGUGCCAAAUAGGACGAAAUGUGCAUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((.................(...........)...))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((.(......).))........).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((.(.((.(......).))........).))......
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((.......((((((............)).)))).))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	((((((.......((((.................)))).))))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	((((((........(((.................)))..))))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((((.......((((.................)))).))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	...(.....................................)...
DotKnot	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
Fold	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((..))))))))((((((((...))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.((.....(((..(((........))).........)))...)).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((..(((......))).........)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((((.((((...((((.....)).))....)).))..))))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((.......((((.................)))).))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	........((.(....)....................))......
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((...........))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	((((((((....))(((((............)).)))..))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
RDfolder	[ FASTA input ]	[ sec struct ]	((((((.......((((...............))))...))))))
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((.......((((.................)))).))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..((((.................................))))..
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((((((((.(((.(...............).)))))).))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((......(.((.(......).))........)....)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((((......(..(((.................))).).)))))
Sfold	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((((.......((.((.....))))............))))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((((.(((((..((((.....)).))...))).))..))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((((.......((((((............)).)))).))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.(((((.......((((((............)).)))).))))).

---

RNA: RFA_00672

			AUCCAGCUCACGAGUCCCAAAUAGGACGAAACGCGUCCUCCAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...((())).))))))
Afold	[ FASTA input ]	[ sec struct ]	((...(((....))).......((((((.....))))))..))
Alterna	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	.........(((.((((......))))......))).......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................(((((.....))))).....
CRWrnafold	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
Carnac(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	...........................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((........((........))...........))))))
CentroidAlifold(20)	[ 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 ]	......................((((((.....))))))....
Cylofold	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	.(((((........(((......)))...........))))).
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............((((......))))................
DotKnot	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
Fold	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
HotKnots	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
IPknot	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((((((((((((..))))))...)))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))......))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))......))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	...............(........)..................
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((..................(((((.....))))))))).
MaxExpect	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
McQFold	[ FASTA input ]	[ sec struct ]	.....((((..)))).......((((((.....))))))....
Multilign(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	...........................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............((((......))))................
NanoFolder	[ FASTA input ]	[ sec struct ]	...........................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((...((..........))........)).))...
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((((.....))))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....)...)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.......)))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((.........))).....
Pknots	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
PknotsRG	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
ProbKnot	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
RDfolder	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
RNASLOpt	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	...........................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.........(((.((((......))))......))).......
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............((((......))))................
RNAfold	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
RNAshapes	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
RNAsubopt	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.....((((..))))((..)).(((((.(....))))))....
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((..(....(((.((((......))))......)))..)..))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((..(....(((.((((......))))......)))..)..))
Sfold	[ FASTA input ]	[ sec struct ]	......(......)........((((((.....))))))....
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
UNAFold	[ FASTA input ]	[ sec struct ]	.....(((....))).......((((((.....))))))....
Vsfold4	[ FASTA input ]	[ sec struct ]	......................((((((.....))))))....
Vsfold5	[ FASTA input ]	[ sec struct ]	...........................................

---

RNA: RFA_00673

			AUCCAGCCGACGAGUCCCAAAUAAAACGAAACGCGCGUCAAAGUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((())))....))))))
Afold	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
Alterna	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((..........))........)))).........
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((((.((..........))........)))).........
CRWrnafold	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((....................................))))))
CentroidAlifold(20)	[ 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 ]	(((((...((((.((.................)).))))....)))))
Cylofold	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)...))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..(((...(((.........................)))....)))..
DotKnot	[ FASTA input ]	[ sec struct ]	.........................(((...[[[.)))....]]]...
Fold	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
HotKnots	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
IPknot	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((.(((((((((((((..)))))))))))).)(((..))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........)))))...)))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..((((((((((......))))).......)))))...)))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((........................................))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...(......((......))(...........))....)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.((((...((((.((.................)).))))....)))).
McQFold	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	................................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........))....)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))...).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....))....))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))...).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)...............................
Pknots	[ FASTA input ]	[ sec struct ]	........((((....[[[.......((.....))))))....]]]..
PknotsRG	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
ProbKnot	[ FASTA input ]	[ sec struct ]	(((((.(.((((.......................))))...))))))
RDfolder	[ FASTA input ]	[ sec struct ]	.........................(((.......)))..........
RNASLOpt	[ FASTA input ]	[ sec struct ]	(((((...((((.......................))))....)))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	........((((.......................)))).........
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAfold	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
RNAshapes	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((((..((((((((((...........).).))))))).)..)))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((...((((..((...........))......))))....)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((((...((((.((..........))........))))....)))))
Sfold	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	................................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.((.................)).))))....)))).
UNAFold	[ FASTA input ]	[ sec struct ]	(((((...((((.((.................)).))))....)))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.((((...((((.......................))))....)))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((...((((.......................))))....)))).

---

RNA: RFA_00674

			AUUCAGCUGACGAGUCCCAAAUAGGACGAAGUGACGCGCGUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))......(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...((...)).))))))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...........))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))...........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................(((((..........))))).....
CRWrnafold	[ FASTA input ]	[ sec struct ]	.............((((.....((((((..........))))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	................................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((...(..............................).))))))
CentroidAlifold(20)	[ 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 ]	.(((((.......((((......)))).....((((()))))))))).
Cylofold	[ FASTA input ]	[ sec struct ]	((((.......))))......(((((((..........)))))))...
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(................................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..((((........(((......)))................))))..
DotKnot	[ FASTA input ]	[ sec struct ]	.............(((.....[[[[[[[....)))...]]]]]]]...
Fold	[ FASTA input ]	[ sec struct ]	.....(((....))).(((....(((((..((...)).))))))))..
HotKnots	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...(.....).))))))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((..((...(((..........[[....)))...]]))))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((.(..((((((..)))))))))).((((..))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))...........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))...........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.((((......................................)))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.(((((.......(((........)))...............))))).
MaxExpect	[ FASTA input ]	[ sec struct ]	..((((........)........(((((..((...)).))))))))..
McQFold	[ FASTA input ]	[ sec struct ]	((((((.......((((......)))).....((((..))))))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	((((((((..[[)))......{{{{{{{...)))]]..}}}}}}}.))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..((((..((...((..........)).............))))))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((............)))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........)).............)).)))..
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((..............))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((..............))).....
Pknots	[ FASTA input ]	[ sec struct ]	((((.......)))).(((....(((((..........))))))))..
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...........))))))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	(((((..................(((((..........))))))))))
RDfolder	[ FASTA input ]	[ sec struct ]	......................((((((..........))))))....
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...........))))))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...(.....).))))))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...........))))))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...(.....).))))))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((((..(((((((((......)))))..........))))))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((...((((.((((......))))...........)))).)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((((...((((.((((......))))...........)))).)))))
Sfold	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))...(.....).))))))))).
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	................................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))...........))))))))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))...(.....).))))))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((.......))).......(((((((..........)))))))...
Vsfold5	[ FASTA input ]	[ sec struct ]	((((.......))))......(((((((..........)))))))...

---

RNA: RFA_00675

			AUCCAACUGACCAGUCGGAAAUAGGACGAAACGCGCGUCCAGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
Alterna	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........(((..(((........))).........)))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........(((..(((........))).........)))......
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	.(((.(((....))).)))....(((((.......))))).....
Cylofold	[ FASTA input ]	[ sec struct ]	......((((....)))).....(((((.......))))).....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	...(.....................................)...
DotKnot	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
Fold	[ FASTA input ]	[ sec struct ]	.(((.(((....))).)))....(((((.......))))).....
HotKnots	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
IPknot	[ FASTA input ]	[ sec struct ]	.(((.(((....))).)))....(((((.......))))).....
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((..)))))))))(((((((((.....))))))..)))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	..........(.........................)........
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.(((........)))........)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((.(((....))).)))....(((((.......))))).....
McQFold	[ FASTA input ]	[ sec struct ]	((((..(((((..))))).....(((((.......))))).))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	((((..(((((..))))).....(((((.......))))).))))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..((....((...((..........))..........))..))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...(....((...((..........))..........))..)...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((.........)))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
ProbKnot	[ FASTA input ]	[ sec struct ]	.(((.(((....))).)))....(((((.......))))).....
RDfolder	[ FASTA input ]	[ sec struct ]	.......................(((((.......))))).....
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	((((.....................................))))
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.(((..(((..)))..))).(..((((((....).)))))..)..
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((((....(((..(((........))).........)))..))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((((....(((..(((........))).........)))..))))
Sfold	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((......((....)).....(((((.......))))).))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((..((((....)))).....(((((.......))))).))))
Vsfold4	[ FASTA input ]	[ sec struct ]	......((((....)))).....(((((.......))))).....
Vsfold5	[ FASTA input ]	[ sec struct ]	......((((....)))).....(((((.......))))).....

---

RNA: RFA_00677

			AUCCAGCUGACGAGUCCUAAAUAGGGUGAAACGCGCGUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((....))).......)).))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................(((((.......))))).....
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((..((((..((((....)))).........))))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	((((((..((((.......................))))))))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	((((((..((((.(((((....))).......)).))))))))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((((..((((..((((....)))).........))))))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	...(.....................................)...
DotKnot	[ FASTA input ]	[ sec struct ]	((((((..((((...(((....)))(((...))).))))))))))
Fold	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((..((((...((.......)).........))))))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((..(((((((.(((..)))(((..))))))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((.....................................))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((........((((......)))).............)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((((..((((.(((((.....)))......)).))))))))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((((..))))))........))))))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	(((((((([[[[))(((((..)))))((.....))]]]]))))))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((((.......))))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((((.......))))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	((((((((....)).(((....)))(((.....)))...))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((..((((...(((.....))).........))))))))))
RDfolder	[ FASTA input ]	[ sec struct ]	......................((((((.......))))))....
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((....)))))........))))))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((..((((...(((....)))(((...))).))))))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((((..(((((((((((..)))).(..)..)))))))))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((.....((.((((......))))........))...)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((((...((((.((((......))))........)))).)))))
Sfold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......)).......)).))))))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......)).......)).))))))))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((((..((((.(((((.....)))......)).))))))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((((..((((..((((....)))).........))))))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.(((((..((((..((((....)))).........))))))))).

---

RNA: RFA_00678

			AUCCAGCUGACGAGUCCCAAAUAGGACGAACGCACUUCCUAGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))..(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(((.((.((.((.((((......))))...))))....)).)))
Alterna	[ FASTA input ]	[ sec struct ]	(((.((.......((((......))))...........)).)))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((((......)))).......).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................(((.(......).))).....
CRWrnafold	[ FASTA input ]	[ sec struct ]	.....................(((((..........)))))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((................................))))))
CentroidAlifold(20)	[ 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 ]	.............((((......)))).................
Cylofold	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..((((..((..........................))))))..
DotKnot	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
Fold	[ FASTA input ]	[ sec struct ]	....((.((.((.((((......))))...))))))........
HotKnots	[ FASTA input ]	[ sec struct ]	.....((......((((......))))....))...........
IPknot	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((.(((((((((..))))))..)))))...)))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..(((((((((......))))......)))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......)))).......))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	..((.....((..((..........))........))...))..
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((......................)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	........(.(..((((......))))....))...........
McQFold	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
Multilign(seed)	[ FASTA input ]	[ sec struct ]	............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........)).........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......(((((......))))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))...).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)......((((........)))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)...........................
Pknots	[ FASTA input ]	[ sec struct ]	.((.....))((.((((......))))[[[))...]]]......
PknotsRG	[ FASTA input ]	[ sec struct ]	....((.((.((.((((......))))...))))))........
ProbKnot	[ FASTA input ]	[ sec struct ]	.......((.((.((((......))))...))))..........
RDfolder	[ FASTA input ]	[ sec struct ]	.....................(((((..........)))))...
RNASLOpt	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	......(((..............................)))..
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	............................................
RNAfold	[ FASTA input ]	[ sec struct ]	.....((......((((......))))....))...........
RNAshapes	[ FASTA input ]	[ sec struct ]	.....((......((((......))))....))...........
RNAsubopt	[ FASTA input ]	[ sec struct ]	....((.((.((.((((......))))...))))))........
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	....((.((((((((((......)))))))).))))((...)).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((.(......(.((..............))......).).)))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((.((..((.(.((((......)))).......).)))).)))
Sfold	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............((((......)))).................
UNAFold	[ FASTA input ]	[ sec struct ]	.....((......((((......))))....))...........
Vsfold4	[ FASTA input ]	[ sec struct ]	...........((((((......)))........))).......
Vsfold5	[ FASTA input ]	[ sec struct ]	...........((((((......)))........))).......

---

RNA: RFA_00680

			AUCCAGUUGACGAGUCCCAAAUUGGACGAAACGCGCGUCAAACUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((())))....))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........))))).)))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........)))).........
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((((.((((......))))........)))).........
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	((((((((.....((((......)))).............))))))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((....................................))))))
CentroidAlifold(20)	[ 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 ]	((((((((((((.((((......))))........)))).))))))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)...))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..(((...((...........................))....)))..
DotKnot	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
Fold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........))))).)))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((..(((((..)))))(((...))))))).))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........)))))...)))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........)))))...)))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((.........(((........))).................))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.((((......))))........))))....)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((((((((((.((((......))))........))))).)))))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))))).))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	................................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........))....)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	........(..(....).............((....))).........
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....))....))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	........((.(....)..............(....))).........
PPfold(seed)	[ FASTA input ]	[ sec struct ]	................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....).............((....))..........
Pknots	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))(.....).)))).))))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))))).))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((((((((.((((.(...)))))........))))).)))))))
RDfolder	[ FASTA input ]	[ sec struct ]	.(((((((...........)))))))......................
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((((.....((((......)))).............))))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	................................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))))).))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((((((((((((...(((...))).((...)).))))))).))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((...((((.((((......))))........))))....)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((((((..((((.((((......))))........))))...))))))
Sfold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........))))).)))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	................................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((((((((((.((((......))))........))))).)))))).
UNAFold	[ FASTA input ]	[ sec struct ]	((((((((((((.((((......))))........)))).))))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((((((((((.((((......))))........)))).))))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.(((((((((((.((((......))))........)))).))))))).

---

RNA: RFA_00684

			AUCCAGCCGAUGAGUUCCAAACAGGACUAAACGCGCUUCUUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((.((.(.(((((......))))).).))......))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((((......))))........).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	(((((..((...(((((......))))).....)).....)))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	((((((......(((((......)))))...........))))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	(((((((((...(((((......)))))...)).))....)))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((((......(((((......)))))...........))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................
DotKnot	[ FASTA input ]	[ sec struct ]	....(((.....(((((......)))))......)))........
Fold	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
HotKnots	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
IPknot	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((((((((....))))))))))).)))....))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..(((((((((......)))).......)))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Mastr(20)	[ FASTA input ]	[ sec struct ]	.............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.((((((((...(((((......)))))...)).))....)))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((......(((((......)))))...........))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	((((((..(((([[[[[....))]]]]].........))))))))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.............................................
Pknots	[ FASTA input ]	[ sec struct ]	....(((((......(((.....)))[[[[.)).)))..]]]]..
PknotsRG	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).)))....))))
ProbKnot	[ FASTA input ]	[ sec struct ]	(((((((((.(.(((((......))))))..)).))....)))))
RDfolder	[ FASTA input ]	[ sec struct ]	............(((((......))))).................
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((......(((((......)))))...........))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............((((......))))..................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
RNAshapes	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).)))....))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((.((((.............))).)..............))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((......(.((((......))))...........).)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.............................................
Sfold	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).)))....))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............................................
UNAFold	[ FASTA input ]	[ sec struct ]	(((((((((...(((((......)))))...)).))....)))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.((((.......(((((......)))))............)))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((.......(((((......)))))............)))).

---

RNA: RFA_00685

			AUCCAACCGAUGAGUCCCAAAUAGAACGAAACCUGCGUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
Alterna	[ FASTA input ]	[ sec struct ]	(((((...((((.((...............))...)))).)))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((.(......).))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	(((((...................................)))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	(((((..................(.(((.......))).))))))
Cylofold	[ FASTA input ]	[ sec struct ]	(((((....................(((.......)))..)))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................
DotKnot	[ FASTA input ]	[ sec struct ]	(((((...((((.........(((........))))))).)))))
Fold	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
HotKnots	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
IPknot	[ FASTA input ]	[ sec struct ]	(((((...(((.........................))).)))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((((((((((((..)))))))))))..).))..)))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((....(((..(((........))).........)))..))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.((((...((((((..................)).)))).)))).
McQFold	[ FASTA input ]	[ sec struct ]	(((((...((((.......................)))).)))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.............................................
Pknots	[ FASTA input ]	[ sec struct ]	(((.....)))..(((((.....).(((.......)))...))))
PknotsRG	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
ProbKnot	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
RDfolder	[ FASTA input ]	[ sec struct ]	(((((...((((.......................)))).)))))
RNASLOpt	[ FASTA input ]	[ sec struct ]	(((((...((((.......................)))).)))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
RNAshapes	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((((.((.(........)..))(((...)))......))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((...((((.((.(......).))........)))).)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.............................................
Sfold	[ FASTA input ]	[ sec struct ]	(((((...((((.......................)))).)))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............................................
UNAFold	[ FASTA input ]	[ sec struct ]	(((((...((((((..................)).)))).)))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.((((...((((((..................)).)))).)))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((...((((((..................)).)))).)))).

---

RNA: RFA_00695

			CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUCGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAAGUUCACCACGACUCCUCCUUCUCUCACAAGUCGAAACUCAGAGUCGGAACAG
Reference structure (ext)		[ sec struct ]	((((((.......((((..............................................................................))))...((((.)))).)))).))
Afold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....)))).))
Alterna	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((..(((((((((.......(((((((..((((........)))))))))))..))).).)).)))...))))..))).....))))....)))).))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.......(((................................................................................))).............)))).))
CentroidAlifold(20)	[ 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 ]	....((((((...(((...((((....((((..((((.((.(((((((...((((.......)))))))))))..)).))..))..))))))))..))).....))))....)).....
Cylofold	[ FASTA input ]	[ sec struct ]	..........(((((.....(((((....))))).......(((((((..................)))))))..[[[[[[.....)))))................]]]]]]......
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(................................................................................................)......)))).))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
DotKnot	[ FASTA input ]	[ sec struct ]	....................(((((....)))))..(((..(((((((..((((........)))))))))))..[[[[[[...............)))........]]]]]]......
Fold	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
HotKnots	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
IPknot	[ FASTA input ]	[ sec struct ]	..(((((((......((..(((((...[[[))......((.(((((((..................)))))))..))..........]]].)))....)).....)))....))))...
MCFold (ext)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((((((....(((..(((.....((((..((...((.(((((((..................)))))))..)).....))..)))).))).)))......))))....)))).).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.((......((...................................................................))...................))..................
Mastr(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
MaxExpect	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((...(((........))).)))))))..))..)).))..))))))))..))).....))))....))))...
McQFold	[ FASTA input ]	[ sec struct ]	......(((..((((.(((((((((....))))).......(((((((..................)))))))..[[[[[[...))))))))...............]]]]]]...)))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..((((..((...((..................................................................................))...........))))))...
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((.(.((..................................................................................))....)......)).)))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Pknots	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
PknotsRG	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((((((.(.(((...((((....((((..........(((((((..((((........))))))))))).............))))))))..)))....)))))....)))).))
RDfolder	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
RNASLOpt	[ FASTA input ]	[ sec struct ]	..((((((((..........(((((....))))).......(((((((..((((........)))))))))))..(((((...............)))))....))))....))))...
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
RNAfold	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
RNAshapes	[ FASTA input ]	[ sec struct ]	...(((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....)))....
RNAsubopt	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(.((((........).)))((((((....))))))..(((.(((((((..((((........)))))))))))))).)(((.(((..((((((((......)))).))))..)))).))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((.(.......(...................................................................................................)...).))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
Sfold	[ FASTA input ]	[ sec struct ]	..((((((((...(((...(((.....((((..((.(.((.(((((((..................)))))))..))...).))..)))).)))..))).....))))....))))...
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.......................................................................................................................
UNAFold	[ FASTA input ]	[ sec struct ]	..((((((((...(((...((((....((((..((.((((.(((((((..((((........)))))))))))..))..)).))..))))))))..))).....))))....))))...
Vsfold4	[ FASTA input ]	[ sec struct ]	...........((((......((((....)))).(((..((((......)))).(((.....))).((((......))))....))).)))).....((((.........)))).....
Vsfold5	[ FASTA input ]	[ sec struct ]	...(((....(((((.....(((((....))))).......(((((((..................)))))))..[[[[[......)))))....]]]]]............)))....

---

RNA: RFA_00703

			CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAACGACUCCUCCUUCUCUCACAAGUCGAAACUCAGAGUCGGAAAG
Reference structure (ext)		[ sec struct ]	((((((.......((((.....................................................))))...((((.)))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
Alterna	[ FASTA input ]	[ sec struct ]	(((((((((....(((...((((....(((......((.((((.........)))).))...)))))))..)))......)))....))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((.....((.((((.........)))).))..))))))))..))).....))))....))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.......(((.......................................................))).............))))))
CentroidAlifold(20)	[ 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 ]	((((((((((...(((...((((....((((....(((.((((.........)))).)).)))))))))..))).....))))....))))))
Cylofold	[ FASTA input ]	[ sec struct ]	(((((.....(((((........((((....))))....[[[(.......{{{{{{.....)))))...........)]]].}}}}}})))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.......................................................................)......))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
DotKnot	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((........((((.........)))).....))))))))..))).....))))....))))))
Fold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((((((.....(((.(((.....(((....((...((((.........))))....))))).)))...)))....))))....))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	.............................................................................................
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((((((....(((..(((..(........)..)))...............................)))......))))....))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((....(((...((..............)).....................)))...............................)))...
Mastr(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
MaxExpect	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((....((((.........)))).))..))))))))..))).....))))....))))))
McQFold	[ FASTA input ]	[ sec struct ]	((((((((((.....(((.........((((..((((..((((.........))))...)))))))).....)))....))))....))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
NanoFolder	[ FASTA input ]	[ sec struct ]	(((((.((..<<<<([[[[[[..(((({{{.))))))..((((..]]]..aaaaaa}}}(()>>>>....))]]]..)))).AAAAAA)))))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((.........................................................))...........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((.........................................................))....)......)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Pknots	[ FASTA input ]	[ sec struct ]	(((((((((..((((.((((.((((((....))))....((((.........)))).))))))))))...(((....))))))....))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((((((.(.(((...((((....((((........((((.........)))).....))))))))..)))....)))))....))))))
RDfolder	[ FASTA input ]	[ sec struct ]	..................................................((((((....(((...........))).....)))))).....
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((((((.((((.((((...((((....))))....((((.........))))...))))))))............))))....))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............(((.......................................................)))...................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................................................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((((((((.((((..((((.(.(((((..))))))((..((.(........)))..)))))).)))))).)(((......)))...))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((..........(..................................................................).....)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
Sfold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...(((.....((((..(.....((((.........))))..)..)))).)))..))).....))))....))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............................................................................................
UNAFold	[ FASTA input ]	[ sec struct ]	((((((((((...(((...((((....((((..((.((...((......))...)).))..))))))))..))).....))))....))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	...........((((.((((.((((((....))))....((((.........)))).)))))))))).....((((.........))))....
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((......))))....((((((((....))))....((((.........)))).........))))...((((.........))))....

---

RNA: RFA_00704

			AUUUAGCUGACGAGUCCCAAACGGUACGAAACUGGCGUCCUUGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(((.((..((((..((((....))...))......)))))).)))
Alterna	[ FASTA input ]	[ sec struct ]	(((.((..((((....((....(((.....))))))))))).)))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((.(......).))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((((.((.(......).))........))))......
CRWrnafold	[ FASTA input ]	[ sec struct ]	..(((...(((((((...............)))..))))..))).
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	........(((..((.((....)).))(.......))))......
Cylofold	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	...(....(((.........................)))..)...
DotKnot	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
Fold	[ FASTA input ]	[ sec struct ]	.....(((.....((.((....)).))......))).........
HotKnots	[ FASTA input ]	[ sec struct ]	.....((((.[[[[..[[[..))))(((....]]]))).]]]]..
IPknot	[ FASTA input ]	[ sec struct ]	.............................................
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((..(((((((((((((...)))))))))..))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	..((.............................))..........
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((((.((((......))))........)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.....((......)...(....)............).........
McQFold	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	...(((..((.(.((..........))....).....)))))...
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	........((((....)...................)))......
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	........((.(....)....................))......
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)............................
Pknots	[ FASTA input ]	[ sec struct ]	.....((...[[[[.......((((.....))))))...]]]]..
PknotsRG	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
ProbKnot	[ FASTA input ]	[ sec struct ]	.....(((....)))..............................
RDfolder	[ FASTA input ]	[ sec struct ]	..........((((..(((.............)))....))))..
RNASLOpt	[ FASTA input ]	[ sec struct ]	..........((((.......((((.....)))).....))))..
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............(((......)))....................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	........((((.......................))))......
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	..........((((..(....((((.....))))..)..))))..
RNAshapes	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
RNAsubopt	[ FASTA input ]	[ sec struct ]	..........((((..(....((((.....))))..)..))))..
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	......(.(((..)))((((((......))).)))....(..)).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((.(...((((..(.(..........).).....)))).).)))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(((.((..((((..((...........))......)))))).)))
Sfold	[ FASTA input ]	[ sec struct ]	..........((((..(....((((.....))))..)..))))..
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	........((((.((.((....)).))........))))......
UNAFold	[ FASTA input ]	[ sec struct ]	.....(((.....((.((....)).))......))).........
Vsfold4	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......
Vsfold5	[ FASTA input ]	[ sec struct ]	........((((.........((((.....)))).))))......

---

RNA: RFA_00705

			AUCCAGUUGAUGAGUCCCAGAGAAGGACGAAACGUGCAUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((.......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((((.(((((.((((.......))))....))).))..))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((.......))))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	..............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	((((((.......((((.......))))............))))))
Carnac(20)	[ FASTA input ]	[ sec struct ]	..............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..((...(((.........)))..........))))))))
CentroidAlifold(20)	[ 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 ]	((((((..((((.((((.......))))........))))))))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((((.......((((.......))))............))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(..............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..............................................
DotKnot	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
Fold	[ FASTA input ]	[ sec struct ]	((((((.(((((.((((.......))))....))).))..))))))
HotKnots	[ FASTA input ]	[ sec struct ]	((((((.(((((.((((.......))))....))).))..))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((..)))))).((((((((...))))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..(((((((((.......)))).......)))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	..............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	...(......................................)...
Mastr(20)	[ FASTA input ]	[ sec struct ]	..............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.(((((.(((((.((((.......))))....))).))..))))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	..............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	...(....((.(.(((.........)))....).....))..)...
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...(....((.(.(((.........)))....).....))..)...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	..............................................
Pknots	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	((((((.(((((.((((.......))))....))).))..))))))
RDfolder	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
RNASLOpt	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((..((((.((((.......))))........))))))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((((((..(((((((((.......))))...(..))))))))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((......(.((((.......))))...........).)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	..............................................
Sfold	[ FASTA input ]	[ sec struct ]	((((((.((....((((.......))))........))..))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	..............................................
UNAFold	[ FASTA input ]	[ sec struct ]	((((((.(((((.((((.......))))....))).))..))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((.......))))........))))))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((.......))))........))))))))).

---

RNA: RFA_00706

			CAAUUGCUGAGGAGUCCCAUAAUAGGACGAAACGGCCGUCCAGUGC
Reference structure (ext)		[ sec struct ]	((((((.......((((.......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(....((((....((((.......))))....)))).........)
Alterna	[ FASTA input ]	[ sec struct ]	....(((((.((.((((.......)))).......))...))))).
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((((.......))))........).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	..............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	..((.((((....((((.......))))....)))).)).......
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............((((.......))))..................
Carnac(20)	[ FASTA input ]	[ sec struct ]	..............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..................................))))))
CentroidAlifold(20)	[ 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 ]	.....((((....((((.......))))....))))..........
Cylofold	[ FASTA input ]	[ sec struct ]	.....((((...............[[[[[...))))]]]]].....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(..............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..............................................
DotKnot	[ FASTA input ]	[ sec struct ]	.....((((.[[[((((.......))))....))))..]]].....
Fold	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
HotKnots	[ FASTA input ]	[ sec struct ]	.....((((.[[[(((({{{....))))....))))..]]].}}}.
IPknot	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((....))))))))(((((((...))))))))))).
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((.......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	..............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	..((...........(........).................))..
Mastr(20)	[ FASTA input ]	[ sec struct ]	..............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
McQFold	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
Multilign(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	..............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((...........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((...........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	..............................................
Pknots	[ FASTA input ]	[ sec struct ]	((.....)).((....))......(((((.......))))).....
PknotsRG	[ FASTA input ]	[ sec struct ]	.....((((.[[[((((.......))))....))))..]]].....
ProbKnot	[ FASTA input ]	[ sec struct ]	..((([[[[....[[[....)))..]]]....]]]]..........
RDfolder	[ FASTA input ]	[ sec struct ]	..(((.......))).........(((((.......))))).....
RNASLOpt	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAfold	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
RNAshapes	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
RNAsubopt	[ FASTA input ]	[ sec struct ]	.....(((..((....))......(((((.......))))))))..
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	((..))((((((.(..((.(........)).)..))))..)))...
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	..((....((.(.((((.......))))........).))..))..
RSpredict(20)	[ FASTA input ]	[ sec struct ]	..............................................
Sfold	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	..............................................
UNAFold	[ FASTA input ]	[ sec struct ]	.....((((....((((.......))))....))))..........
Vsfold4	[ FASTA input ]	[ sec struct ]	..((((.((........)))))).(((((.......))))).....
Vsfold5	[ FASTA input ]	[ sec struct ]	..((((.((.((...)))))))).(((((.......))))).....

---

RNA: RFA_00707

			GCACUGCUGAGGAGUCCCACAAUAGGACGAAACGACCGUCCAGUAC
Reference structure (ext)		[ sec struct ]	((((((.......((((.......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(......((.((....)).))...(((((.......)))))....)
Alterna	[ FASTA input ]	[ sec struct ]	....(((((.((.((((.......)))).......))...))))).
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((((.......))))........).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........((.(.((((.......))))........).))......
CRWrnafold	[ FASTA input ]	[ sec struct ]	((.....((.((....)).))...(((((.......))))).))..
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............((((.......))))..................
Carnac(20)	[ FASTA input ]	[ sec struct ]	..............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..................................))))))
CentroidAlifold(20)	[ 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 ]	..........((....))....(.(((((.......))))).)...
Cylofold	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(..............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.........(............................).......
DotKnot	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
Fold	[ FASTA input ]	[ sec struct ]	..........((....))......(((((.......))))).....
HotKnots	[ FASTA input ]	[ sec struct ]	.......((.((....)).))...(((((.......))))).....
IPknot	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((((....))))))(((((((...))))))).))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((.......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.((((..(((((.((((.......))))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.((.....(((..(((.........))).........)))...)).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...(..(..(((......))).........))....)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	..........((....))......(((((.......))))).....
McQFold	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
Multilign(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	..............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((...........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....).......(((((.......))))).....
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((...........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....).......(((((.......))))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)........((...........))......
Pknots	[ FASTA input ]	[ sec struct ]	.((....)).((....))......(((((.......))))).....
PknotsRG	[ FASTA input ]	[ sec struct ]	....(((...((....))......(((((.......))))).))).
ProbKnot	[ FASTA input ]	[ sec struct ]	....(((.................(((((.......))))).))).
RDfolder	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
RNASLOpt	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAfold	[ FASTA input ]	[ sec struct ]	.......((.((....)).))...(((((.......))))).....
RNAshapes	[ FASTA input ]	[ sec struct ]	.......((.((....)).))...(((((.......))))).....
RNAsubopt	[ FASTA input ]	[ sec struct ]	....((((..((....))......(((((.......))))))))).
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	...(.((((.(((((..(.............)..)).)))))))).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(.(((...((.(.((((.......))))........).)).))).)
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(.((((..((.(.((((.......))))........).)))))).)
Sfold	[ FASTA input ]	[ sec struct ]	..........((....))......(((((.......))))).....
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	........................(((((.......))))).....
UNAFold	[ FASTA input ]	[ sec struct ]	.......((.((....)).))...(((((.......))))).....
Vsfold4	[ FASTA input ]	[ sec struct ]	....(((((.((.((((.......)))).......))...))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	....(((((.((.((((.......))))..........))))))).

---

RNA: RFA_00708

			GCACUUCUGAAGAGUCCCAUGCUAGGACGAAACAGCCUUCCAGUAC
Reference structure (ext)		[ sec struct ]	((((((.......((((.......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(.....(((....((((.......))))....)))..........)
Alterna	[ FASTA input ]	[ sec struct ]	..(((...((((.((((.......))))........)))).)))..
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.((((.......))))........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	..............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	......((((((.((((.......))))........)))).))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	..............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..((....((.........))...........))))))))
CentroidAlifold(20)	[ 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 ]	......(((....((((.......))))....)))...........
Cylofold	[ FASTA input ]	[ sec struct ]	.............((((...[[[.)))).....]]]..........
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(..............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..............................................
DotKnot	[ FASTA input ]	[ sec struct ]	(((...[[[....[[[[..)))..]]]]....]]]...........
Fold	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
HotKnots	[ FASTA input ]	[ sec struct ]	(((.{{(.{{{{.{{{{..)))..}}}})}}.....}}}}......
IPknot	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((..)))((((((...))))))(((((..))))).)))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((..(((.......))).........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	..............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((..........(..........)................))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	..............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
McQFold	[ FASTA input ]	[ sec struct ]	........((((.((((.......))))........))))......
Multilign(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	..............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((...........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((...........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	........(....((...........))...........)......
PPfold(20)	[ FASTA input ]	[ sec struct ]	..............................................
Pknots	[ FASTA input ]	[ sec struct ]	....(((.[[[[.((((.......))))))).....]]]]......
PknotsRG	[ FASTA input ]	[ sec struct ]	........((((.((((.......))))......[[))))..]]..
ProbKnot	[ FASTA input ]	[ sec struct ]	......((([[[.((((.......))))....))).]]].......
RDfolder	[ FASTA input ]	[ sec struct ]	...................((((.(((...........))))))).
RNASLOpt	[ FASTA input ]	[ sec struct ]	.............((((.......))))..................
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAfold	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
RNAshapes	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
RNAsubopt	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	......((((((.((..(.(..........))..))))).)))...
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(.(((......(.((((.......))))...........).))).)
RSpredict(20)	[ FASTA input ]	[ sec struct ]	..............................................
Sfold	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
TurboFold(20)	[ FASTA input ]	[ sec struct ]	..............................................
UNAFold	[ FASTA input ]	[ sec struct ]	......(((....((((.......))))....)))...........
Vsfold4	[ FASTA input ]	[ sec struct ]	........((((.((((.......))))........))))......
Vsfold5	[ FASTA input ]	[ sec struct ]	..((((.....))))....((((..................)))).

---

RNA: RFA_00709

			AUCUAGCUGACGAGUCCCGAAUAGGAGGAAGUGCUCGUUCAAUAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((......(((((((.((........))....)))))))....))
Alterna	[ FASTA input ]	[ sec struct ]	........(((((((((.........))....)))))))......
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((..(((......))).........))))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	...((...(((((((.................)))))))...)).
Carnac(seed)	[ FASTA input ]	[ sec struct ]	........(((((((.................)))))))......
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((.................................))))))
CentroidAlifold(20)	[ 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 ]	........((((((((((........))..).)))))))......
Cylofold	[ FASTA input ]	[ sec struct ]	........(((((((((......))).......))))))......
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................
DotKnot	[ FASTA input ]	[ sec struct ]	..(((...[[[[[[[......)))........]]]]]]]......
Fold	[ FASTA input ]	[ sec struct ]	.......((((((((.((........))....))))).)))....
HotKnots	[ FASTA input ]	[ sec struct ]	.......((((((((.((........))....))))).)))....
IPknot	[ FASTA input ]	[ sec struct ]	........(((((((.((........))....)))))))......
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((..((((((((((((....))))..).)))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	..((.........((((......))))..............))..
Mastr(20)	[ FASTA input ]	[ sec struct ]	.............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	........(((((((.((........))....)))))).).....
McQFold	[ FASTA input ]	[ sec struct ]	........(((((((.................)))))))......
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.............................................
Pknots	[ FASTA input ]	[ sec struct ]	.(((....[[[[[[(((......))))))....]]]]]]......
PknotsRG	[ FASTA input ]	[ sec struct ]	.(((....[[[[[[[.((.....)).)))...]]]]]]]......
ProbKnot	[ FASTA input ]	[ sec struct ]	.......((((((((.................)))))).))....
RDfolder	[ FASTA input ]	[ sec struct ]	.........((((((((.........)))....))))).......
RNASLOpt	[ FASTA input ]	[ sec struct ]	........(((((((.................)))))))......
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	........(((((((.((........))....)))))))......
RNAshapes	[ FASTA input ]	[ sec struct ]	........(((((((.((........))....)))))))......
RNAsubopt	[ FASTA input ]	[ sec struct ]	.......((((((((.((........))....)))))).))....
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.......((((((((((((......))).)..)))))).))....
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	((.(....((.(..(((......))).......))).....).))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.............................................
Sfold	[ FASTA input ]	[ sec struct ]	.......((((((((.((........))....)))))).))....
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............................................
UNAFold	[ FASTA input ]	[ sec struct ]	........(((((((.((........))....)))))))......
Vsfold4	[ FASTA input ]	[ sec struct ]	........((((((...................))))))......
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((...[[[[[[[......)))).......]]]]]]]......

---

RNA: RFA_00710

			AUCUAAAUGACGAGUCCUAAAUGGAACUAAACACAUGUGUUUGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	(((...........(((.....)))...(((((....))))))))
Alterna	[ FASTA input ]	[ sec struct ]	(((.........(((((.....)).)))(((((....))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	.........(((.((.(......).))........))).......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	.((((................))))..((((((....))))))..
Carnac(seed)	[ FASTA input ]	[ sec struct ]	..............(((.....)))....................
Carnac(20)	[ FASTA input ]	[ sec struct ]	.............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..(((..(((........))).........)))))))))
CentroidAlifold(20)	[ 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 ]	..............(((.....)))..(((((((())))))))..
Cylofold	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(.............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	.............................................
DotKnot	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
Fold	[ FASTA input ]	[ sec struct ]	............(((((.....)).))).((((....))))....
HotKnots	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
IPknot	[ FASTA input ]	[ sec struct ]	............(((((.....))).))(((((....)))))...
MCFold (ext)	[ FASTA input ]	[ sec struct ]	((((((((((.((.((((..).)))))))))(((..)))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((.........(((........)))..............))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
McQFold	[ FASTA input ]	[ sec struct ]	..............(((.....)))..(((((((..)))))))..
Multilign(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	.............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	.............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	.............................................
Pknots	[ FASTA input ]	[ sec struct ]	..((........))(((.....)))..((((((....))))))..
PknotsRG	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
ProbKnot	[ FASTA input ]	[ sec struct ]	.............((((.....))).)((((((....))))))..
RDfolder	[ FASTA input ]	[ sec struct ]	(((.........(((..........)))(((((....))))))))
RNASLOpt	[ FASTA input ]	[ sec struct ]	...........................((((((....))))))..
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	.............................................
RNAfold	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
RNAshapes	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
RNAsubopt	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.(((.(.(...........).))))..(((((((..)))))))..
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((.(........((...............))........).)))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	.............................................
Sfold	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	.............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.............................................
UNAFold	[ FASTA input ]	[ sec struct ]	..............(((.....)))..((((((....))))))..
Vsfold4	[ FASTA input ]	[ sec struct ]	.((((................))))..((((((....))))))..
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((................))))..((((((....))))))..

---

RNA: RFA_00711

			CGACUGCUGAGGAGUCCCACAAUAGGGCGAUACGGACGUCCAGUGC
Reference structure (ext)		[ sec struct ]	((((((.......((((.......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((((..(((....((((.......))))....)))..))).....)
Alterna	[ FASTA input ]	[ sec struct ]	....(((((....((((................))))...))))).
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((.(.((((.......))))........).))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	..............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	.((((.......))))...((...(((((.......)))))..)).
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.............((((................)))).........
Carnac(20)	[ FASTA input ]	[ sec struct ]	..............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((..................................))))))
CentroidAlifold(20)	[ 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 ]	.((((.......))))........(((((.......))))).....
Cylofold	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(..............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..............................................
DotKnot	[ FASTA input ]	[ sec struct ]	....((((..[[[[[[[........))))....]]]].]]].....
Fold	[ FASTA input ]	[ sec struct ]	.((((.......)))).(((....(((((.......))))).))).
HotKnots	[ FASTA input ]	[ sec struct ]	.((((.(...).))))........(((((.......))))).....
IPknot	[ FASTA input ]	[ sec struct ]	.....((((....((((........[[[.....))))]]]))))..
MCFold (ext)	[ FASTA input ]	[ sec struct ]	..((((((((((....))))))))))(((((..(((..))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.((((.......))))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	..............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	...(......................................)...
Mastr(20)	[ FASTA input ]	[ sec struct ]	..............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....
McQFold	[ FASTA input ]	[ sec struct ]	.((((.......)))).(((....(((((.......))))).))).
Multilign(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	..............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	..............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((...........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((...........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	..............................................
Pknots	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....
PknotsRG	[ FASTA input ]	[ sec struct ]	.(((..(((....((((.......))))....)))..)))......
ProbKnot	[ FASTA input ]	[ sec struct ]	.(((([[[....))))........(((((.......)))))]]]..
RDfolder	[ FASTA input ]	[ sec struct ]	.((((.......)))).(((....(((((.......))))).))).
RNASLOpt	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	..............................................
RNAfold	[ FASTA input ]	[ sec struct ]	.(((..(((.(..((((.......))))..).)))..)))......
RNAshapes	[ FASTA input ]	[ sec struct ]	.(((..(((....((((.......))))....)))..)))......
RNAsubopt	[ FASTA input ]	[ sec struct ]	.(((..(((.(..((((.......))))..).)))..)))......
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.....((((.((((((((((........)).).)))))))))))..
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	..(((......(.((................))......).)))..
RSpredict(20)	[ FASTA input ]	[ sec struct ]	..............................................
Sfold	[ FASTA input ]	[ sec struct ]	..............................................
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	..............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	..............................................
UNAFold	[ FASTA input ]	[ sec struct ]	.(((..(((....((((.......))))....)))..)))......
Vsfold4	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....
Vsfold5	[ FASTA input ]	[ sec struct ]	.((((.......))))........(((((.......))))).....

---

RNA: RFA_00715

			GGCUAGCAGUGGAAUCCAAAUAGGACGAAACGCGCGUCCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((.....))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	............................................
Alterna	[ FASTA input ]	[ sec struct ]	.(((...)))...(((((....(((((.......))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........(..(..((.......)).........)..)......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	........(..(..((.......)).........)..)......
CRWrnafold	[ FASTA input ]	[ sec struct ]	.............(((((....(((((.......))))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	.........(((...)))..........................
Carnac(20)	[ FASTA input ]	[ sec struct ]	............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((................................))))))
CentroidAlifold(20)	[ 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 ]	.............((((....((((((.......))))))))))
Cylofold	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((..(............................)))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	..((..................(((...........))).))..
DotKnot	[ FASTA input ]	[ sec struct ]	.............(((((....(((((.......))))))))))
Fold	[ FASTA input ]	[ sec struct ]	..(((....))).(((((....(((((.......))))))))))
HotKnots	[ FASTA input ]	[ sec struct ]	.............(((((....(((((.......))))))))))
IPknot	[ FASTA input ]	[ sec struct ]	.............((((....((((((.......))))))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((..)))(.((..)))(((((((((((.....)))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((..((((.(((......).))........))))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((..((((.(((......).))........))))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.(((.....((........................))...))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.((((...((....(((.....)))((.......)))).)))).
MaxExpect	[ FASTA input ]	[ sec struct ]	..(((....))).((((....((((((.......))))))))))
McQFold	[ FASTA input ]	[ sec struct ]	.............((((....((((((.......))))))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	............................................
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((...((...((.........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	........((.(....)...................))......
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((...((.(.((.........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....).....(((...........))).....
PPfold(seed)	[ FASTA input ]	[ sec struct ]	............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)...........................
Pknots	[ FASTA input ]	[ sec struct ]	..(((....))).(((((....(((((.......))))))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	.............((((....((((((.......))))))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	..(((....))).((((....((((((.......))))))))))
RDfolder	[ FASTA input ]	[ sec struct ]	.....................((((((.......))))))....
RNASLOpt	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	............................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	............................................
RNAfold	[ FASTA input ]	[ sec struct ]	.............(((((....(((((.......))))))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	.............(((((....(((((.......))))))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	.............((((....((((((.......))))))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((..........).))..(..((((((....).)))))..)..
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(.(((...(..(..(((.....))).........)..).))).)
RSpredict(20)	[ FASTA input ]	[ sec struct ]	(.(((...(..(..((.......)).........)..).))).)
Sfold	[ FASTA input ]	[ sec struct ]	..............(((....((((((.......))))))))).
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
UNAFold	[ FASTA input ]	[ sec struct ]	.............((((....((((((.......))))))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	..............((((....(((((.......))))))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	..............(((....((((((.......))))))))).

---

RNA: RFA_00716

			ACUCCGUGACAAGUCUCGAAUAGGACGAAAUGUGCGUCCUAGAU
Reference structure (ext)		[ sec struct ]	((((((......((((......))))...(((()))).))))))
Afold	[ FASTA input ]	[ sec struct ]	((..((.((....)).))..(((((((.......)))))))).)
Alterna	[ FASTA input ]	[ sec struct ]	............((((.....((((((.......))))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	.......(((..((((......)))).........)))......
CMfinder(20)	[ FASTA input ]	[ sec struct ]	............................................
CRWrnafold	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
Carnac(seed)	[ FASTA input ]	[ sec struct ]	............................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	............................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((................................))))))
CentroidAlifold(20)	[ 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 ]	.....(.(......).)...(((((((.......)))))))...
Cylofold	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
DAFS(seed)	[ FASTA input ]	[ sec struct ]	(((((..(.............................))).)))
DAFS(20)	[ FASTA input ]	[ sec struct ]	............................................
DotKnot	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
Fold	[ FASTA input ]	[ sec struct ]	..((.(.((....)).))).(((((((.......)))))))...
HotKnots	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
IPknot	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(.((((((((..))))))..(((((((((...))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.((((..((((.((((......))))........)))))).)).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	............................................
Mastr(seed)	[ FASTA input ]	[ sec struct ]	........((..((..........)).........)).......
Mastr(20)	[ FASTA input ]	[ sec struct ]	............................................
MaxExpect	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
McQFold	[ FASTA input ]	[ sec struct ]	.......(((..))).....(((((((.......)))))))...
Multilign(seed)	[ FASTA input ]	[ sec struct ]	............................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	............................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	............................................
NanoFolder	[ FASTA input ]	[ sec struct ]	..(((({(((..))).((..[[[[[[[..)}))]]]]]]]))).
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((..((...((..........))..........)).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	............................................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	...((..((.(.((..........))....).....)).))...
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	............................................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	............................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	............................................
Pknots	[ FASTA input ]	[ sec struct ]	......(((......)))..(((((((.......)))))))...
PknotsRG	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
ProbKnot	[ FASTA input ]	[ sec struct ]	..(.((..........))).(((((((.......)))))))...
RDfolder	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
RNASLOpt	[ FASTA input ]	[ sec struct ]	....................(((((((.......)))))))...
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	....(((..........................)))........
RNASampler(20)	[ FASTA input ]	[ sec struct ]	............................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	............................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	............................................
RNAfold	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
RNAshapes	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
RNAsubopt	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	.(..((((((..))))))..((((((.(......))))))).).
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(.(....(((..((((......)))).........)))...).)
RSpredict(20)	[ FASTA input ]	[ sec struct ]	............................................
Sfold	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	............................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	............................................
UNAFold	[ FASTA input ]	[ sec struct ]	....((.((....)).))..(((((((.......)))))))...
Vsfold4	[ FASTA input ]	[ sec struct ]	............((((.....((((((.......))))))))))
Vsfold5	[ FASTA input ]	[ sec struct ]	............((((.....((((((.......))))))))))

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RNA: RFA_00717

			AUCCAGCUGACGAGUCCCAAAUAAGACGAACGCGCGUCUGGAU
Reference structure (ext)		[ sec struct ]	((((((.......((((......))))..(((())))))))))
Afold	[ FASTA input ]	[ sec struct ]	(((((((((.((.(((........)))...)))).).))))))
Alterna	[ FASTA input ]	[ sec struct ]	((((((...(((.(((........))).......)))))))))
CMfinder(seed)	[ FASTA input ]	[ sec struct ]	........((((.(((........))).......)))).....
CMfinder(20)	[ FASTA input ]	[ sec struct ]	.............(((........)))................
CRWrnafold	[ FASTA input ]	[ sec struct ]	((((.(((....)))........(((((......)))))))))
Carnac(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Carnac(20)	[ FASTA input ]	[ sec struct ]	...........................................
CentroidAlifold(seed)	[ FASTA input ]	[ sec struct ]	((((((........((........))...........))))))
CentroidAlifold(20)	[ 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 ]	((((((.((.((.(((........)))...))..)).))))))
Cylofold	[ FASTA input ]	[ sec struct ]	((((...................(((((......)))))))))
DAFS(seed)	[ FASTA input ]	[ sec struct ]	((((((........((........))...........))))))
DAFS(20)	[ FASTA input ]	[ sec struct ]	...(...................................)...
DotKnot	[ FASTA input ]	[ sec struct ]	((((((...(((.(((........))).......)))))))))
Fold	[ FASTA input ]	[ sec struct ]	(((((((((.((.(((........)))...)))).).))))))
HotKnots	[ FASTA input ]	[ sec struct ]	(((((((((.((.(((........)))...)))).).))))))
IPknot	[ FASTA input ]	[ sec struct ]	((((((.......(((........)))..........))))))
MCFold (ext)	[ FASTA input ]	[ sec struct ]	(((((((((.((((((((((....)))))))))))))))))))
MXScarna(seed)	[ FASTA input ]	[ sec struct ]	.(((((...(((.((((......)))).......)))))))).
MXScarna(20)	[ FASTA input ]	[ sec struct ]	.(((((...(((.((((......)))).......)))))))).
Mastr(seed)	[ FASTA input ]	[ sec struct ]	.((((....((..(((........)))........)).)))).
Mastr(20)	[ FASTA input ]	[ sec struct ]	.(((((...(((.((((......)))).......)))))))).
MaxExpect	[ FASTA input ]	[ sec struct ]	.((((((((.((.(((........)))...)))).).))))).
McQFold	[ FASTA input ]	[ sec struct ]	((((((...(((.(((........))).......)))))))))
Multilign(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Multilign(20)	[ FASTA input ]	[ sec struct ]	...........................................
Murlet(seed)	[ FASTA input ]	[ sec struct ]	...........................................
Murlet(20)	[ FASTA input ]	[ sec struct ]	...........................................
NanoFolder	[ FASTA input ]	[ sec struct ]	((((((.(([[[.[[[.)).....]]].......]]]))))))
PETfold_2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((....(.(.(((........)))...).....).)))..
PETfold_2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)..........................
PETfold_pre2.0(seed)	[ FASTA input ]	[ sec struct ]	..(((....(.(.(((........)))...).....).)))..
PETfold_pre2.0(20)	[ FASTA input ]	[ sec struct ]	...........(....)..........................
PPfold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
PPfold(20)	[ FASTA input ]	[ sec struct ]	...........(....)..........................
Pknots	[ FASTA input ]	[ sec struct ]	((((((((...............))(((......)))))))))
PknotsRG	[ FASTA input ]	[ sec struct ]	((((((.((.((.(((........))).....)))).))))))
ProbKnot	[ FASTA input ]	[ sec struct ]	(((((((((.((.(((........)))...)))).).))))))
RDfolder	[ FASTA input ]	[ sec struct ]	.......................(((((......)))))....
RNASLOpt	[ FASTA input ]	[ sec struct ]	.............((((......(((((......)))))))))
RNASampler(seed)	[ FASTA input ]	[ sec struct ]	...........................................
RNASampler(20)	[ FASTA input ]	[ sec struct ]	...........................................
RNAalifold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
RNAalifold(20)	[ FASTA input ]	[ sec struct ]	...........................................
RNAfold	[ FASTA input ]	[ sec struct ]	((((((.((.((.(((........))).....)))).))))))
RNAshapes	[ FASTA input ]	[ sec struct ]	((((((.((.((.(((........))).....)))).))))))
RNAsubopt	[ FASTA input ]	[ sec struct ]	((((((.((.((.(((........))).....)))).))))))
RNAwolf (ext)	[ FASTA input ]	[ sec struct ]	(((((((...((((((........))))..))...).))))))
RSpredict(seed)	[ FASTA input ]	[ sec struct ]	(((((........((..............)).......)))))
RSpredict(20)	[ FASTA input ]	[ sec struct ]	((((((...(((..((...........)).....)))))))))
Sfold	[ FASTA input ]	[ sec struct ]	((((((.((....(((........))).......)).))))))
TurboFold(seed)	[ FASTA input ]	[ sec struct ]	...........................................
TurboFold(20)	[ FASTA input ]	[ sec struct ]	.(((((.......(((........)))..........))))).
UNAFold	[ FASTA input ]	[ sec struct ]	(((((((((.((.(((........)))...)))).).))))))
Vsfold4	[ FASTA input ]	[ sec struct ]	.(((((.((.((..((...........))...)))).))))).
Vsfold5	[ FASTA input ]	[ sec struct ]	.............((((......(((((......)))))))))

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