lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-572.97) is given below.

1. Sequence-
CUUCACUCUUCUAUUCUAUCUCUAUUCGUUUUACUCUCUUUUGCAAAUUAAGACACAAUC
UUGAUUCUCCUUCAUAUUUUCUAUUUGUUGCUCAUAUUUUCUUGAAAAACAACUAGAAAG
AUCAAAUGGGUCGAGCCAAGAACUGGGAUGCCUAACUUGUUUCUUGUAAGUUAUUUGCAA
UCUCAUAAAACUGAGCUAAAAACUGAUUUGAUGGGUAAUUUUUCCAACUUUGUUGUGUGU
UCUGUUACAUGCUUUUUUCAACCUUGGUUGUGGGAAAAUCUUGUAAAGUUGCUUGCUUUU
GCACUGAAUCGUGUUUUCUUGUUCUUGCAAGUGUUCACAUGUAUGGCUAUAGGUGGUGGA
GAUAAAGAAUCUAUCUUUUUGCUGUAGUGGUUUCUGCGUUACCACUAUUUCUCAUCCAUU
UUGAAGAUUUUGGUCUUUGCAUUUUUUCUCUUUUUGCUCAUAUUGUCUUGAAAAACAACA
AAAAGAUCAAAUGGGUCGAGCAAACAACUGGGAUUCCUAGAGGUUUCCUGUAAGUUGUUU
GUAAUCUCAUAAAACUAAGCUAUAAACUGAUUCGAUGGUUAUUUUUUUCAGGGAUGGCUU
UUGUUUGUUGGAAAUUCUCUUUCAGUUGCUUGCUUUUUUUAAUGAAUUGUGUUUUCUCGU
UCUUACAAGUAUUGGCAUGGAUGGUUAUAUAAAGAACCUGUCUUUUUGCUGUAGUAGUCU
CUGCAUUACCAUUAUUUCCCUCCCAUUUUGCACGAUGUAGUCUCUGCAUUUUUCUCUUUU
UUGCUCAUAUUUUGUUGAAAAACAACAAAAAAGAUCAAAUUGGUCGAGCCAAGAACUGGU
CUUCCUUAUAGGUUUCUUGUCAGCUCUUUGUGAUCUCUUAAAGUUCUACUUUUGGUUCUG
UGAUCAAACUGAUUUGAUGGGUACUUUUUCAACUUCGUGGUGUGUCUUCCUGCUUAGUUG
UGGUUCUGUUAAAUGGUUUUUUUUCAGGGAUGGUGGCCUUUGGUUGUGGGAAAAUCUUGU
GAAGUUGCUUUGCUAUGUUUACUGAAUUAUUUGUUCUUGUUCAUAUAAGCACUUACAUGU
UUAUAUGGUGGAGAUAAAGAAUCCGUGUUUUUGCUGUAGUUAUUUCUGCUUUACCAUUUA
UUUCUCUUCCAUUUUGAACAUUUUGGUCUUUGCUUCUUUCAUCUUUUUGCUCAUAUUUUC
UUGAACAAAACAACAAAAAAGAUCGAACGGGUAGAAGCAAGAAUUGGGUUUCUUGUAAGA
UUCGUAAGUUGUCCCCUUUUUGGUUUUAUGAUCAAACUGAUCUGAUGGAUUUCUUCCUAC
UUUGAUGUGUGUAUGGUUUUAUCAAGGCUGGUCUUGUUUGAUGAUAAUCUUCUGAAGUUG
CUUGCUUUUUUUCUUUUACUGUAUUGUAUGGAUAUCUAUAAGAAGUGAAGAUAAACAUUC
UAUCUGUUUUUGCUGUUGUGGUCUCUGCAUUUCCAUUAUUUCUCUCCCAUUUGCACAAUC
CGUCUUCAACUGCAGCAGCUGCUAUUAUUAAUUGUCUCAUGUAUCUGGGUUCGAGCGGUG
GAACCAGUCAAUAAGCUGUCUACAUCUCGCUUCUUGGGAUGCUGGCCUUCCUCGUACCUU
GCUAACACGGGGUUCUUUGUGCACCGAGCUGCCGUUCCCCAUAAUCUCAACCUUGGAAAU
CUUGAAAUCUCUAAGUUGUCCCCUUUUUGGGUCUCUGAUCAGACCAUUAUGAUGGAUGAU
UCCUACUCUGGUGUGUGUAUGGUUUUUAGCAUGUUUGGUCUUGUUUGUGGAAAUAUCUUC
UCAAGAUGCUUGCUUUUUUGUUCUAUUGUGUCUUCUUGUUCUUGCAUUUACGUGUAUGGC
UAUUAGGGUAUAUGCGGAGAAGAUGAAGAAUCUAUCUUUUUGGCUGAAAUGGUCUAAGCA
UUUACAUUAUUUUCUGUCAUUUUGCAUAAUCUGGCUUCAAUUAUAACAGCUAAUGUUACU
AAUCUUCUCCUCAAUCUCAAAUUAGGAAAAUCUUGAAAUAUCUGUCAAGUUUGUUCCAGC
UCAGAUCUUAUUAAGAGUUGUUUGUUUUUUGUUGGUCUUGUAUCUUUCUAAUUGAUAUUA
CUACUUUUUGUGGUAUAUCUACUAACCUAACUACAUUUCUUUUCCACUUUUUGCUAGUUU
UAUUCUCGAUGUUGGUAUAUGGAAGAUCUGGGUCACUGAAUUUCUGUGGUUAGUCUUACU
AUCUGCUGUUCCAUUUGCUUUCUUUCGUGCUAUUCUUUUAUGUCUUUUCUUUGCUUCAAA
UUCUUAUUUAUUUUUGGGGGGUUUGUAGGGGUUUCUAGCAGAAACAGUCUCUUUACCCCA
CAAAAAGGUAGGGGUAGGGGUUGCAGAGCUUGGCGUCCUAUAAAUAUUUUGGACAUGAAA
ACCUCAGUACUUUUUUAAAGGGUUAUUGCAAUUGAGCUAAGUGAACAUGAGUUACGUAAU
CUGAGAAGAAAGUUGUUUAUAUUCCACUGAGUUCUUUUAAGG

2. MFE structure-
......((((((...........(((((((((((((((..(((((((((((((.....))))))))............(((((.(((((..(((........)))..))))).)))))((((...(((((..((((...(((((.((((((.(((((((.......)))))))...(((((.((((.(((..((((....
((((((......(((.....((((((((......((((((......))))))..(((((((...(((..(((((((..((.((((((((.....)).))))))..))...(((....(((((....)))))....)))......(((...((((((..............))))))....)))((((((((.........
))))))))))))))))))..)))))))..(((((((((....((((((.....................))))))......)))))))))(((((....((((((((((((((..((....))..))))...))))))))))...))))).((((.(((((((...((((.................))))..)))))))
..))))))))))))..)))..))))))....))))..))).))))))))).........(((((((((.((..(((..((((((((........)))).))))......(((((......))))).(((((.....(((((.((((((.(((.(((((((...)))))))...........(((((((.((((((((...
..)))))))).((((((..((((((((((((((((((........(((((((((.......))))...)))))........)))))).....))))))...))))))..)))))).)))))))......(((((..((((........)).))..)))))......))).)))))).........)))))))))))))..
)).)))))))))......(((((...((...))....))))).((((.....))))....(((((((((((......)))))))))))..(((((((..(((....((..(((((((((((......((...((((.....(((...........))).....))))....))............((((.(((.......
.))).))))((((((..((.....(((((((((((((((((((......))))))).......((((((......((((......((((.(((((((.((((....(((.....)))..((((((((............))))))))..))))..))))))).))))......))))..))))))..(((.(((((.(((
...(((((........)))))..)))))))).)))..))))))))))))))..))))))((....((((......................))))....))......)))))))))))..))....)))..)))))))..)))))).)))))(((..(((((..((((......)))))))))..)))((..(((((..(
((.......((((((...........))))))........))))))))..)).))))))))).))))((((.(((((.((......)).)))))))))..((((((..((((..((((.((.((((.......(((....))).....)))).)).....(((((((((((((...((....((..((((((..((((((
(((((((((..................)))))))..(((....)))....((((((((.((....)).))))))))))))))))(((((..........(((((((..(((((..((((..................................))))..)))))..))))))).........))))).............
....((((...(((((........)))))....)))).((((((((((....(((((.(((..(((....((((((...(((((.........)))))((((((.....)))))).....))))))..))).))).))))).((((.....((((((..((......))..))))))..)))))))))))))).......
.....((((.((((...)))).))))..))))))..))..))...))))))..........(((....(((((((((..(((((((((..((((((.(((((....((((((((((...))))))...))))..))))).)))))))))))))))..)))..))))))...)))((((............))))..))))
))))))).))))....))))))....)))))..)))...)))))).))))))...........)))))).................................

You can download the minimum free energy (MFE) structure in Vienna Format

II. Results for thermodynamic ensemble prediction

1. The free energy of the thermodynamic ensemble is [-618.49] kcal/mol.

2. The frequency of mfe structure in ensemble 8.35142e-33.

3. The ensemble diversity 614.56.

4. You may look at the dot plot containing the base pair probabilities [below]

Download Dot plot JPG EPS

III. Graphical output

1. A note on base-pairing probabilities:--

The structure below is colored by base-pairing probabilities. For unpaired regions the color denotes the probability of being unpaired. The reliability information of RNA secondary structure plot in the form of color annotation, Positional entropy ranging from red (low entropy, well-defined) via green to blue and violet (high entropy, ill-defined).

Download RNA structure JPG EPS

2. Here you find a mountain plot representation of the MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure. Additionally we present the positional entropy for each position. The resulting plot shows three curves, two mountain plots derived from the MFE structure (red) and the pairing probabilities (black) and a positional entropy curve (green). Well-defined regions are identified by low entropy.

Download mountain plot JPG EPS