lncRNA Structure Prediction

Species Name : Withania somnifera Sequence Id : GBHJ01033075.1

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-406.72) is given below.

1. Sequence-
AAAUUUUCCUUUAUAGUUUUCGGGCAACUUUAUUUUCCAAGGAUGACCAGCAGUGACCAU
CAUCCUAGAUGCAAAGCAAGUCUAAGGGCACACUUGUUUGUACUAAAAUGGAGGUCUUAA
UCUGAACGGUUCGUAUCUUAGAUCAUUAAGAGCGUUGCUUACGCCAAGAUUUAAACAUUU
AUUUUCCUUUUCAAAAGAAAAAAGAUUUAAAAUGUUAAAAUCUUCACCACCACUUUGUCG
ACAACAACCUAUCUCCACCACUAACCACCAGGGGCGGACCUAGAGGGGUGUUAGGGGGUU
CACACGAACCCCAUCGGCAAAAAAUUACAUUAAAUGUAUAACGUAUAUUCUCUAUAUUUA
UGUACAUAUACUAAAUUUGAACCUCUUCAACAAGAAGAAAAAGAUAGUUCAGUGGCACAC
AGUCUCUGAAAUGUUGCUUUCCGUGUUGCUAAGGUUCCGGGUUUGAACCUGAAGGCCAGC
AUCUUCUUUUUUUAGUUAGCAAUAUUUUUUUCAUUUAAUUCCAUAAAGGAACACAUCGUU
CCCUUUCCUUAUUUAAAAUAAAAAUGGUUGGAUUUGUAAUCCCAAUUACCAAAAUUAAAG
UUCUAAUUUCCAACCCAAAAUCAAAUCUCAGAACUUCUUGGAUUCUUCCUUCUUUACCCA
AAAUUCAAGAGACAAAAAUCAAAAUCAUCUUUCAUCCUCUCCAGUUGAAUUUCAAACCGC
AAUCUAAAGCCGAGGUAAUCUCUUCUCUCUAUUUUUCUUAAAAUUUUUUGGUCUCUCUUU
GGCUAUCUUCAUUCUUAUGUUGUAAAAUUUUUCGUGAUUUUUUCUUCACUCUUUUUGGAG
UUUAUACUUAUUAUCCUAGUUCUAGAUUGACGUAUUGUGAAGGACUAAUGUUUUAUUGUA
CUUAGCACCUUAGUUUUAUAUGGACAUAUUGUAAAGGGCUAACUUUUUUGCUUUACUGUA
AUUAGUCUUAUUAGUUUCAGGUCUUUUGCGACGAGACUAACUUUUUGUACUUAUAGACUA
UAUACUACCGCAUCUCUUGGAACUAUAGUUUCUUGGUUUAUUCAUAGGUUUCUAUUAUUU
AUUUUUCGAACCCCUGAGUGAAAAUCCUAAAUCCACCACUGGGGCCAGAUCUAGAGGGGG
AGAAGGGUUCACCCGAAACCCAUCAGCAAAAAAUUACACUAUAUAUGUAAGGUAUUUUAU
AAUACUUUAUGUAUACAUAUAGAUUUUGAACCUCCUAAACAUCAAAUUGAAGAUUGGCUU
AGUGACUGAGGUUCCAAGUUCAAAACUCAAACACUAUAUUUUUAUUUUUCAAACCUCCUU
AGUGAAAAUCCUGGAUCCGUCACUGCUAACCACCUAUGCCAUCACAAUUACCAUCACCAC
AAUCAACCAACCGCUAUCGCCAACCACCAACCAACUCUAUCAUCACAACCACCACUAUCG
GUCACUACCACAUUUACCUUCAUGAUUAAAAUUAUUCCACGGUCAUGGCCACCACUAUCG
GCUCCGCUACUAUAGACAAUUUCUACUACCAACCACCUUCACAAUCACAGCUAGCACCUU
CACUAACUACCACCAACACCAUCAUCAACCACCACAUUCUUCUAGCACCACCAUAACAUC
GUCAACUACUAAUAUCAACCAAUUCGAUCAUUAAAACUACUACCAACUGCCACCAUUGCG
CCAGUCACUAUAACACCAACCUCUUCACCAUCAUAACUAUCACAACCAUCAUUACUAGCC
ACUAGCACCAAUCAUCAAUAUCACCACCACAACAUAAACCAUCUCAACUAUCACUAGCAA
AUAUAAAUUUUUCACUUGCACUCAAGGGUGUGCCUUAGUGGUCAAUGAGGUGGGUAAAAA
ACCAUAAGGUCUAAAGUCUCAGGUUCAAAUCCUAGCGGAGACAAAAAAAUACUAGGUGAU
UCUUUCCAUCUGUUCUAGCCUUGGUGGAUAGAGUUUUCUGGUAGCAGUUGCUGGUAAAAG
GUGGUAGGUAUUCUUUCCAUAUGUUUCACUUUUUUAUCAAAUAAUGAUUUUAUUUUAUUA
AUUUUAUCAAAUAAGGAUUAAAGUAAUAUACUUU

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

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

II. Results for thermodynamic ensemble prediction

1. The free energy of the thermodynamic ensemble is [-441.28] kcal/mol.

2. The frequency of mfe structure in ensemble 4.41973e-25.

3. The ensemble diversity 473.13.

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



Download Dot plot

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

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

* Results have been computed using RNAfold ViennaRNA-2.5.0.
* An equivalent command line call would have been RNAfold -p -d2 --noLP < test_sequenc.fa > test_sequenc.out
* A dot plot into the mountain plot coordinates transform using mountain.pl test_sequenc.fa | xmgrace -pipe