lncRNA Structure Prediction

Species Name : Withania somnifera Sequence Id : GBHJ01025556.1

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-832.10) is given below.

1. Sequence-
CUAGGGCCCAAAUAACGGCACACAUAGUCAGCCCAGAAAUUUUGGGCUAAGCCCAAUAGA
AGAAUAGGCAAGUCAUACAUAUAAAGACCAAAUAACAGAGGCCCAAUACCUAAGGGAACA
AUACAACAAUUUACGGGCCAGACAGGAAACUCAUACGAAAAUGGCAUGCAAGCAGGCCCG
GUAACAGUCUAUAGUCAACUUGGGUCCCGAAACAAGAGAAAAGGAGCAAUAUACACGAUA
CAUAUAAUAUGUAUAUACUACACAUUUAUACCCAACACAUGUACUAGUAGGAAAUUUAUU
UCUAAGCAUAAGAUAUUCAUAAAGAAUUAUAAGGUCGAUGUUAAUUAGGAAAAAGCUAUU
GAGUUGCUCUAAAUUUAUACAUGUCAUAACAUGUCUAUACAGAUUUUUAUUUUUUUCAAA
AAGGGCCCAAAUCAUUAACAUAGCACCUAGCAGGAAAUGACACAAUUGGUUGGCAUGGAA
AGCUAGGGAAAAAGGCUAUUAGUCAUUAUCAUGAAAAGGGGUAAGAAAUCAACAAGGAUA
AAUGAGAGAGUUAAGAAAACAUUUUAGUUAUCUAAGCAUUCAAACUCGGUCAAAUUAAGU
CUUCAACACAUUAAUCAAAAUAGAUUUCCUCAUUAUAAGCAUUAAGAGUGAAAGAAAAUA
AUUUCAAAGAUUUGUAGUUGAAACUGACACCUCAUUUUGAUUAGACACGAGGGCAAGCAG
AAUCAGUCAUGCACACACUUUCCAUGCAUUAAGAUUCAGCCUACUGACUACAAUAAUCUA
UCAUGCUCAUGUGAGAUAGCAAAUAACUUAGCAUGCUUGUCAAAUUAAUACACACUUACU
AGAUCAAUAUCAUAGCUGAUGACAUUAACAAAAUGCACCAUUUAGAACUGAUCAAGGCAG
CACAAGAGAGGGAUAUGGGAGCGCUGGGCUAUAAUGAAACCAGAAGCAAGUAAUGCAAGG
UAGUCUACACAAGGAUUCAAUUAUCACACCAAUAUAGAAUCAGACACAGGCGAAUAUAAC
ACACUGAGAUGCAGCAGACUUAAACCAAGUAAGACUAUGAGAGCACUAAGUGAACAGCAC
GUAUACAUGGAUGCUUAGACCAUAAUUUCAUCAAAAUUAUAUUAAACAAUGGCUUAUAGA
UAGUCUAAAAUAUCAUGGUACGGAAGAUCCUAUAUACAUACUAAUGCUAGUUAAACUUUU
UCAUAUCAAGGCACCUAACUGGUUAUACAGAAUAAGGUAAGUCAGUUUGAAAUUAAACCA
AGUUGCAGGGAUGACUAAGAGUUCAGUAAACAUCAUACAGAGAAACAUAAAAUAAGGUUU
UACUAAAAAGCAGGAGAUCAGGCAGCUGAGCAGAGACUUAUGCGAAAUAAUUUCACAUUU
AUUGCAGAAAAUAGGUUAGUUCAUGACUGGUUUUAAUUGAGGCUUAGACAAGUAGAGAUA
AACAAGGAAAGCAGCUCAUGAACAAGUGGUUUAUUUACUGGUUCGGAUCAUAAGAAUGAU
UAUAAGGCCUCAACACUUUGGUCACUUGAGCAGAAAGUAGAACAAGAAAGAGAAGCAUCU
AUCACAUCUUUUCAAGAAAAAAAAUAAAAGCCUUUUAAGACAAAAGAAGUUAAGCUUGAG
ACAAGUUCAAUUCACAUCAUUAGUCAAAAAACACCAUUUAACCAGUUCACAUACAACCCU
CAUUAAUUCUACAGUUAGCCUCAAACAAAAGAUGCACAAGGAGGACACCUACUUCUAUCA
UUUUUAUUCAGGCCUUUCACCAGACAAAUAGUUACUUAUAACAGGUCAUUUUCAGGCAAG
AGAUCUACACAUCAGCUUCAUGAUAGAACACAUGGGAUCAAUUAAAUAUAUACAACUAGA
UCAUCUAAGAAUAUGAUAUCACUUUGACAUCUAAGCCAUUUCAGAAAACAAGAUAAGAGA
GAGGACAAGACUGUACAGGGACCUUACGAACUUCAGUCCAAGCAAAAACCAUUCAAUCAG
UAGUUUGCACAGACAGAAGGCAUGCAAGGGACUUAAUGCAUAUUCUCAUCACUUAAUGUC
AUUCAACAAGAAUAUAAAAGGCAUCAUAAAUCUAGCAUAAGGUUACAGUCAGGACAGACU
UGACACAACCAAGGCUGAUCAUUCUUGGAACAACACACUAAGUUAUUACCUUCCUUAAGA
GAGCAUGACAAAAACUAAAAAUAAAUGAUAACACUAACCAGACACCAGACCAUCAAUCAG
UAAACUUAAUUUAUCCAACAAAAUCACAGAUGAGGUUUAGGAGGGACCCUUCUAAAACAC
UGUACAGAGGAUACAUGCAUAUAAUAUGAUACAAAAGAUAGACAGUGUGCCUACCAACAU
GGUUCAAAACAUAUAAUCAUUCAUCCUUAUAAACAUCAAUCAUGCAAGAUCAAAUAGAUG
GUUGAAACAGAAUAAGCAUACUGGGUCUAAUUUAGGGAAAAGUUAUCAAUAUUUUAACUG
GUAAAAAGAGAUUUGCGUGAAAAGGAUUCAAUUUAGACUAAACAAGAGUUUUAGGCACCU
AGAUGCAUCAAAUCAUCAUGUCAUGGGGUAUAUGGAACAAGAGCUGAUCUAAGGAGUGUC
AUAACUAAGAAUUCUAUGCAGCACACAGCCACUAAGGCCUUUGCAUUUAGCAUGUAGACA
CUGUACAACAUUUCAGUUGUUAUAUUUUUGCAAAUGUAUCAGCAUAACAUAUGACAGAUA
GAUACAAGGACUUUAUAUCACCUAUGAACAUAUGGAACUAAGGAUCAUAUUAAUCAACUA
GACAGGGCUAGAUUAGAAACAUGCCAGAUAUAGUCAACAUGCAGGUUUAGAGAGGGAAAA
ACUUUAAAAGUAAACCAAUAGAUAGACUGGAGAGACACAUUCAACUUACAGUAAGCUUGA
UUCUAAGAGAAAAUGCCAUUUUAAGGAAAAUGCAUGAUCAAACAUGGUCCGCUUGAACAC
UGACAAGUAAGUAUGCUAGAUAAAAUGCCAAAACAUUAUAAGUUAGGUCUUAUUGCUUCA
AAAUAAUUAUUCUUUACAAGCAACUAAACCAGUUCUACAGACAUUAUACUAAAUACUAUA
UUAGCACAGCCAGUGAACCAACUAUGAAGACAAGACAAGUAUAAAACAGGAAUCAUUUUC
AGAUUUGCCAAAGUUAAAUUUAAGGAAAAAAUAGCUUUGAAAACAGAGUUUGCAAAGGCA
UUACAUGCCCUUAUGUCACUCAUCCCUUUAAAACAUACACCUAUGGAUUCCUAGGAGGUA
GCUUGAACCGAAUAUCAAACUACACUCCUCUCCUUGGGCAUUCUCAUAAGAUACCAAGUU
AAUGGAUAAGUAAAAAAAAAAGAUUUCAACAUCAAAGUCAUGCCAUUAAUAUCUUACAAG
UCUUCUCCUUUAUCCUUCAUUCACUAAGGUUCCUUAUGUAGGAUAAAAAAGGUAUGAGGU
AAAUAAGCUAAAAACUCAUUUGCUUCUAAUUUUGAGACAGUUUUGAAAUCAAAAGAUCCU
CAGAAACCACUUAACACAGACCAUAUAGGGAUUGAUUUAAAAAAUGAGUGUGGGGUGGGU
UGAGGGAACUUAAUUUAGGACUUGAGGGGUGUCAAGAAGGCCAUUUUAAGACCAACUUGG
GACAAUAGAUAAGUGGCAUAAGAUUACCUCCCCUAUCCUUCAAGUUCUUUUUAGGCAACC
UUGAUGCCCUAAUUGCCAUUUAAAAGAAAGAAAAUAAAUUCUUUCUGGAAGGACUUGGCA
AGUAGUUCAUGGAGAAAAUCAUUUGAAUAUCAAAAACAUAGUGACCUUGCACAUAGACAA
CUUAACUGGGCAUGACCCUAAUACUGGAAUAAGGAUGAGAAAUCCAUAAGACAAGCAAUU
UAGAACCUAAGAACCAACUUAAAACCAAUACCAAACGGUAGACAGACUAUAACACACCUU
GAACUCAGACUUGAAAGAAACAGCACAGAAAAUAGUAAAAUCAAACUCAUUCAAAACUUU
UUUUUGUAUUGUGUACUAUCUGUUGAUAUUAUAUCAUGCCUUUUUGGGGUUAUUUUUGGG
UCUUAUGCCGGGGUUUUAUCGAAAACAACCUCUCUAUCUUUACUGCAUUCUACCCUCCCC
GAACCCACUUUGUGAGAAGAUACUGGGCAUGUUGUUGUUGUAAACUCAUUCAGACAGUGG
CAUCACUAAACAACAUAUAGAUUUGAAAAAUAUAUCACUGAACCAGUGGAAACAAAACAU
AAGCCUCUAAUAGCUAAAACCACC

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 [-907.07] kcal/mol.

2. The frequency of mfe structure in ensemble 1.48721e-53.

3. The ensemble diversity 1155.93.

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