Welcome to the Multilign Web Server

The Multilign server takes three or more sequences, either DNA or RNA, and folds them into their common lowest free energy conformations. Additionally, it creates an alignment file of the sequences. Note that sequences must be entered as a group in this server. Sequences can be entered either as a FASTA file with multiple sequences, or manually in the sequence box.

If you plan to leave this page while waiting for calculations to complete, please make sure you have entered a valid email address below. Leaving this page without entering a valid email address will render results inaccessible.

If you need specific help using the Multilign server, please click here.

February 14, 2018:
RNAstructure tools have been updated to version 6.0.1 which includes several improvements.
Please contact us with any questions or issues regarding this update.

Select Sequences Input:

Select Sequences File:

- OR -
Enter your sequence content below (replaces upload if present).
Sequence content should be entered in FASTA format, with a proper FASTA header on a line preceding each sequence.
Please enter headers and nucleotides only, no comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.

Sequences: (Example sequences have been displayed.)

> RA7680
GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU CCACCA
> RD0260
GCGACCGGGG CUGGCUUGGU AAUGGUACUC CCCUGUCACG GGAGAGAAUG UGGGUUCAAA UCCCAUCGGU CGCGCCA
> RD0500
GCCCGGGUGG UGUAGUGGCC CAUCAUACGA CCCUGUCACG GUCGUGACGC GGGUUCgAAU CCCGCCUCGG GCGCCA

Select Nucleic Acid Type:

DNA:
RNA:

Select Multilign Options:

Default Data If a default value is left blank, the value is treated as if it was not changed at all. Iterations: Maxdsvchange: Maximum % Energy Difference: Maximum Number of Structures: Structure Window Size: Alignment Window Size: Gap Penalty: Temperature (K):

Optional Data

Allow Single Base Pair Inserts:

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Address to Email Results:

RNAstructure

Web Servers for RNA Secondary Structure Prediction

Welcome to the Multilign Web Server

Select Sequences Input:

Select Nucleic Acid Type:

Select Multilign Options:

Designate Address to Email Results: