Welcome to the Predict a Secondary Structure Common to Two Sequences Web Server

The Predict a Secondary Structure Common to Two Sequences server takes two sequences, determines common secondary structures, and and calculates base pair probabilities. Additionally, it creates two alignment files of the sequences. Both sequences, as well as the resulting alignments, can be restrained using constraint files. Note that if an error is encountered in calculations, it may still be possible to do other calculations on one or both component sequences independently without errors. Note also that the server assumes the sequences are RNA.

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 Predict a Secondary Structure Common to Two Sequences server, please click here.

Note: The maximum sequence length has been increased for several tools. Please see Sequence Limits for details.

Select Sequence 1 Input:

- OR -
Enter your sequence title and content below (replaces upload if present).
Please enter nucleotides only, no headers or comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.




Select Sequence 2:

- OR -
Enter your sequence title and content below (replaces upload if present).
Please enter nucleotides only, no headers or comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.




Select Dynalign Options:

If a default value is left blank, the value is treated as if it was not changed at all.




Select PARTS Options:


If a default value is left blank, the value is treated as if it was not changed at all.

Specify the minimum and maximum probabilities to show on the dot plot.
If a specified probability is out of range, it is ignored.



Designate Address to Email Results: