Click on the menu at the left to see which of the following sequence input methods are available.
Type in sequences
When this option is available you may directly input multiple sequences by typing them. Sequences must be input in FASTA format.
Upload sequences
When this option is available you may upload a file containing sequences in FASTA format.
Databases (select category)
When this option is available you may first select a category of sequence database from the list below it. Two additional menus will then appear where you can select the particular database and version desired, respectively. The full list of available sequence databases and their descriptions can be viewed here.
Submitted sequences
This option is only available when you have invoked the current program by clicking on a button in the output report of a different MEME Suite program. By selecting this option you will input the sequences sent by that program.
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Select an available sequence database from this menu.

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Select an available version of the sequence database from this menu.

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Select an available tissue/cell-specificity from this menu.

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Selecting this option will filter the sequence menu to only contain databases that have additional information that is specific to a tissue or cell line.

This option causes MEME Suite to use tissue/cell-specific information (typically from DNase I or histone modification ChIP-seq data) encoded as a position specific prior that has been created by the MEME Suite create-priors utility. You can see a description of the sequence databases for which we provide tissue/cell-specific priors here.

Note that you cannot upload or type in your own sequences when tissue/cell-specific scanning is selected.

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Enter text naming or describing this analysis. The job description will be included in the notification email you receive and in the job output.

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Data Submission Form

Perform motif discovery on DNA or RNA datasets for short regular expression motifs.

Select the type of control sequences to use

Select the sequence alphabet

Use sequences with a standard alphabet or specify a custom alphabet.

Input the sequences

Enter sequences in which you want to find motifs


Input job details

(Optional) Enter your email address.

(Optional) Enter a job description.

Advanced options hidden modifications! [Reset]

How should the search be limited?

Can motif sites be on both strands?

Warning: Your maximum job quota has been reached! You will need to wait until one of your jobs completes or 1 second has elapsed before submitting another job.

This server has the job quota set to 10 unfinished jobs every 1 hour.

Note: if the combined form inputs exceed 80MB the job will be rejected.