I have found a sequence repeated in various bacteria. There is strong evidence that it is part of a regulatory element. But I would like to find which part of this element is more conserved. Is there a web tool or similar software to find out?
WebLogo might be useful to start with:
http://weblogo.berkeley.edu/logo.cgi
The best way is to generate a multiple alignment of your sequences and then use LOGO application, has already suggested. Moreover you can take a look to the overall alignment and conservation levels at each positions using JalView or GeneDoc. If you have some experience with LaTex you can use the powerful TexShade package that can apply several visualization styles based on conservation and allow a fine tuning of visualization parameters, including LOGO visualization.
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