Did you try with another browser on Mac, like Safari or Opera?

Yes. I tried Safari on Mac. It works as expected. See attached images from Safari and Firefox.

Maybe it's related to HWA and font rendering in Firefox. Options > Advanced > General > disable hardware acceleration and restart FF. Then test.

Tried disabling HWA. Does not help.

Argh. Do you know if it's possible to test a public demo of this application? Maybe there is a regression in FF9 (and even FF9+), who knows...

It is a website that anyone can access. All you need is input protein sequences which can be downloaded for free from a database like uniprot.

Anyhow, I just realized that the additional information I have posted along with the question is buried under the 'More System details...' link. Please follow these steps to see what I am talking about:

1. Go to http://www.ebi.ac.uk/Tools/msa/clustalw2/

2. Enter the following as-is in the 'STEP 1' box: ('>Seq1' should be in first line and the sequence should be in the second line. Leave an empty line and do the same for seq2)

>Seq1

ACDEFGHIKLMNPQRSTVWY

>Seq2

ACEEFGGIKLMNPQRRTVWY

3. Hit 'Submit' A sequence alignment will appear. In firefox, the protein sequence is displayed in sans-serif font instead of monospace.

Sorry, I missed too the details about your STR. I tried with FF9.0.1 on Win 7, the alignment is fine (see my pic). Did you test with a new Firefox profile? I could be help.

Indeed your alignment looks exactly how it is supposed to look. When I try it from Firefox installation on Ubuntu Linux machine, I get the expected monospace alignment. It appears to be a mac-specific thing.

I have tried using a new profile. I see the alignment in serif fonts but that is probably because I changed the default to sans-serif in my profile. I also deleted the entire firefox directory from the User's Library folder in Mac and fired up the browser hoping that I will start with a clean slate. Inspite of that I still see the alignment in serif and not monospace.

I have observed the same behavior in Firefox 8 also.

I asked Mac user (OSX 10.7.2) to test with FF9, he got the same result as me, see http://imgur.com/ktpOS

So I think you changed the settings about fonts and now, rendering is badly affected. Anyway using a new fresh FF profile should fix the issue if the font settings are limited to the profile (I don't know Mac OSes), but that's clearly an issue on your side.

I have completely deleted the Firefox app from my computer using AppCleaner and installed it fresh. In spite of that I have the exact same problem. What else can I do?!

I figured it out! Thank you for all your replies.

When completely deleting Firefox app did not fix the problem, I suspected that it may be an issue with the fonts. So, I went to the FontBook app and noticed that there was an issue with the Courier font (which is the default monospace font). Once I fixed that, everything is working fine.

Great. I hope you have kept a backup of your profile anyway... ;)