Online servers will not be able to analyze to this huge data. It can be done by stand alone version of multiple sequence alignment tool.

Dear

Please check some infromations concerning sequence alignment:

-Jaroszewski, L. et al. 2011. Nucleic Acids Res. 39(Web Server issue):W38-44).

-Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ; Gish; Miller; Myers; Lipman (October 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–10.

-Hauswedell H, Singer J, Reinert K (2014-09-01). "Lambda: the local aligner for massive biological data". Bioinformatics. 30 (17): 349–355.

Thank

http://molbiol-tools.ca/Alignments.htm

You can try stand alone blast from ncbi

Hello

I have never heard of such online services. How about stand-alone software?

Mauve (http://darlinglab.org/mauve/mauve.html) is a classical tool made for multiple genome alignment. If you need faster software, you might want to try Mugsy (http://mugsy.sf.net/).

Good luck

Try EBI's MUSCLE http://www.ebi.ac.uk/Tools/msa/muscle/

All online services put certain limits on data size as they don't want their servers to be overwhelmed by a single user.