Why does the MEME web application limit the sequence file to 60,000 bytes?

[CharlesEGrant]

The problem is that the running time of MEME grows as the square of the size of the input file. Files much larger than 60kb would end up monopolizing the server. 

Depending on the nature of your sequence data you may be able to get around the size limit by using MEME-ChIP rather than MEME. MEME-ChIP randomly samples 600 sequences from your data and trims each sequence to the central 100 positions before analyzing it with MEME. This was intended for use with ChIP-seq data where there is a lot of redundancy in the sequence data, but it can be applied to other data sets as well.

Alternatively, if you install your own copy of the MEME Suite software you adjust the maximum allowed size for sequence input using the '-maxsize' command line option to the MEME command line.