server for finding kmers in set of sequences
One Codex is powerful and user friendly, and works in a similar way to Kraken underneath
https://www.onecodex.com/

The Kaiju web server might be of interest and is more sensitive than exclusively k-mer based methods
http://kaiju.binf.ku.dk/server

The title of this question is misleading – it sounds like you're actually looking for a webserver for taxonomic classification using k-mers.