Hi @Manolis1
Please see the tools in the group “Motif Tools”. Galaxy EU https://usegalaxy.eu has a few more tool options than Galaxy Main https://usegalaxy.org.
Screenshot for EU:
Depending on how your motif was generated/formatted already, you may be able to go straight to the FIMO tool.
There are many more motif discovery/analysis tools in the ToolShed that could be installed into your own Galaxy server. Some of those are also likely hosted by other public servers. There isn’t a good way to batch search by tool against all of them (yet!), so you would just need to review to see if any of the servers have tools that meet your needs: https://galaxyproject.org/use/
Others might know more about the best tool/s or public server/s to use … so more replies are welcomed.