Hi 

Please suggest me some good motif discovery tool that should work on the mentioned data details.

I have certain number of sequences out of which a subset of sequences have have a common motif. 

Have you tried any of the packages in the MotifDiscovery view?

http://bioconductor.org/packages/release/BiocViews.html#___MotifDiscovery

I would start by exploring these options. In particular motifRG and rGADEM look promising even though I have no particular experience with these tools...

H.