I am looking for a sequencing protocol and associates tools to discover one or more consensus sites from DNA fragments digested by a novel enzyme.

The template is plasmid sized and fully characterised, so I can map reads against it.

The fragments range from 10's of bases to 100's and are quite many so I will need to rely on sequencing depth to score the discovered motifs. The small fragments are too short for direct sequencing so I will likely need to concatenate them first without loosing the restriction information.

Does anyone have a primer or links? Thanks