Most Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse Genetic Distances

Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance
I would like to know what is the most sensitive method to search sequences ranging from 100bp to 1000bp against a whole genome assembly of another species, for genetic distances similar to human-mouse.
As an example, if I have human sequences ranging from 100-1000bps, what is the most sensitive tool and parameter options to find hits in the mouse genome?
I've been recommended to look at blast and blast+, but it would be great to hear about specific parameter settings or different options.