protein and even raw-text dot-plots support added to UGENE 1.10. Now you can use it even to compare you programming language source files
about huge number of sequences:
1) open them all as a single sequence (use merge option). The regions for original sequences will be highlighted with annotations.
2) Run dot-plot for this merged sequence and see the matches.
If you can describe the algorithm to use to filter the results, there will be possible to use UGENE Workflow Designer as a runner for the batch job to produce only filtered results.