I'm looking for a tool to search for an unusual criteria of repeats. Specifically, I'm trying to find pseudo-repeats that are:
- ~ 1000-2000 bp long
- interspersed fairly rarely (~ once every 1-20 Mb) - which means, they cannot be tandemly repeated!
- chromosome specific
These repeats need not be completely homologous (70-80% sequence homology is OK). The motivation is that I'd like to develop chromosome-specific DNA-FISH probes that are degenerate - that is, they label multiple regions of the same chromatin fiber.
I gave RepeatMasker a shot but it isn't quite amenable to making this strange search. Recommendations greatly appreciated!