I'm looking to run miRNA target prediction analysis on a miRNA dataset in an aphid species. I'd love to be able to use one of the programs that combine MiRanda, PITA, RNAHybrid, etc.; however, they all seem to only be available for select species: human, mouse, fly, and maybe more.

Are there any that will allow me to submit a custom miRNA dataset and run it against any genome?

Even if there was a tool to make comparing the outputs of these programs easier, I'd appreciate that. I don't have any experience with SQL Databases that people seem to use for this.