Useful Links:

Repbase update, a database of sequences representing repetitive DNA of different classes (including SINEs) from different eukaryotic species (Jurka 2005).
GeneDoc, a multiple sequence alignment editor (Windows only) with a highly convenient Find tool (F9) that allows fuzzy string search in the sequences.
Genomic tRNA Database, a database of tRNA genes and sequences from a variety of species (Juhling 2009).
mfold, a tool for predicting the secondary structure of RNA using thermodynamic methods.