Starting with IGV v2.3.46, released March 2015, you can do a BLAT (BLAST-like Alignment Tool) search from a feature, alignment, or region of interest, of a sequence up to 8 kb in length.
The default search engine is the BLAT server hosted at the UCSC Genome Browser. UCSC's BLAT search supports most UCSC derived genomes including human and mouse genomes. Change to use a different BLAT server in Advanced Preferences.
BLAT Feature Track
Each query sequence appears as a new Blat feature track in the lower panel of IGV's display. The Screenshot (2015.04.01) shows five different Blat feature tracks for the following sequences:
Manipulate this track just like other feature tracks as outlined in the Feature Tracks section of the Pop-up Menus page.
BLAT Results Panel
Results are presented in a new window that displays the query sequence, location of hits, match score, and other metrics as shown in the Screenshot (2015.04.01). Hits are listed in descending order of alignment score.
For the example hit highlighted in the Screenshot above, the original search sequence is returned as the top hit. The read used in the search was an aligned RNA-Seq read spanning an intron (example b), which the BLAT results show is a singly gapped alignment as indicated by the 1 under the column T gap count.
For example, for ROI2 (marked 1 above), clicking on the second hit in the results panel (marked 2 in Screenshot below) navigates the view away from chromosome 19 to the hit locus on chromosome 22 (marked 3). This same region contains a hit for example c, a BLAT search done with an exon feature. Because the exon feature has a higher alignment score than ROI2, its Blat feature is shaded darker.