Using BLAT command line tool to blat split sequences
The FAQ offers an answer:


  I'm setting up my own Blat server and would like to use the same parameter values that the UCSC web-based Blat server uses. 
  
  We almost always expect there to be some small differences between the hgBlat/gfServer and the stand-alone command-line blat. The best matches can be found using pslReps and pslCDnaFilter utilities. The web-based blat is tuned permissively with a minimum cut-off score of 20, which will display most of the alignments. Other than to confirm that your command-line blat is working, there is little use in perfectly replicating the web-based blat results. We advise deciding which filtering parameters make the most sense for the experiment or analysis. Often these settings will be different and more stringent than those of the web-based blat. With that in mind, use the following settings to replicate the search results of the web-based blat:
  
  [ . . . ]
  
  standalone blat:
  
  blat search:

blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 database.2bit query.fa output.psl