# Using BLAT command line tool to blat split sequences

I have the nucleotide sequence:

AATTGAGGCACATTTTTTTTTAGACAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTGATCATAGCTCACTGCAGCCTCGACCTCCTGGGCTCAACAAAGCACACAGTGGGCGGATCCCCACCAG

When I blat this on UCSC Genome Browser, the first hit is a match which spans 6572 basepairs on chromosome 19, and essentially matches the first portion of the sequence to one spot on the genome, and the second portion to another part of the genome approximately 6.5kb downstream.

However when I use the BLAT command line tool, it doesn't find the second half of this match, it only matches the first portion.

Here are the flags I'm using:

-t=dna

-q=dna

-minIdentity=90

-out=blast8

How do I get the command line tool to mimic the behavior of BLAT on UCSC Genome Browser?

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