[Genome] BLAT- commandline and web results differ

[Tan Hui Hui Jenny]

Hi,

I have tried to replicate the web BLAT results on the standalone blat
The options I used were:
blat -stepSize=5 -minScore=0 -minIdentity=0 -mask=lower   (.....etc
etc....)

These are exactly the instructions given at
http://genome.ucsc.edu/FAQ/FAQblat#blat5.

However, some sequences that I expected to show 100% hits against some
human chromosomes did not have a hit at all in the standalone blat
whereas they appeared in the web BLAT results.

Can someone shed light on the discrepancy or what did I go wrong? 

Thanks for ur time in answering this.....

-jenny