[Genome] possible reasons for sequence masking

[Vanessa Bauer]

Hello,

Sorry to bother you but I was unsuccessful answering the following 
question from browsing your web site.  In short, I am curious if 
there are various reasons for sequences to be masked in an alignment. 
We have downloaded introns for a specific set of loci (roughly 8500) 
for  Drosophila genomes from the Comparative Genomics "group" 
(multiz15way alignments).  We our now attempting to get this data in 
the format that we want (i.e.,  each alignment block linked to its 
corresponding transcript and to mask any part of a intron that is 
also, at times, coding sequence) using the dm2 annotation.  We have 
noticed upper and lower case letters in the alignments.  While I did 
notice that repeats are masked on the web site I was also wondering 
if there is any other reason for masking.  More specifically, have 
intron sequence that are also coding  (due to alternative splicing or 
coding regions within introns of other coding regions) been masked?

thanks, Vanessa