[Genome] lower case Letters and repetetive sequences

[shlomit farkash]

Hello,

 

First, thanks a lot for this very helpful site and for your helpful
assistance in the past...

 

I have downloaded genome version (hg17), I assumed that the lower case
letters are repetitive sequences, however, when I was looking for a
pattern of 18bp, I found many patterns that were in lower case and
appeared only once in the genome... since it surprised me, I tried to
look for one of these 18bp patterns (for example: gaattcaaaggctaatgg in
BLAT, but it failed (it found no matches)...

My question is if there is a way to make sure that the sequence indeed
occur only once although it is a repetitive sequence (use BLAT in the
command line with some flags?), I have many such examples and the only
explanation I have is that sequences that were defined as repetitive
sequences don't have a clear consensus, but rather fall into some
defined categories

 

What do you think and am I missing anything here? 

 

Thanks a lot,

Shlomit Amar-Farkash