[BiO BB] checking conservation of short sequences

[T Joshi]

Hi,
I have some small short sequences of less than 40nt. I want to check
if they are evolutionarily conserved across some species.

One way I could do so is to download conservation track from UCSC in
.aln format and use that with clustalw or clustalx for alignment  with
my query sequences. Blastn also doesn't have any database containing
information on conservation.

Could you suggest some other way by which I could do so without
downloading the conservation track ?

Thanks a lot..