David:
> 
> Question I: what are the small letters and what are the capitals here?
> Are these already masked, exons/introns or what?
> (I downloaded some of these sequences and repeatmasked myself. My pasked 
> sequences overlap with some of "yours" written in small letters.)
> 

In case of mouse the sequences are extracted from softmasked genomic builds 
retrieved from UCSC. So, small lettres = repeats, capital letters = no repeats.

> Question II: Is the strand "honored" by these tool?
> I guess I remember from my old experience that there was an issue although I 
> can not recall what exactly.

Yes, if the strand is explicitly specified. If it is not specified it is 
assumed to be +.

Thanks for using Galaxy.

anton

> 
> Thank you in advance,
> 
> David
> 
> 
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