To perform a screen of genomic regions your alignments need to fulfill some
requirements: The identifier of the first sequence in the first alignment
is used as reference. Each provided alignment must contain a sequence
with this identifier and at least for this reference sequence correct
genomic positions must be provided in the alignment. The identifier can be
of the form species.chrom. In that case each alignment is required
to have a sequence from the reference species. Refer to the help pages for additional information an examples.