What does the divergent sequences checkbox do?
If you try to align sequences from two different species (or finished mRNAs to draft sequence) using the standard parameters, usually you will get many, many short exons. To force the alignments to be longer and to have more gaps and mismatches (as you will see in interspecies comparisons), the BLAST parameters need to be changed. The mismatch penalty is lowered, and the gap opening and extension penalties are lowered. This encourages BLAST to merge nearby alignments into a single exon; we find that with these parameters, the gene models look much more realistic. What happens when I pick “large intron sizes”? Spidey tries to keep its models compact, so it has a maximum allowed intron size (two, actually — a smaller size for internal introns, and a larger size for the first and last introns). In some cases, though, the intron size of the correct model is larger than Spidey’s maximum intron size, so Spidey cannot arrive at the correct model. If you know that the introns are especially l
