Search with stop codons for last exon
The last exon does not have a splice site pattern at the 3' end but its end is determined by a stop codon (TAG, TAA, TGA). So the algorithm tries to find duplicated exons followed by a stop codon (and not with a splice site pattern at the 3' end of the exon).
Auto: This option makes it possible to autodetect, whether the last exon in the Scipio result is the end of the protein. It searches for duplicated exons with stop codons (instead of a splice site pattern) if the last exon ends at the end of the protein sequence and is followed by TAG, TAA or TGA.
Enable: This option forces the algorithm to look for duplicated exons followed by stop codons for the last exon (and does not use the splice site pattern).
Disable: This option forces the algorithm to use splice site patterns of the last exon to look for duplicated exons as if it is a normal exon in the middle.