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