Search with start codon for first exon
The first exon does not have a conserved splice site pattern at the 5' end but its beginning is determined by the start codon (ATG) coding for a Methionin. So the algorithm tries to find duplicated exons beginning with ATG (and not with a splice site pattern at the 5' end of the exon).
Auto: This option makes it possible to autodetect, whether the first exon in the Scipio result is the beginning of the protein. It searches for duplicated exons with the ATG start codon (instead of a splice site pattern) if the first exon begins at the start of the protein sequence and starts with ATG.
Enable: This option forces the algorithm to look for alternative exons with ATG as start codon for the first exon (and does not use the splice site pattern).
Disable: This option forces the algorithm to use splice site patterns of the first exon to look for duplicated exons as if it is a normal exon in the middle.