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