For each ortholog set several different statistics are shown. "Totally Conserved Introns" is the number of introns in totally conserved positions (i.e. in positions with introns in all four species). "Gained Introns" is the number of raw gains. "Lost introns" is the number of raw losses. "Other Introns" is the number of other passing introns. "Fail/Homology Positions" is the number of positions that failed because of low conservation or adjacency to a gap. "Fail/Nearby Intron" is the number of positions that failed because of a nearby intron.
Clicking on any alignment opens it up. Each intron position is color-coded and can be clicked to view an explanation of either the reason it failed the filter (light gray) or, if it passed, the evolutionary classification it was assigned: raw gain (blue), raw loss (red), conserved (green), or other (dark gray).