Columns are organized by exon type: Constitutive, Cassette, Multiple Splice, Intron Retention, and all exons counted together (All Exons). Rows 1–2 show ExAlt performance using an input exon and default parameters from Table 2 (ExAlt-Exon) and no informant species (ExAlt-Exon-ab initio). Rows 3–5 show ExAlt performance using an input coding frame with default parameters (ExAlt-Frame), no informant species (ExAlt-Frame-ab initio), and at most 1 exon predicted per test sequence (ExAlt-Frame-Single). Rows 6–8 show ExAlt performance using no gene structure information with default parameters (ExAlt-Default), no informant species (ExAlt-Default-ab initio), and at most 1 exon prediction per test sequence (ExAlt-Default-Single). Output is shown for three single isoform gene finders N-SCAN, Augustus, and SNAP.