| GeneSeqer | GenomeThreader (w/out intron cutout) | GenomeThreader (with intron cutout) | |
| total output | gsq-OSchr10.out9 | gth-OSchr10.out9 | gth-OSchr10-IC.out9 |
| parameter settings | parameters.gsq | parameters.gth | parameters.IC.gth |
| alignments the same | struct_same.gsq | struct_same.gth | * |
| struct_same.IC.gsq | * | struct_same.IC.gth | |
| alignments similar, but on opposite strands | strand_diff.gsq | strand_diff.gth | * |
| gene structures differ, but at same locus | struct_diff.gsq | struct_diff.gth | * |
| struct_diff.IC.gsq | * | struct_diff.IC.gth | |
| cDNA maps to different locus | locus_diff.gsq | locus_diff.gth | * |
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