You can now export genomic regions from Wormbase directly: In the upper right drop-down menu button, select "Download Track Data". Click the "Configure..." button. Dump selected features using version 3 Across currently visible region. Check "Save to File". Check "Embed DNA sequence". UNCHECK "Include track configuration data". Click "Go". Open the resulting .gff file in the latest ApE.
Alternatively, you can export a genomic region (from the genome viewer) as a FASTA formatted file (using the menu on the upper left). You can add the feature tracks by downloading the GFF3 feature track files using the same menu. In ApE, open the FASTA file, then use the Features menu to open the GFF3 track info.
Another way to go is to take the gene model (from a gene page), paste it into an ApE window and then select all, make a new feature (Feature menu), and in the edit feature window that appears press the "upper case only" button.
If you think that ApE doesn't find all of the ClaI sites (or XbaI or BclI) that you KNOW are present in your sequence, turn off the Dam/Dcm methylation on your sequence and try again.
See here for more information.
Click here to make a voluntary donation in support of ApE.