Additional File 3: List of software parameters that differ from default.

Program	Parameter	
SeqClean	-l 50	
RepeatMasker	-lib arthropodRepeats.fasta
this “custom” repeats library is a download of all Arthropod and shared (ancestral) repeats from RepBase Update (23) in August 2008	
CrossMatch	-minscore 20
-masklevel 100	
CAP3	-d 400
-o 21
-s 900	
BLAST (for clustering)	-p blastn -q -3 -G 2 -E 4 -K 0 -v 1 -b 1000 -e 1e-4	
BLAST (for annotation)	-v 200 -b 5 -e 0.01	
Interproscan	-trlen 30 -goterms -iprlookup -appl blastprodom fprintscan hmmpfam hmmsmart profilescan