Table 3. Summary of high-probability CyHV-3 pre-miRNAs Identified using both approaches.

Pre-miRNA candidate a	Pre-miRNA candidates from non-coding regions identified by both programs or multiple times by the same program (automated approach)				High probability pre-miRNA candidate(non-automated approach)	High probability CyHV-3 pre-miRNA
	miRDeep2		MIREAP
	H361 Isolate	N076 Isolate	H361 Isolate	N076 Isolate
MR5057	Yes	Yes	Yes	Yes	Yes	Yes
MD11776	Yes	Yes	Yes	Yes	Yes	Yes
MD11410	Yes	Yes	Yes	No	Yes	Yes
MD9812	Yes	No	Yes	Yes	Yes	Yes
MD1111	Yes	No	Yes	No	Yes	Yes
MR6201 b	Yes	No	Yes	No	No	No
MD11704 b	No	No	Yes	Yes	No	No
MR5075	No	No	No	No	Yes	Yes

^a Pre-miRNA candidates are referred to using IDs originally assigned to the same predicted hairpin structures by VMir.

^b Classified as putative CyHV-3 pre-miRNA due to non-compliance with Points (ii) and/or (ix) of pre-miRNA identification criteria.