Table 1. Primer and probe sequences used in this study.

Target organism	Name	Target gene	primer/probe	Sequence (5′→3′)	References
C. hominis	Ch001	DNA-J like	Forward	ATC CTA CGT CTA ACT TCA CGC	This study
			Reverse	GAA GCT CTT CAT ATG CCT TAT TA
			Probe1	TTA TAG GGA TAC CAG TCG ATT CTG ATG AC
	Ch003	NTF2	Forward	AGC ATT ATT GGA TGT TGT AG	This study
			Reverse	TAA TAA AAA TCA ATC AGT GGT
			Probe1	CTG CTA ATA CTA GTA ATA CTA GTA GTA ATC
	CRULib13Ch2	Unknown	Forward	TCC TTG AAA TGA ATA TTT GTG ACT CG	[30]
			Reverse	AAA TGT GGT AGT TGC GGT TGA AA
			Probe3	CTT ACT TCG TGG CGG CGT
	JVAG14	Unknown	Forward	ACT TTT TGT TTG TTT TAC GCC G	[29]
			Reverse	AAT GTG GTA GTT GCG GTT GAA
			Probe1	ATT TAT TAA TTT ATC TCT TAC TTC GT
C. parvum	Cp001	DNA-J like	Forward	ATC CTA CGT CTA ACT TCA CGT	This study
			Reverse	GTA GCT CCT CAT ATG CCT TAT TG
			Probe1	TTA TAG GGA TAC CAG TCG ATT CTG ATG AT
	Cp003	NTF2	Forward	AGC ATT ATT GGA TGT TGT AT TAG	This study
			Reverse	TAA TAA AAG TCA ATC AGT GGC
			Probe1	CTG CTA ATA CTA GTA ATA ATA GTA GTA ATA
	CRULib13Cp2	Unknown	Forward	TCC TTG AAA TGA ATA TTT GTG ACT CG	[30]
			Reverse	TTA ATG TGG TAG TTG CGG TTG AAC
			Probe3	TAT CTC TTC GTA GCG GCG TA
	JVAG24	Unknown	Forward	ACT TTT TGT TTG TTT TAC GCC G	[29]
			Reverse	AAT GTG GTA GTT GCG GTT GAA
			Probe1	ATT TAT CTC TTC GTA GCG GCG
Cryptosporidium spp.	CRU18S	18S rRNA	Forward	GAG GTA GTG ACA AGA AAT AAC AAT ACA GG	[30]
			Reverse	CTG CTT TAA GCA CTC TAA TTT TCT CAA AG
			Probe5	TAC GAG CTT TTT AAC TGC AAC AA
	JVA	18S rRNA	Forward	ATG ACG GGT AAC GGG GAA T	[24]
			Reverse	CCA ATT ACA AAA CCA AAA AGT CC
			Probe1	CGC GCC TGC TGC CTT CCT TAG ATG

¹Probes labeled with 6-carboxy-fluorescein (FAM) and black hole quencher (BHQ).

²Forward primer is the same.

³Probes labeled with VIC and with minor groove binding non-fluorescent quencher (MGB).

⁴Forward and reverse primers are the same.

⁵Probes labeled with 6-carboxy-fluorescein (FAM) and with minor groove binding non-fluorescent quencher (MGB).