Table 2. Sequences for each of the validated taxon-specific qPCR assays.

Species	Oligo	Sequence	Rxn [] (nM)	Amplicon ln
westslope cutthroat	F	5’-CCTAAAACTATTTATTAAAGAACCAGTTCG-3’	100	88
	R	5’-AAGTGTAAGGGCGAGTCTRGGG-3’	900
	P	6FAM-5’-CCACCTCCTCTCCCT-3’ -MGBNFQ	250
Yellowstone cutthroat	F	5’-CGACCTTCCACCTCCTCC-3’	600	152
	R	5’-AGCTAGACTGGATAGCTCAAGC-3’	900
	P	6FAM-5’-CTCGCCACACCTATACT-3’ -MGBNFQ	250
rainbow trout	F	5’-AGTCTCTCCCTGTATATCGTC-3’	300	102
	R	5’-GATTTAGTTCATGAAGTTGCGTGAGTA-3’	600
	P	6FAM-5’-CCAACAACTCTTTAACCATC-3’ -MGBNFQ	250

Target species, oligonucleotide (forward primer; F, reverse primer R, probe; P), oligonucleotide sequence, and optimized reaction concentration of the oligonucleotide (nM), and amplicon length (bp). The induced mismatch (mismatch between both target and non-target taxa to increase specificity) in each reverse primer is underlined.