Table 1.

Oligonucleotide probes

Target species	Probe name	Probe sequence (5' -> 3')a	Length (nt)	GC content (%)	TM (° C)
Internal positive control	uni_16S_05b	TTACGACCTCGATGTTGG	18	50	48.4
P. vannamei	Pvannam_16S_01	TGTCTCAATTATATTTATTGAATTTA	26	15	46.6
P. vannamei	Pvannam_16S_02	TTACAATAAGTTACCTATATTATAAA	26	15	45.1
P. vannamei	Pvannam_16S_02_MM	TTACAATAAGTTAtCTATATTATAAA	26	12	43.7
P. vannamei	Pvannam_16S_03	GAGTTTAGGTAACGTTTGTT	20	35	45.5
P. vannamei	Pvannam_16S_04	GTTCTTAAGTTATTTAATGACAG	23	26	45.5
P. vannamei	Pvannam_16S_04_2MM	GTTCTTAAGcTATTTAATaACAG	23	26	46.2
P. vannamei	Pvannam_16S_04_3MM	GTTCTTAAGTTAaTTAATaACAt	23	17	42.3
P. vannamei	Pvannam_16S_05	AATGACAGAAATTTCTGGAAA	21	29	46.4
P. vannamei	Pvannam_16S_06	GATCCTCTACTAGAGATCA	19	42	45.0
P. vannamei	Pvannam_16S_06_2MM	GATCCTCTttTAGAGATCA	19	37	44.0
P. monodon	Pmonod_16S_01	CAAAAAGTAATCTGTCTCAG	20	35	45.4
P. monodon	Pmonod_16S_01_MM	CAAAAAGTAAgCTGTCTCAG	20	40	48.4
P. monodon	Pmonod_16S_02	GCTTAAATACTTTAAGGGGA	20	35	45.3
P. monodon	Pmonod_16S_03ac	ACAATAATTTGATTAAATTATAAATT	26	8	43.6
P. monodon	Pmonod_16S_03bc	ACAATAAATTAGTTAAATTATAAATT	26	8	43.2
P. monodon	Pmonod_16S_04	GGAATATAATTAGTAACTGTTC	22	27	43.0
P. monodon	Pmonod_16S_04_MMa	GGAATATAATaAGTAACTGTTC	22	27	43.0
P. monodon	Pmonod_16S_04_MMb	GGAATATAATgAGTAACTGTTC	22	32	45.1
P. monodon	Pmonod_16S_05ac	AGTATAATTGAAGAATAATTGATC	24	21	45.3
P. monodon	Pmonod_16S_05bc	AGTATAATTGAAAAATAATTGATC	24	17	43.8
P. monodon	Pmonod_16S_06	ATTGATCCTTTATTAAAGATTAA	23	17	43.9
Negative control	NK01 b	TACCAACTTCGCTAACTCA	19	42	48.5
Negative control	NK02 b	ATATTCTGCCCGCAGTTA	18	44	48.2
Negative control	NK03 b	TTGTGCCATTCTTGAAAGATC	21	38	49.6

^aLowercase letters indicate mismatch (MM) positions (i.e. positions with bases complementary to related species)

^bPublished in Kappel et al. (2020) [6]

^c“a” and “b” represent two types of probe, each for a distinct P. monodon 16S rDNA cluster