TABLE 2.

Oligonucleotide probe set used in this study

Name	Sequencea	Positionb	Length (nt)	Tm (°C)	GC (%)	Coordinate(s)c
Entamoeba
Ehlocus1-2.3	CTGGTTAGTATCTTCGCCTGTCACG	1	25	59.3	52	A3, C3
EssrDNA.1	AATGAATTGCGATAAGTGATAGGAAC	171	26	55.0	35	B3, D3
E. histolytica
Ehlocus5-6.1	TCTTTGAGACTTATTTCTACTTTATTTCTT	37	30	53.7	23	A1
Ehlocus5-6.2	TGTACGTCTTTAACTTTAAAAACAA	415	25	54.7	24	B1
Ehlocus1-2.1	ATATTCTTATCACTTCCTACTACTCTTATT	116	30	53.6	27	A2
Ehlocus1-2.2	TACTACTCTT*(6)CTTACTATACCT*(6)CTTACTAC	331	30	54.5	33	B2
EhlTS.1	AATCTACAAAGAAAATAATAATAAGTAAGA	54	30	50.4	17	A4
EhlTS.2	AATATCAATAGACAGACCAGACCAATA	368	27	54.8	33	B4
EhlTS.3	GCAAGTACAACAGAGAAGAAGTAGC	304	25	53.1	44	A5
EhSA.1	ACTTTTCCCCTCAATTATTTCGTTTT	76	26	55.1	31	A6
EhSA.2	AAGACAGGTATTTAAAGATCATAATAAACT	401	30	53.5	23	B6
Ehprrdx.1	GAAAGAATGTTGTAAAGAATGTTGTTGTCC	9	30	61.6	33	A7
Ehprrdx.2	AACAGAAATGATTGGATATAGTGAACTT	224	28	54.8	29	B7
Ehcp1.1	TATGGTTCAATGTACTAGGGAAGATG	73	26	55.1	39	A8
Ehcp1.2	AGTTATACAAGAGTGGAGCATATACAG	342	27	55.4	37	B8
E. dispar
Edlocus5-6.1	CTATATTCTTTTTATGTACTTCCCTTA	33	27	54.3	26	C1
Edlocus5-6.2	TTCCTTTTATACAAATACTCTCATG	356	25	51.4	28	D1
Edlocus1-2.1	GTCACTTATACTATTAACTTTATCTATTCC	102	30	52.2	27	C2
Edlocus1-2.2	CCTACTATACCTACTACTCTTACTACTCCT	428	30	54.1	40	D2
EdITS.1	AATCTACAAAGAAAATAATAA*AAGTAAGA	54	29	55.9	17	C4
EdITS.2	TTAACCAGATATCTATAAGTGAGTTAATA	356	29	53.7	24	D4
EdITS.3	TTAGTAGAAGTGAGAAGTAGCTAGTG	303	26	50.1	39	C5
EdSA.1	GTTTTTGTTAAGTTTTTGGTATTACTG	110	27	55.5	26	C6
EdSA.2	GAGCCAGGTATTTAAAGATCATATCAA	401	27	58.2	33	D6
Edprrdx.1	GAGAAAGAATGTTGTAAAGAGTATTGTTGT	6	30	58.2	30	C7
Edprrdx.2	AACAGAAATGATTGGATATAGTGAAGTT	194	28	56.8	29	D7
Edcp1.1	GTACTAGAGATAATGGAAACAATGG	84	25	52.2	36	C8
Edcp1.2	GTGGTGCATACAGTGATACTAAATG	353	25	51.8	40	D8
G. lamblia
Glhsp.1	AATTGATTAGTATTAGTAGGATGCCT	46	26	52.6	31	E1, G1
Glhsp.2	CTTGGCGTTCCCGAAGTCTGTC	113	22	59.8	59	F1, H1
girAB.1	TCAAGCTCAGCAACATGAACCAGC	36	24	58.8	50	E5, G5
girAB.2	ATGGAGAACGAGATCGAGGTCCG	84	23	60.4	57	F5, H5
gdhAB.1	GAGCAGATCCTGAAGAACTCCCT	49	23	57.0	52	E8, G8
gdhAB.2	GACAACGAGGTCATGCGCTT	134	20	54.1	55	F8, H8
Assemblage A
tpiA.1	ATGGGTTTGAAGCATGTGATAGTAG	29	25	55.8	40	E2
tpiA.2	TATGACGATGATCGACATTCTTACG	505	25	55.7	40	F2
girA.1	ATGTACCTAACGATCAAGGAGGAGA	246	25	57.3	44	E3
girA.2	AGAACGCAGAAAGGAAGAAGATGTA	442	25	56.9	40	F3
girA.3	ATCGCACACCTCGACAGGCTCAT	150	23	60.1	57	E4
girA.4	CCACGACAGAAGCGCTCACAAACA	561	24	60.0	54	F4
gdhA.1	AATCTTTCGATTCTCAAGTTCCT	20	23	57.6	35	E6
gdhA.2	GGTACCTGTACGGACAGTACAAG	246	23	57.8	52	F6
gdhA.3	TTGACCCAAAGGGCAAGTCCGA	113	22	61.8	55	E7
c4A.1	GCCATGATGAAAGGGAGTGCTGTA	37	24	58.9	50	E9
c4A.2	TGGACCCCACTGTTCAAAAGAAGA	158	24	58.5	46	F9
c4A.3	CATCCAAAGATATGAATGAGCTTCC	218	25	57.4	40	E10
c4A.4	CAGATGGAATCAAGCTTCTTAGCG	362	24	58.4	46	F10
Assemblage B
tpiB.1	CTGAGCCATGTAATAATAGGACACT	145	25	54.9	40	G2
tpiB.2	GCCAATAACACTATGGAGGTGAATA	289	25	55.4	40	H2
girB.1	ATGTACCTGACGATCAAGGAGGAGA	246	25	57.5	48	G3
girB.2	AGAACGCCGAGAGGAAGAAGATGTA	442	25	60.6	48	H3
girB.3	ATCGCGCACCTCGACAGACTCAT	150	23	60.4	57	G4
girB.4	CCACGACAGAGGCCCTCACAAACA	561	24	61.9	58	H4
gdhB.1	AACCTCTCGATCCTTAAGTTCCT	20	23	55.0	44	G6
gdhB.2	GTTATCTGTTTGGACAGTATAAGCG	246	25	54.5	40	H6
gdhB.3	TCGATCCTAAGGGCAAGTCGGA	113	22	60.2	55	G7
c4B.1	GGCTATGACGAAAGAAGATGCTGTA	36	25	57.8	44	G9
c4B.2	AGCCGGATGCTCATTGTTGCG	68	21	60.8	57	H9
c4B.3	TATCTGAGAAGGACATGAAGGACCT	215	25	55.7	44	G10
c4B.4	ATCCAGCTTCTCAGTGCTTCTCTG	370	24	56.0	50	H10
C. parvum
dhf.1	GGATAGGAATTAACGGACAATTACC	45	25	58.3	40	I1
dhf.2	TCAATAGAGAATCTTATGAATGATGACT	281	28	54.8	29	J1
dhf.3	AATGTGACTCGAATAAGAAGAATGC	120	25	54.7	36	K1
dhf.4	AAGCCGATCCTAATGTTGTTGTATT	240	25	55.8	36	L1
ptg.2	GAGTGATGATTCCAGGTTCTTTAGG	415	25	55.9	44	J4
Cphsp.1	TGCCGTACAGGATCTCTTATTATTG	6	25	55.2	40	K4
cowp.1	TCTCCTGCTTCAACTGTATGTCCTA	133	25	57.7	44	I6
cowp.2	TGTGTTAGAAGAAGCCAATATGACT	391	25	54.9	36	J6
rDNA.1	TTTACTTTGAGAAAATTAGAGTGCTTAAA	106	29	54.3	24	K6
rDNA.2	TAACAGTCAGAGGTGAAATTCTTAGAT	249	27	55.2	33	L6
RAPD.1	CATACAGGTGAGGAAGTTGATCTAT	75	25	52.7	40	I7
RAPD.2	ATCGCAATAATCCTTGTAACTTGTG	372	25	56.5	36	J7
TRAPC2.1	CCTTGAGTTGTACTGTCTCTGAATG	14	25	56.1	44	K7
TRAPC2.2	GGAGGAAAGACCTTCAGATTGTTTA	324	25	55.4	40	L7
Type 1
dhfI.1	CTGTTTTGAGCAGTGGGATAGGAAT	16	25	58.8	44	I2
dhfI.2	CAAAGATAACTAATAATAAATGTGACTCG	89	29	57.2	28	J2
ptgI.1	TTAGATCCAGTTAGTTTGATTCCATTC	161	27	57.3	33	I3
ptgI.2	ATCCAATCTCAGATGAGATCATGAAT	214	26	55.3	35	J3
Cphsp.2	TGGTATCTTGAATGTATCTGCTGTT	297	25	53.5	36	L4
p23I.1	CCAATTAGCAACCAAGCCCAACAAA	188	25	64.4	44	I5
p23I.2	TACACTC*(3)GAGTACTTAACATGGGTT	427	25	53.5	40	J5
Type 2
dhfII.1	CTGTTTTGAGTAGAGGAATAGGAAT	16	25	53.6	36	K2
dhfII.2	CAAAGATAACTAGTAATAATTGTGACTCG	89	29	56.5	31	L2
ptgII.1	TTGGATCCAGTCAGTTTGATTCCGTT	161	26	61.8	42	K3
ptgII.2	ATCCAATATCAGATGAGATAATGAAT	214	26	53.4	27	L3
ptg.1	TTATCGGTATCATATCTTGCTGCTAA	117	26	55.0	35	I4
p23II.1	CCAATCAGCAACCAAGCTCAACAAA	188	25	61.4	44	K5
p23II.2	CTCAGAGAGTACTTAACATGGGTT	431	24	51.0	42	L5
Internal positive control
fliC.1	AACGGTTAGCAATCGCCTGACCTGCGGCGTCATCCTTCGCGCTGTTAATACGCAAGCCAGAAGACAGACG		70	80.6	56

^aMismatched nucleotides between homologous target sequences are underlined, and deleted nucleotides are designated by an asterisk (with the number in parentheses).

^bThe first nucleotide of the probe corresponding to the position within an amplicon starting from the 5′ end.

^bThe position of each probe on the microarray is represented by coordinate number corresponding to Fig. 2B.