. 2011 Jul 22;125(6):879–885. doi: 10.1007/s00414-011-0605-2

Table 1.

Genotyping details of Y-SNP multiplex 1

Locus	Mutation	PCR amplification				Single-base extension
Locus	Mutation	Primer sequences (5′-3′)		Conc. (μM)	Amplicon size (bp)	Primer sequence (5′–3′) (5′ aspecific tail in lowercase italics)	Conc. (μM)	Length (nt)	Orientation	Alleles (dye)
M91	ins T	F	CAAAAATCCCCCTACATTGC	0.600	144/143	g CTACAGTAGTGAACTGATTAAAAAAAA	0.300	28	R	a (yellow), i (green)^a
M91	ins T	R	GCAGTGCCCTTCCAAATAAA	0.600	144/143	g CTACAGTAGTGAACTGATTAAAAAAAA	0.300	28	R	a (yellow), i (green)^a
M60	ins T	F	TCTTTACATTTCAAAATGCATGACT	0.600	128/129	ct(gact) ₆ TAACCACTGTGTGCCTGAT	0.600	45	R	a (yellow), i (green)^a
M60	ins T	R	GAGAAGGTGGGTGGTCAAGA	0.600	128/129	ct(gact) ₆ TAACCACTGTGTGCCTGAT	0.600	45	R	a (yellow), i (green)^a
M145	G->A	F	GCATACTTGCCTCCACGACT	0.200	96	ct(gact) ₃ gac TAGGCTAAGGCTGGCTCT	0.450	35	R	G (yellow), A (red)
M145	G->A	R	CCTCCCACTCCTTTTTGGAT	0.200	96	ct(gact) ₃ gac TAGGCTAAGGCTGGCTCT	0.450	35	R	G (yellow), A (red)
M174	T->C	F	TCTCCGTCACAGCAAAAATG	0.450	178	ct(gact) ₅ g ATACCTTCTGGAGTGCCC	0.100	41	F	T (red), C (yellow)
M174	T->C	R	AGGAGAAGGACAAGACCCATC	0.450	178	ct(gact) ₅ g ATACCTTCTGGAGTGCCC	0.100	41	F	T (red), C (yellow)
M96	G->C	F	TGAGCTGTGATGTGTAACTTGG	0.200	117	act(gact) ₁₀ gac TGGAAAACAGGTCTCTCATAATA	0.200	69	F	G (blue), C (yellow)
M96	G->C	R	CACCCACTTTGTTGCTTTGT	0.200	117	act(gact) ₁₀ gac TGGAAAACAGGTCTCTCATAATA	0.200	69	F	G (blue), C (yellow)
M216	C->T	F	CCTCAACCAGTTTTTATGAAGCTA	0.100	102	ct(gact) ₆ g CTGCTAGTTATGTATACCTGTTGAAT	0.075	53	R	C (blue), T (green)
M216	C->T	R	TTCTAAATCTGAATTCTGACACTGC	0.100	102	ct(gact) ₆ g CTGCTAGTTATGTATACCTGTTGAAT	0.075	53	R	C (blue), T (green)
M89	C->T	F	CAGCTTCCTGGATTCAGCTC	0.200	105	ct(gact) ₁₃ ga AACTCAGGCAAAGTGAGAGAT	0.300	77	R	C (blue), T (green)
M89	C->T	R	CACTTTGGGTCCAGGATCAC	0.200	105	ct(gact) ₁₃ ga AACTCAGGCAAAGTGAGAGAT	0.300	77	R	C (blue), T (green)
M282	A->G	F	TGTGCAACCTCAACTTTGCTT	0.750	106	t(gact) ₁₅ GAAAGCAAAATCTCAATATGATAA	1.000	85	F	A (green), G (blue)
M282	A->G	R	TGTGATCAACTTCTTTCCCTCA	0.750	106	t(gact) ₁₅ GAAAGCAAAATCTCAATATGATAA	1.000	85	F	A (green), G (blue)
P257	G->A	F	ACCCCTCAGTCTCTCCGATT	0.200	71	(gact) ₉ g ATTATCCCACTGCATTTCTG	0.300	57	F	G (blue), A (green)
P257	G->A	R	TCATCTCCAACCCCCATCT	0.200	71	(gact) ₉ g ATTATCCCACTGCATTTCTG	0.300	57	F	G (blue), A (green)
M69	T->C	F	GGAGGCTGTTTACACTCCTGA	0.300	87	(gact) ₁₀ g GGCTGTTTACACTCCTGAAA	0.150	61	F	T (red), C (yellow)
M69	T->C	R	TCTCCCCTTAGCTCTCCTGTT	0.300	87	(gact) ₁₀ g GGCTGTTTACACTCCTGAAA	0.150	61	F	T (red), C (yellow)
M522	G->A	F	TCCAATTCCCATGTCCTCTC	0.100	109	t(gact) ₁₁ CTACTACGCCTCTCTTGTCC	0.075	65	F	G (blue), A (green)
M522	G->A	R	CAGTGCAGAAAATCACGGTAGA	0.100	109	t(gact) ₁₁ CTACTACGCCTCTCTTGTCC	0.075	65	F	G (blue), A (green)
M258	T->C	F	TTCAGGATTTGTCAAGGATGG	0.200	108	t(gact) ₃ gac GGGATTCCAAGTTCCCA	0.300	33	R	T (green), C (blue)
M258	T->C	R	GCTATGACTAAGAGGGATTCCAA	0.200	108	t(gact) ₃ gac GGGATTCCAAGTTCCCA	0.300	33	R	T (green), C (blue)
M304	A->C	F	TTGTAACAAACAGTATGTGGGATTT	0.200	88	act(gact) ₁₁ ga TTATACCAAAATATCACCAGTTGT	0.300	73	R	A (red), C (blue)
M304	A->C	R	CGTCTTATACCAAAATATCACCAGTT	0.200	88	act(gact) ₁₁ ga TTATACCAAAATATCACCAGTTGT	0.300	73	R	A (red), C (blue)
M9	C->G	F	CTGCAAAGAAACGGCCTAAG	0.100	90	t(gact) ₇ g CGGCCTAAGATGGTTGAAT	0.100	49	F	C (yellow), G (blue)
M9	C->G	R	AACTAAGTATGTAAGACATTGAACGTTTG	0.100	90	t(gact) ₇ g CGGCCTAAGATGGTTGAAT	0.100	49	F	C (yellow), G (blue)

^a a ancestral, i insertion