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

Table 2.

Genotyping details of Y-SNP multiplex 2

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)
M9	C->G	F	CTGCAAAGAAACGGCCTAAG	0.300	90	t(gact) ₇ g CGGCCTAAGATGGTTGAAT	0.100	49	F	C (yellow), G (blue)
M9	C->G	R	AACTAAGTATGTAAGACATTGAACGTTTG	0.300	90	t(gact) ₇ g CGGCCTAAGATGGTTGAAT	0.100	49	F	C (yellow), G (blue)
M526	A->C	F	TAGAGGCAGGGTGTTGCTCT	0.300	100	ct(gact) ₁₀ ga TGTCATCAGGCTGAATCATAC	0.450	65	F	A (green), C (yellow)
M526	A->C	R	TACTTTGGGAGGCTGCTGTT	0.300	100	ct(gact) ₁₀ ga TGTCATCAGGCTGAATCATAC	0.450	65	F	A (green), C (yellow)
M147	ins T	F	CCTGAATAAGCTGGTGAAAGAAA	0.500	114/115	ct(gact) ₁₁ ga CCTGTCTCTGAAAGAAAAAAA	1.000	69	R	a (yellow), i (green)^a
M147	ins T	R	GGAGACCCTGTCTCTGAAAGAA	0.500	114/115	ct(gact) ₁₁ ga CCTGTCTCTGAAAGAAAAAAA	1.000	69	R	a (yellow), i (green)^a
P308	C->T	F	GCTACCAATACCCCCAAAGA	0.050	108	gactgac GAAATGATTAAGTAAGTGCCTTCT	0.150	31	R	C (blue), T (green)
P308	C->T	R	CCTGGAATATGGCACGAAAT	0.050	108	gactgac GAAATGATTAAGTAAGTGCCTTCT	0.150	31	R	C (blue), T (green)
P79	T->C	F	TTGCTTAGTATAATGTCTTTCATGCTC	0.500	101	ct(gact) ₄ g TGCTCATTCGCATCTTTG	1.000	37	F	T (red), C (yellow)
P79	T->C	R	AAATGAGGCTAATCAATGGAACA	0.500	101	ct(gact) ₄ g TGCTCATTCGCATCTTTG	1.000	37	F	T (red), C (yellow)
P261	G->A	F	TCCTAGAAGGTAACCCACTACCC	0.500	93	t(gact)7gac TTTTTGTTTTTATTAATGAATGCTA	1.000	57	R	G (yellow), A (red)
P261	G->A	R	TGTGCATATGTTATCCACCATGT	0.500	93	t(gact)7gac TTTTTGTTTTTATTAATGAATGCTA	1.000	57	R	G (yellow), A (red)
P256	G->A	F	TCTTGGTTTTCCCATTGACC	0.200	91	t(gact) ₁₃ ga TGCCCTACACTAGATAGAAAGG	0.150	77	F	G (blue), A (green)
P256	G->A	R	CATCTCCCAACTTGTCTGTGC	0.200	91	t(gact) ₁₃ ga TGCCCTACACTAGATAGAAAGG	0.150	77	F	G (blue), A (green)
M231	G->A	F	AACAACATTTACTGTTTCTACTGCTTTC	0.300	119	act(gact) ₃ g CGATCTTTCCCCCAATT	0.450	33	R	G (yellow), A (red)
M231	G->A	R	TTCACATCATCCAGTACAGCAA	0.300	119	act(gact) ₃ g CGATCTTTCCCCCAATT	0.450	33	R	G (yellow), A (red)
M175	5 bp del	F	CCCAAATCAACTCAACTCCAG	0.300	101/96	t(gact) ₁₀ CACATGCCTTCTCACTTCTC	0.600	61	F	a (red), d (green)^a
M175	5 bp del	R	TTCTACTGATACCTTTGTTTCTGTTCA	0.300	101/96	t(gact) ₁₀ CACATGCCTTCTCACTTCTC	0.600	61	F	a (red), d (green)^a
M45	G->A	F	CATCGGGGTGTGGACTTTA	0.400	109	act(gact) ₆ g AATTGGCAGTGAAAAATTATAGATA	0.750	53	F	G (blue), A (green)
M45	G->A	R	CCTCAGAAGGAGCTTTTTGC	0.400	109	act(gact) ₆ g AATTGGCAGTGAAAAATTATAGATA	0.750	53	F	G (blue), A (green)
M242	C->T	F	AAAAAGGTGACCAAGGTGCT	0.400	46	ct(gact) ₆ g CGTTAAGACCAATGCCAA	0.100	45	R	C (blue), T (green)
M242	C->T	R	AAAAACACGTTAAGACCAATGC	0.400	46	ct(gact) ₆ g CGTTAAGACCAATGCCAA	0.100	45	R	C (blue), T (green)
M207	A->G	F	GGGGCAAATGTAAGTCAAGC	0.300	83	(gact) ₁₄ g AATGTAAGTCAAGCAAGAAATTTA	0.300	81	F	A (green), G (blue)
M207	A->G	R	TCACTTCAACCTCTTGTTGGAA	0.300	83	(gact) ₁₄ g AATGTAAGTCAAGCAAGAAATTTA	0.300	81	F	A (green), G (blue)
M412	G->A	F	GGCACTCCTCCGTCATCTT	0.300	114	ct(gact) ₁₆ GGGTACAATCTGATGAGGC	0.300	85	F	G (blue), A (green)
M412	G->A	R	GGTGAAGTGGACCCTATCCA	0.300	114	ct(gact) ₁₆ GGGTACAATCTGATGAGGC	0.300	85	F	G (blue), A (green)
P202	T->A	F	AAACTTCCCAGTTTGTGGTTC	0.300	125	ct(gact) ₁₂ ga CCAGTTTGTGGTTCTTTGTTA	0.300	73	F	T (red), A (green)
P202	T->A	R	TGATCCCTTAATTAATAGCAAGACC	0.300	125	ct(gact) ₁₂ ga CCAGTTTGTGGTTCTTTGTTA	0.300	73	F	T (red), A (green)
P326	T->C	F	TTCAGATATCAGGCCGCTTT	0.200	61	t(gact) ₃ CCTAAGCAGAGGAAAATAGTACAG	0.150	37	R	T (green), C (blue)
P326	T->C	R	GAGCTGTCAGCCTGCCTAAG	0.200	61	t(gact) ₃ CCTAAGCAGAGGAAAATAGTACAG	0.150	37	R	T (green), C (blue)

^a a ancestral, i insertion, d deletion