Table 2. Primer sets used for ChIP-PCR.

Genomic site	primer name	description	length	Position Assembly March 2006	Ta
ZXDA	BS254/255	F: 5′ TCAATTAAGGTGGGAGGCAG 3′ R: TGTGAGGTAATTATGGCAAAGTC 3′	217 bp	chrX:57949717-57949933	59°C
1 (Xp sat jxn)	BS236/237	F: 5′ ATTTTCCCAGCACCATTTTTCAA 3′ R: 5′ CTGTCAAGATGGTATGGGCTGTGT 3′	397 bp	chrX:58104524-58104920	56°C
2 (HSAT4)	BS392/393	F: 5′ TGTGGTCAGCGAGATGTCTC 3′ R: 5′ AGTTTCCTGTGTGACCCCAG 3′	159 bp	chrX:58259011-58259169	64°C
3 (HSAT4-γ jxn)	BS222/223	F: 5′ CCAGGCATTCAAGCGGGAGAG 3′ R: 5′ CGGCGGAAGTTATCGTTGAGAG 3′	355 bp	chrX:58296350-58296704	60°C
4 (γ-satellite)	BS160/161	F: 5′ TTC AAC GTA CCC CTG AAA GCC TGG 3′ R: 5′ CTA TTT TGT CCC AAG CCT GCC 3′	339 bp	chrX:58329603-58329941	58°C
5 (γ-ALR jxn)	BS226/227	F: 5′ AGCCCGAGGAAAATACTGGTGAGG 3′ R: 5′ GCTGTCTTTCTAGTTTTTGTCGTGGGTTAT 3′	224 bp	chrX:58335817-58336040	62°C
6 (Xp mono-HOR jxn)	BS240/241	F: 5′ AACGCTGCGCTATCAAAGGGAAAGT 3′ R: 5′ GGACATGTGGAGCGCTTTGTGC 3′	313 bp	chrX:58577182-58577494	64°C
7 (α-satellite)	BS13/14	F: 5′ ATAATTTCCCATAACTAAACACA 3′ R: 5′ TGTGAAGATAAAGGAAAAGGCTT 3′	535 bp	chrX:61610033-61610567	55°C
8 (Xq HOR-mono jxn)	BS258/259	F: 5′ GACCTCAAAGCACTCTAAATACAC 3′ R: 5′ CTTCACATAAAAACTAGACAGACAG 3′	495 bp	chrX:61642633-61643127	61°C
9 (Xq sat jxn)	BS238/239	F: 5′ CCTGCTGAATCAAAACAATGGT 3′ R: 5′ CAAAGAAGGCTGGGTGAGAAG 3′	389 bp	chrX:61962313-61962701	59°C
10 (Xq jxn+150 kb)	BS260/261	F: 5′ TGCCTCCATGATTCAGTTACCA 3′ R: 5′ AATCTCCCTCCTCTTACCCTCTA 3′	475 bp	chrX:62111658-62112132	58°C