Evolutionary-new centromeres preferentially emerge within gene deserts

Table 2 Duplication analyses in ENC regions

						Non-redundant WSSD base pair (bp)
ENC	Start (HAS hg17)	Start+1M	End (HS A hg17)	End+1M	Size	HSA	PTR	PPY	MMU
Narrow interval
MMU2 (HSA3)	164,221,008		164,539,729		318,722	0	0	0	0
MMU4 (HSA6)	145,651,644		145,845,896		194,253	0	0	0	104,409
MMU12 (HSA2)	138,847,788		138,947,383		99,596	0	0	0	0
MMU13 (HSA2)	86,680,785		86,885,407		204,623	24,002	0	0	0
MMU14 (HSA11)	5,856,181		5,864,725		8,545	0	0	0	0
MMU15 (HSA9)	122,486,836		122,532,865		46,030	0	0	0	0
MMU17 (HSA13)	61,178,154		62,520,878		1,342,725	24,879	15,879	103,912	85,133
MMU18 (HSA18)	50,313,129		50,360,135		47,007	0	0	0	0
PPY11 (HSA11)	20,180,424		20,332,556		152,133	0	0	126,135	0
Larger interval
MMU2 (HSA3)		163,221,008		165,539,729	2,318,722	0	0	0	24,053
MMU4 (HSA6)		144,651,644		146,845,896	2,194,253	0	0	0	115,053
MMU12 (HSA2)		137,847,788		139,947,383	2,099,596	0	0	17,001	1,706
MMU13 (HSA2)		85,680,785		87,885,407	2,204,623	1,227,738	309,321	0	19,317
MMU14 (HSA11)		4,856,181		6,864,725	2,008,545	0	0	13,379	0
MMU15 (HSA9)		121,486,836		123,532,865	2,046,030	0	0	0	0
MMU17 (HSA13)		60,178,154		63,520,878	3,342,725	160,4637	98,004	144,056	85,133
MMU18 (HSA18)		49,313,129		51,360,135	2,047,007	0	0	0	0
PPY11 (HSA11)		19,180,424		21,332,556	2,152,133	0	0	784,808	0

We estimated the number of duplicated base-pairs predicted in each of the ENC intervals using the WSSD method; duplications >10 kb and >94% were detected with the exception of the macaque, where a threshold of >88% was used due to the greater sequence divergence of the human and macaque genomes. The analysis was performed separately for each of the four primate species. Two different ENC intervals were considered: a narrow interval, as defined in Table 1 (upper dataset) and a larger interval adding 1 Mbp to each side of the region (lower dataset).

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