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Table 1.

Duplication Content of Pericentromeric and Subtelomeric Compartments

Method		Sequence		All pairwise		Interchromosomal pairwise		Intrachromosomal pairwise
Method		Kb	% genome	Kb	% pair	fold[i]	Kb	% pair	fold[i]	Kb	% pair	fold[i]
Assembly-Based[ii]
Peri^2Mb	86,000	3.2%	11,548	11.8%	3.7	7,348	14.5%	4.5	6,341	10.0%	3.1
Sub^500kb	21,000	0.8%	1,290	1.3%	1.7	1,062	2.1%	2.7	376	0.6%	0.8
Repeat-Based[iii]
Peri^alpha	58,561	2.2%	9,999	10.3%	4.7	7,565	14.9%	6.9	5,106	8.1%	3.7
Peri^αβCERγ	76,143	2.8%	16,245	16.7%	5.9	11,689	23.0%	8.1	8,618	13.6%	4.8
Peri^duplicons	23,425	0.9%	9,995	10.2%	11.8	8,824	17.4%	20.0	3,556	5.6%	6.5
Peri^ALL	92,090	3.4%	22,769	23.3%	6.8	17,350	34.2%	10.0	10,863	17.2%	5.0
Sub^1kb	23,535	0.9%	7,038	7.2%	8.3	5,179	10.2%	11.7	3,261	5.2%	5.9
PeriSub^ALL	106,678	4.0%	25,157	25.8%	6.5	18,763	37.0%	9.3	12,211	19.3%	4.9
TOTAL ASSEMBLY	2,692,604	—	97,514	—	—	50,752	—	—	63,160	—	—

[i] Fold enrichment calculated by percent of total pairwise in compartment/percent genome size of compartment.

[ii] Assembly-based compartments relied solely on positions assigned within assembly. Peri^2Mb included all sequence within 2Mb of the defined centromeric ends of the assembly. Sub^500kbincluded all sequence within 500 Kb of the defined telomeric end.

[iii] Repeat-based compartments relied solely on a minimum amount of pericentromeric and/or subtelomeric repeats within a given 400 Kb region. Peri^alpha required a minimum of 10 Kb. Peri^αβCERγ required a minimum sum of 10KB for alpha satellite, beta satellite, CER, and/or gamma satellite. Peri^duplicons required at least 1Kb of CAGGG repeat (Eichler 1999) or the Duplicon4 repeat (Horvath 2000). Peri^ALLcombined all of these compartments together. Sub(1Kb) utilized TAR and TTAGGG repeats to detect subtelomeric regions. PeriSub^ALLcombines the sequence found in Peri^ALL and Sub^1Kb.