TABLE 3.

Clusters of plasmids based on nucleotide sequence similarity within the Egyptian S. aureus strains.

Cluster ID (replicon)	Cluster details				Closest relative (by BLAST homology)
	Strains	Avg. length (bp)	%GC	% Pairwise identity	Description	Accession #	Length (bp)
A (rep7a)	AA29, AA35, AA57, AA64	3,909	29.3	99.5	Unnamed3	CP033985	3,785
B (rep20)	AA2, AA3, AA4, AA45	27,938	29.1	100	pGR2A	CP010403	28,895
C (rep16)	AA17	20,970	28.7	80.7	pPS00087.1A.1	CP022721	20,730
	AA30				pl1_M2024	CP047022	19,760
	AA41				pWBG757	GQ900397	20,730
	AA1, AA59, AA65, AA68, AA69, AA78				pWBG750	GQ900392	20,653
	AA51				p18809-P04	CP002146	28,404
D (rep5a)	AA5, AA32	34,114	30.3	100	pIT4-R	CP028471	34,104
E (rep20)	AA6, AA8, AA53	16,610	28.1	99.2	pM121	CP007671	20,409
F (rep20)	AA35	21,196	28.4	80	Unnamed1	CP030394	25,071
	AA36				Unnamed1	CP030413	20,403
G (rep21)	AA35	3,112	29	99.5	pV605	CP013960	43,115
	AA4				SAP104A	GQ900450	3,011
	AA57, AA64				pV605	CP013960	43,115
H (rep10)	AA1	2,560	30.8	96.8	Unnamed1	CP029648	2,473
	AA17				pSau-2716Lar	MH423311	3,267
	AA35				Unnamed	CP047816	2,473
	AA63				Unnamed2	CP047819	2,477
I (rep21)	AA53	3,123	29.1	98.8	3	LR130517	3,011
	AA63				Unnamed1	CP034006	3,011
J (rep10)	AA13	2,556	31	98.9	pUSA05-1-SUR24	CP014446	2,415
	AA29				pSR265	MN251859	2,413
	AA53				p19321-P01	CP002148	2,473
	AA64				SAP078B	GQ900431	2,415
	AA65				pSR241	MN251858	2,402
K (rep7a)	AA53, AA63	3,901	29.6	98.8	pOC160-2	LC012933	3,788