TABLE 2.

Sequence of recombinant junctions in molecules recovered from cells transfected with linear substrates encoding sequence-tagged (mismatched) termini^a

Sequence-tagged mismatches at homologous endsb	Fraction of recovered molecules with sequence Xc for nucleotide:				Predicted effect of resection polarity on junction sequence
	G	A	T	C	3′ to 5′	5′ to 3′
Left end
	5/16	3/16	6/16	2/16	G or T	A or C
Right end
	5/16	8/16	1/16	2/16	G or A	T or C

^aDuplex oligonucleotides were ligated to all four ends of two linear recombination substrates, adding 20 nt of sequence identity to each end interrupted by a single, central, mismatched base pair. These substrates were transfected into virus-infected cells (Fig. 3), and recombinants were recovered in E. coli (6) and sequenced (25). 

^bDiagrams illustrate the base substitutions used to differentiate all eight 3′- and 5′-ended strands. The left end of the linear insert is identical to the vector end shown immediately below it, except that T · G and A · C mismatches differentiate insert from vector ends. T · C and A · G mismatches similarly differentiate the right end of the insert from its vector target. See Materials and Methods for sequence details. 

^cTop-strand sequence (as drawn) at variant site.