Figure 1.

Origin of filler DNA sequences for T-DNA/plant DNA junctions and for junctions between linked T-DNAs. The sequence of each junction for which the origin of the filler DNA (represented by different types of lines) was determined is presented and so are the border characteristics for each junction. The T-DNA end sequences are given in uppercase, plant DNA sequences in lowercase, and intermediate filler DNA in bold lowercase. All sequence motifs, identical to sequence blocks occurring in the plant DNA surrounding the T-DNA integration point or the T-DNA plasmid sequence, are positioned above and below the junction sequence, respectively. All sequence motifs for which the origin could be indicated on the figure are given consecutive numbers, and corresponding motifs have the same number. Motifs designated by uppercase letters are identical to sequence blocks found in the plant DNA target, for which the originating sequence are not represented on the figure. Motif A is identical to a sequence block occurring in the target site deletion, whereas motif B is either identical to a sequence block from the T-DNA target site deletion or from the plant DNA adjacent to the opposite T-DNA end of the same T-DNA insert. For sequence motifs that are identical to T-DNA plasmid sequence blocks that are not present on the figure (internal T-DNA plasmid sequences), the position of the original sequence was determined, and its position is given between parentheses. Inverted, direct, and chimeric sequence motifs are indicated with arrowed, solid, and dotted lines, respectively. LB and RB, Left and right border T-DNA ends for linked T-DNAs, respectively. For junction kd12-1, the italicized sequences correspond to the Arabidopsis genomic DNA. Asterisk, Base mismatch with the original sequence; double slash, Both junction sequences correspond to one and the same T-DNA insert (see “Experimental Setup”).