. 2019 Nov 19;14(11):e0220584. doi: 10.1371/journal.pone.0220584

Table 4. XerC/D sites in HPC229 plasmids.

Plasmid	XerC/D-site^a	Nucleotide sequence^b			cr length (bp)	Position in plasmid (start-end)	Search method^c
Plasmid	XerC/D-site^a	XerC	cr	XerD	cr length (bp)	Position in plasmid (start-end)	Search method^c
pAbe229-15	XerC/D_1	`···········`	`··c···`	`···········`	6	2,174–2,201	*
	XerC/D_2	`g··········`	`cc····`	`···········`	6	6,904–6,931	*
	XerC/D_3	`·c···tc····`	`·a·a·t`	`···········`	6	9,477–9,504	*
	XerC/D_4	`·c···tc····`	`·a·a·t`	`···········`	6	10,204–10,231	*
	XerC/D_5	`·a··aac····`	`tac·c·a`	`·····cg····`	7	13,062–13,090	**
pAbe229-9	XerC/D_6	`g··········`	`c··cc·`	`···········`	6	3,622–3,649	*
	XerC/D_7	`·c····c····`	`··t···`	`·········t·`	6	4,473–4,500	*
	XerC/D_8	`·····a·····`	`atca·-`	`····a·gg··a`	5	6,778–6,804	**
	XerC/D_9	`···········`	`·a·a·t`	`·········g·`	6	6,828–6,855	*
pAbe229-114	XerC/D_10	`···········`	`··t···`	`·········t·`	6	59,663–59,690	*
pAbe229-114	XerC/D_11	`taac··a····`	`c·ccc·`	`·········t·`	6	82,467–82,494	**
pAbe229-4	XerC/D_12	`···········`	`c·t·c·`	`·········t·`	6	2,889–2,916	*
	consensus^d	`atttCgtATAA`	`ggggta`	`TTATGTTAAaT`

^aThe numbers assigned to the different XerC/D-like recognition sites in HPC229 plasmids were arbitrarily chosen.

^bIn each of the inferred XerC/D sites the presence of the same nucleotide in a given position is denoted with a dot sign (.), otherwise the corresponding nucleotide is indicated in lowercase letters; cr: central region.

^cXerC/D sites in HPC229 plasmids were detected by using Fuzznuc (http://www.bioinformatics.nl/cgi-bin/emboss/fuzznuc) using as query NNTNYKYATAANNNNYWTTATSTKAWNN (*) [13], or by visual inspection (**).

^dNew consensus inferred from the XerC/D-like sites identified in HPC229 plasmids. Only XerC/D sites displaying a cr of 6 nucleotides in length were considered for this purpose.