TABLE 2.

Sequences of primers used in this study

Primera	Primer sequence (5′-3′)	Coordinateb (5′ end)	Size (bp)c	Use
LJ-F	GTGAATCTTGATGAGACGCTCTG	872910	1,011	PCR
LJ-R	GGTGAGCCAGGCTTATTTGGG	873920		PCR
SCE4.LJ-F2	GGATCATCAACCGAAGAGGTAGA	This study		Sequencing
SCE4.LJ-R2	GCCTGCATCACCACATTCCTCATA	This study		Sequencing
SCE4.LJ-F3	GGTTAGCTCTTCCATCGACAACA	This study		Sequencing
SCE4.LJ-R3	GGTCTGGAAATACCACAGCGT	This study		Sequencing
aldA-F	GCATCTGATTATGACCAAAGAATAGG	875610	1,116	PCR
aldA-R	GTCAATGGATGAAGCCACACAGTG	876725		PCR
tagA-F	GGTGGTAAGATATTCACTCTTAATG	877014	351	PCR
tagA-R	GAGACATCTATAGAATACTGGCTG	877364		PCR
tcpI-F	GCCGTCTCCGCATTAAGCTCTGCAC	887200		PCR
tcpI-F2	GCCAACGTAATGATGCACGCAAGTA	888350	1,212	PCR
tcpH-R2	CGTTACACCAAGTGCTACAACGAAT	889561		PCR
tcpA-F(cla)	CACGATAAGAAAACCGGTCAAGAG	M33514	617	PCR
tcpA-R(cla)	ACCAAATGCAACGCCGAATGGAGC	M33514		PCR
tcpA-F(elt)	GAAGAAGTTTGTAAAAGAAGAACAC	890480	471	PCR
tcpA-R(elt)	GAAAGGACCTTCTTTCACGTTG	890951		PCR
tcpQ-R	GAGGACTGTTCTGCAATCTGCTCAT	892609		PCR
tcpF-F	GAGTTCCACATGCAGAAACAGGA	899444		PCR
tcpF-R	GCCACGAATGTGGCTGTTATCTTATC	899724		PCR
toxT-F	ACTGTATAGCAAAGCATATTCAGAGA	899658	1,115	PCR
toxT-R	CAGTGATACAATCGAAAATAGGATC	900772		PCR
acfB-R	GAGCGTGCTTTATCATGGTCGAT	902296		PCR
int-F	GAAGTAATGAAACCGATAAGTGG	913253	347	PCR
int-R	TGCTTTGTACCAGTCACAGATAG	912907		PCR
RJ-F	TCGTTAGCGTGTCGGTTCGCAGG	914405	1,499	PCR
RJ-R	TGCTTTGTACCAGTCACAGATAG	912907		PCR
ig-1-F	GAGCCTGTGACACTCACCTTGTAT	1566438	629	PCR
rstA-R	GCATAAGGAACCGACCAAGCAAGAT	1565810		PCR
rstC-R	GCTCAGTCAATGCCTTGAGTTG	1564169		PCR
orfU-F	GGTGTTATTTGATGGCTGCATG	1570758	3,713	PCR
ctxB-R	GCTTCAGTAAGATATGCAATCCTCAG	1567046		PCR
tcpE-F2	GCTCCTGACAATGGCTGTTTATTCA	898458		PCR
tcpF.n-F2	GCTATTCCTACTCCAGACCAACTA	This study		Sequencing
toxT.n-F2	GAGTTTGATTGTCGATCTCAGTT	This study		Sequencing
toxT-R2	CACAGTTCCAGAGGAGCAGAT	This study		Sequencing
tcpJ-R2	GGGCACATGGAGCGATTTGAAT	900876		Sequencing
tcpJ-R	GCTTGGTCCAAGAGGGATAT	901444		PCR
226.tcpF-F	GGATATTCCTACAGCTGAGCAGTT	This study		Sequencing
226.toxT-R	GGTCATATGTGCTCACTATCTCT	This study		Sequencing

^aLJ, left junction; RJ, right junction; aldA, toxT, and int, genes in the V. cholerae pathogenicity island; ig1, RS, orfU, ctxB, and rstA, DNA segments and genes in the CTXφ prophage; tcpI, tcpQ, tcpF, and acfB, genes in the V. cholerae pathogenicity island VPI. 

^bUnless stated otherwise, the coordinates used here correspond to positions in the complete genome sequence of V. cholerae El Tor N16961 (19), available at http://www.tigr.org/tdb/CMR/gvc/htmls/SplashPage.html. 

^cSize of diagnostic PCR product generated with pairs of primers (only those important to this analysis are given).