TABLE 2.

Primers used in this study

Primer namea	5′-to-3′ sequence	Positionb
Cip-RTdir	TGTTGTTAAATCAGGTAATGTAGG	4291
F-RTrev	TCTTCCGTGCATTGCTTCCAACC	294
F-RTdir	GCGAAATCAAGTTCAATGCTGACGG	1426
C-RTrev	ATCAGCTGCACTTGAAGCGATG	102
C-RTdir	AATGATGGTGCTATAGATGC	1226
G-RTrev	TGCAGATGTATATGACATAGGTAG	318
G-RTdir	CACTTCCAGCATAGATGTTAAGG	2058
E-RTrev	GAGCAGTTATCTTGTACTTAGG	220
E-RTdir	GTCAGTGACTCCTCCAACTA	2463
X-RTrev	AAGCAGATGCAGTTGGTGATG	154
X-RTdir	GATACAACAGGTCTGGTCAG	472
H-RTrev	TCTGTTAATTGAGCATCTCC	227
H-RTdir	TATTGATGCATTGGACGTTG	2067
J-RTrev	GCCTGTGACATATTAGTTCC	280
J-RTdir	AAAGTGTATGGAAATGAACCG	2049
K-RTrev	GAGTATCATTGTCAACATCACC	115
K-RTdir	CAGAGCATCCTGACGTAGTC	1251
M-RTrev	ATTCGTACAATGACCAACCT	336
M-RTdir	GTTCTTTGGAGGTACGATTG	1374
Y-RTrev	ACCAGAGGTAATTGGAGTGG	246
Y-RTdir	GGTCAATCAACAGAGTTAGATAC	1933
N-RTrev	GTTTGGTTTACCAGTCATCC	333
Cip-PE1	CCTAAAGACTTTTTACGCATTG	20
Cip-PE2	TTTAGGCATACTGATATAACTGAA	−121
Cip-PE3	TTAAGCCGTTTACCTCAGGTGC	−512
F-PE1	ATTCTTACTCATTTTACACCTTCC	12
F-PE2	AGAGTAAAATCTGCTCATATGTTT	−35
C-PE1	AACCTTTGATCATGTTCTTACCT	13
G-PE1	TCTTAAGCAACAAGCCATCACTCC	11
E-PE1	AACCTTTTTTTCATATTTACCTCC	14
E-RCdir	TGGTATTGCAACCTGGACCGTAA	1158
E-RCrev	GAAGATCTAACAGTGTGATTTTTC	2658
X-RCdir	GGTAAACCATTTTACATCTGATT	63
X-RCrev	TTCAGTATCTCCAAATGCACC	638
H-RCdir	GCTTTTAACTATGGGGAGGCTT	103
H-RCrev	GCAAAATCGAGAGCATCAATA	2183
J-RCdir	CCTCCTTTCAACTACGCAGAAGCATTT	106
J-RCrev	TTTACCTTCGTCATACATAACCGCAAC	1809
K-RCdir	GATTCCATATGGCTGCGACTACAT ACAAA	72
K-RCrev	GGGCTCGAGTCTGACTACGTCAGGATG	1272
M-RCdir	GGGGTGCACCCGAGGAGCAAA	476
M-RCrev	AACAATCGTACCTCCAAAGAAC	1395
Y-RCdir	AATTCCATATGACGGCAGCATCGG CACGC	76
Y-RCrev	GGGCTCGAGCGAAAGCAAACTTGCT TTTAG	2030
N-RCdir	GGCAGACAGAGGAATAGGGTT	255
N-RCrev	TATCAATCCGCCTGTATCACCTG	1257
16S-RCdir	CCGAATTCGTCGACAACAGAGTTT GATCCTGGCTCAG	8 (E. coli)
16S-RCrev	TACGGTTACCTTGTTACGAC	1494 (E. coli)
16S-RS	CCGTCAATTCCTTTGAGTTT	907 (E. coli)
F-RS	ACTAGTATCCAACGGAG	471
Cip-IPCRdir	GTAAGCACCTGAGGTAAACGG	−536
Cip-IPCRrev	CCATTTATGTAATTAAATGACAAG	−649
N-IPCRdir	CCAAAATGTCACGTTTAGCAAAGGA AGTAT	862
N-IPCRrev	GATACTTATCCAAAGCTGCCTC	879
N-S1	CTTTGGAAGCATACATGAGG	323/orf4
N-S2	CTCATGGAATTCAGGAACTAT	528/orf5
Cip-S1	TACTAAAATCACTTATTGTCAGTAC	650/orf2
Cip-S2	GCATAGCACATATGACCTTC	819/orf2
Cip-S3	TGGCATTGGTAGCTCAGGAT	433/orf1

^aThe primer's name includes the letter or name of the gene followed by the analysis for which it was designed: RT, RT-PCR; PE, primer extension; RC, riboprobe cloning; RS, riboprobe synthesis; IPCR, inverse PCR; and S, sequencing. Dir and rev indicate direct and reverse primers, respectively.

^bThe position indicated refers to the position of the primer 5′ nucleotide on the corresponding gene, with the nucleotide numbering beginning from the first codon of the gene. The sequences of the corresponding genes are described in GenBank under accession no. U40345, U30321, M87018, AF316823, and DQ156106.