TABLE 1.

Oligonucleotides used in this study

Primer no.	Primer	Sequence	Positions	GenBank accession no.	Reference or source
1	5′-CS	5′-GGCATCCAAGCAGCAAG-3′	5298-5314	AF071413	11
2	3′-CS	5′-AAGCAGACTTGACCTGAT-3′	6306-6289	AF071413	11
3	aadA1F	5′-GCTGGCCGTGCATTTGTACG-3′	5487-5506	AF071413	This study
4	ORF513rF1R	5′-GAGCTCTGCACCATCCCAC-3′	527-507	AY079169.1	This study
5	qacEΔ2	5′-ATCGCAATAGTTGGCGAAGT-3′	6383-6392	AF071413	This study
6	ORF513-4F	5′-CTCGCTTGAGGCGTTGCAT-3′	2106-2088	AY079169.1	This study
7	ORF513-4R	5′-ATGCAACGCCTCAAGCGAG-3′	2088-2106	AY079169.1	This study
8	CTX-M-2R/P2b	5′-TCCCGACGGCTTTCCGCCTT-3′	3655-3637	AY079169.1	31
9	CTX-M-2F/P3	5′-ATGATGACTCAGAGCATTCG-3′	2823-2842	AY079169.1	31
10	qacEΔ1B	5′-CAAGCTTTTGCCCATGAAGC-3′	5050-5031	AY079169.1	This study
11	orf5-R	5′-AGTTCTAGGCGTTCTGCG-3′	8157-8140	AF071413	This study
12	orf5-F	5′-CGATATCGACGAGGTTGTGC-3′	7712-7730	AF071413	This study
13	IS1326-F	5′-TACCGGGTCTTATGACCGAGT-3′	10357-10337	AF071413	This study
14	IS1326-R	5′-ACTGTCATAGCGGTTCACGTT-3′	9141-9161	AF071413	This study
15	tniBΔ1F	5′-ATCATCGACCTGTCCCACCT-3′	13201-13182	AF071413	This study
16	tniBΔ1R	5′-AGGTGGGACAGGTCGATGAT-3′	13182-13201	AF071413	This study
17	tniAF	5′-TCGTGCGGAGATCATCAGTCC-3′	14821-14801	AF071413	This study
18	merA1	5′-ACCATCGGCGGCACCTGCGT-3′	17597-17578	AF071413	13
19	merA5	5′-ACCATCGTCAGGTAGGGGAACAA-3′	16360-16382	AF071413	13
20	merR1	5′-GCGGATTTGCCTCCACGTTGA-3′	19278-19260	AF071413	13
21	merT1	5′-CCAGGCAGCAGGTCGATGCAAG-3′	19055-19076	AF071413	13
22	Tn21IR/38	5′-GGGCACCTCAGAAAACGGAAA-3′	19669-19649	AF071413	14
23	TnpR-Fa	5′-ATGCTATGCACCACCACGG-3′	3376-3394	AF071413	14
24	intF1	5′-GGGTCAAGGATCTGGATTTCG-3′	4774-4754	AF071413	This study
25	merA6	5′-GCCGACCAGTTGTTCCCCTACCTGACG-3′	16391-16365	AF071413	13
26	merD1	5′-CGCACGATATGCACGCTCACCC-3′	16211-16233	AF071413	13
27	merA0	5′-GTCGCAGGTCATGCCGGTGATTTT-3′	178950-17974	AF071413	13
28	merP1	5′-GGCTATCCGTCCAGCGTCAA-3′	18520-18501	AF071413	13
29	merC1	5′-CATCGGGCTGGGCTTCTTGAG-3′	18361-18351	AF071413	13
30	merC2	5′-CATCGTTCCTTATTCGTGTGG-3′	17987-18007	AF071413	13
31	IRIn2R	5′-TGGTGCAGTCGTCTTCTGAAAA-3′	15012-15033	AF071413	14
32	tniAR	5′-GGACTGATGATCTCCGCACGA-3′	14801-14821	AF071413	This study
33	IRTn21Fa	5′-GGGTCGTCTCAGAAAACGG-3′	1-38	AF071413	This study
34	TnpR-Ra	5′-CCGTGGTGGTGCATAGCAT-3′	3394-3376	AF071413	This study
35	IRIn2F	5′-TTTCAGAAGACGGCTGCACTG-3′	4046-4066	AF071413	14

^aPrimers 23, 33, and 34 were used in combination with primers 24 and 35 in order to characterize the 5′ end of In117 using appropriate controls.