TABLE 1.

Primers used for characterization of the cap region

Primera	Sequenceb	Use	Reference
FI3	TCTTAGTTCCATGGGATGCTTTCTGTGTG	Long-range PCR, Southern blot probe cap110.58, sequencing of cap region, and in vitro translation of aliB-like ORF 1	11
FI4	CGCTGAACTTTTGTAGTTGCTGTCTGGTCAAC	Long-range PCR and sequencing of cap region	11
aliA_b832	TGCAGGTTTGCTGGTATCTTGAC	Long-range PCR, Southern blot probe cap110.58, and sequencing of cap region	This study
cpsA3	ATCCTTGTCAGCTCTGTGTC	PCR for Southern blot probe cap111.46	14
cpsB2	TCACTTGCAACTACATGAAC	PCR for Southern blot probe cap111.46	14
104_b832.12	GTATCTGAACCTGATTGTCCGC	In vitro translation of aliB-like ORF 1	This study
110_FI3.4	AACACTTGGAACGGAGAATG	PCR detection of aliB-like ORF 1 and RT-PCR	This study
104_b832.14	GCCCTTTGTTATACCTAGATGTTTC	PCR detection of aliB-like ORF 1 and RT-PCR	This study
104_FI3.6	AGATGCCAAATGGTTCACGG	PCR detection of aliB-like ORF 2 and PCR for Southern blot aliB-like ORF 2 probe	This study
104_b832.10	GAAATCTTTTAACAAATAAGGTCCG	PCR detection of aliB-like ORF 2 and PCR for Southern blot aliB-like ORF 2 probe	This study
Rif-399f	GATGAYATCGAYCACCTCGGAAA	RT-PCR, control	18
Rif-525r	GATGTTAGGTCCTTCAGGTGTCTC	RT-PCR, control	18
dexB_f145_XbaI	GCTCTAGAGCTGGCTTTCTCCCGTTTATGACA	PCR for mutant construction	This study
dexB_b1504_BamHI	CGGGATCCCGAGACAGATTTGACGTTTCCTTC	PCR for mutant construction	This study
capN_F1_ClaI	CCATCGATGGTCGTTGGTGCTGGTTTGTCA	PCR for mutant construction	This study
capN_B1_XhoI	CCGCTCGAGGCACTGCTTTGAGGTTGTAGATAA	PCR for mutant construction	This study
cat_Spn_F1_HindIII	CCCAAGCTTGGATTTTTCGCTACGCTCAA	PCR for mutant construction	This study
cat_Spn_B1_HindIII	CCCAAGCTTTCACTTATTCAGGCGTAGCACCAG	PCR for mutant construction	This study

^aPrimers used for primer walking sequencing of the different cap regions are not shown.

^bRecognition sites for restriction enzymes within the primers are underlined.