Table 1.

Predicted base pairs for domain 2 of the FMDV IRES with 18S and 28S rRNA*.

Domain (nt position)	IRES sequence (5′-3′)	rRNA sequence (5′-3′)	nt position	rRNA
D2 37–40	UGAA	UUCG	939–942	18S h23
D2 50–54	GGUCU	GGACC	985–989	18S h23
D2 60–68	GGUCUAGAGG	UUCUUGGACC	965–974	18S h23
D2 36–42	UUGAAAC	GUUUUAA	4357–4362	28S h88
D2 50–72	GGUCUUUCCAGGUCUAGAGGGGU	GCCUCUCCAGUCCGCCGAGGGCGCACC	1436–1461	28S h30ES9
D2 51–56	GUCUUU	GGAGGC	3970–3975	28S h77
D2 51–57	GUCUUUC	GAAAGAU	1523–1528	28S h32
D2 51–57	GUCUUUC	GAGAGAU	2448–2454	28S h52
D2 51–57	GUCUUUC	GAAGGGC	4272–4277	28S h85
D2 51–57	GUCUUUC	GAGAGGC	4908–4914	28S h98ES39b
D2 52–58	UCUUUCC	GGAAAGA	3899–3905	28S h73
D2 67–84	GAGGGGUAACACUUUGUAC	GUGCGGAGUGCCCUUCG	4868–4883	28S h98ES39
D2 68–72	AGGGGU	GCCUCU	4695–4700	28S h97
D2 74–80	ACACUUU	GAGGUGU	3953–3959	28S h76

^*Prediction of base pairs was performed using IntaRNA. Only ribosomal RNA nucleotides located in flexible regions (according to⁵⁴) were considered. Unpaired nts are indicated in bold.