looping through a file on 2 lines in shell

I have a file which looks like this:

>a
TCCACTCCACGC
>b
ACCTCCAG

I want to loop through the file in such a way that it takes into account 2 lines at a time i.e >a and its sequence and then I want to store those 2 lines in a variable and then further use my bioinformatics tools clustalomega

Some thing like this

for lines in test.fa; 
do 
    clustalo -i $capture -o outputfile; 
done

where capture variable first time when the loop goes has this format

>a
TCCACTCCACGC

then next time

>b
ACCTCCAG

How can I do this?