Well, a flute would normally only go down to Middle C, or D, depending upon type. My 'B foot' Boehm System flute goes down to B below middle C, which is not as commonplace as the more usual 'C foot' models.

I'd be inclined to suggest the Clarinet as a more likely possibility. Depending upon type, that could go down to E below Middle C (written), 'extended' models even lower.

Bear in mind that a clarinet is usually a 'transposing' instrument - the usual key is Bb, meaning that a C on the MS would come out of the instrument as Bb, if you follow?

This means that a clarinet playing along with a flute would have the music in a different key - for example, if the flute's music was in C, the Bb clarinet's music would be in D for them both to sound in the same pitch.