Unfortunately not having any luck on iBooks on Mac -- I'm assuming this type of input is just not allowed. (This is the same for a XHTML compatible form in a smart object in PubCoder and a normal form inside of a Hype document)
One option is to allow clicking on individual base pairs to fill in an input field. It seems you will need to simulate a keyboard. (@MarkHunte to the rescue... --> Virtual keyboard for use with Textareas )