threads are formed as messages are posted in response to another. most interfaces I'm aware of group such messages so that they appear together in timelines. your response, as well as karl's, appear next to my initial question in my timeline.
subtoots are reactions posted as standalone messages, so as to separate them from a thread instead of keeping them together. they're used to avoid hijacking threads when going down a tangent, but also to allude to another thread without copying its participants.