I wante to have an idea about the thread count and the number of input sequences
I don't think there will necessarily be more sequences as the number of threads grows, if that's what you're asking. We were told not to assume anything about the input.
there is no such information available, they've said in a number of threads that, they won't be giving us information about the input so that we do not focus on optimizing our programs for a determinated type of input rather than optimizing it to any kind.(by "they" i'm refering to intel guys).
The simplest method is to associate a thread for each sequence but if the thread count is very high compared to the number of sequence, this method is not effective.
When HT kicks in, it may mess up all the "scheduling" if you are using SSE4.2 - in our implementation we had trouble adjusting it and possibly it is still far from acceptable in niche cases.