Lab Grey Dots

I know in the lab, its practically a given that you cant change the grey dots.
What does it actually refer to?

Does it refer to a level of stability then it cannot be changed anymore?
I’ve noticed that the beginning and end of the RNA strands move.
I’m also assuming that the Promoter and the Primer used in the synthesis arent shown in the lab designs.

This was initially covered in the thread…

What are the technical reasons we can’t get the SHAPE data for the beginning or the end?

Berex, I’ll forward this to the synthesis team

Like Berex, I’d like to hear in general why we can’t get data for the beginning or end of the sequences.

I’m also interested in why the data starts at different places for different shapes (for most shapes it seemed to start around nucleotide 4 or maybe 6, but for most rounds of the Branches lab we didn’t have any data until nucleotide 10). Since we’ve had so much trouble getting that first stack right in the labs where we do get the data for at least half of it, it seems like a pretty significant blind spot.