This is complementary answer to what @gc5 provided.
for cases that are using "the second notation" which looks like:
|________________what we are
trying to ...
The reason you aren't finding this information in the literature is that this metric doesn't match the way that most genetic circuits work.
You appear to be thinking about operations in genetic circuits as being like instructions on an electronic processor. In that world, an instruction starts, executes, and stops, and you can measure the amount of energy ...
I would suggest using the FTP at NCBI to download GFF files for whatever organisms you are interested in, as suggested by commenters. GFF files will have annotations for the genome for genes and also for many other features (figure 1).
Not entirely clear about the goals of this, but if you want annotated coordinates of things in genomes GFFs are a good ...