How do i figure out whether a recognition site is conserved or not?

Question

[Mahmoud Reda]

I have two sequences corresponding to the 16s rRNA gene for two strains of a certain species. I simulated the restriction digestion of these sequences using a restriction enzyme.

How do i figure out if a recognition sequence is conserved or not, if the coordinates of the cut are not the same in the sequences?

What i want to say is that they could be different for two reasons: A-not conserved or B-conserved but there was some base insertion that lead to this position mismatch.

I guess i would need some tolerance, how do i figure this tolerance value and how do i apply it?

Edit: i forgot to mention that the sequences are flanked by the same primers motifs.

Sequences: https://pastebin.com/0ua0dw30

Emboss's restrict:

[Mensur Dlakic]

I think the easiest way is to align the two sequences, and then see where GGCC is conserved in both of them. An educated guess is that 1177 in Seq 1 and 1442 in Seq 2 are not conserved, while all the others are.

[Mahmoud Reda]

What's the chance that non conserved restriction sites would produce same restriction pattern (similar fragments size and number) in two sequences?

I'mean, should this be looked at from the side of fragment sizes?

[Mahmoud Reda]

https://www.frontiersin.org/articles/10.3389/fmicb.2016.00643/full

"Restrict from EMBOSS Suit version 6.3.1 with the following parameters: snucleotide1, sitelen = 4, rformat = table, enzymes = enzymes.txt. From the 4379 sequences present in REBASE, we selected the 650 restriction enzymes that were commercially available, which were contained in “enzymes.txt.” From the 650 enzymes, 152 digest all P. salmonis sequences and only 65 recognized conserved restriction sites in the complete set of sequences."