I am trying to compare the sequences of two files of the same circular plasmid, one is a file from my lab and the other was reported back to us from a sequencing company. I know how to align the two, however because it is circular, the plasmid maps don't align with one another properly. It seems that where one sequence begins/ends is not where the other sequence begins/ends. But when I search for a specific sequence pattern, it shows up in both plasmid sequences, just in different locations of their individual sequences. Is there a way that I can align the two sequences in such a way that they begin/end with the same nucleotide order so that I can verify whether or not the two sequences match one another 100%? 

Hello,

Sorry for the delayed answer. Unfortunately, there is no way to align plasmids on each other, but I think you can spin both plasmids manually for them to have the same beginning. You have said that you have a pattern, which you can find in both sequences - I think, we can use this pattern as a marker of, for example, the beginning of the sequence. Do the following:
1. Open your first plasmid as a sequence.
2. Find the pattern.
3. Click right mouse button -> Edit -> Set new sequence origin...
In the appeared dialog the suggested beginning will be the same as the beginning of the found pattern.
4. Click OK.

Now the first sequence is sinned and begins from the pattern you searched. Repeat steps 1-4 with the second sequence.
Now sequence have the similar beginning. Create the alignment again (I suppose, you know how to do it) and sequences will have the same beginning in the alignment