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