Yes, I chose to interpret the problem as described (N characters "in order" with no mention of position) and to interpret the lining up of the positions as merely a typographic choice to make the correspondence more visually obvious.
There certainly are other ways to interpret the problem and I don't even assert that the interpetation that I chose is the most likely to be correct. (:
If my assumption was correct however, then using Algorithm::Diff::LCSidx to compare the pattern against the target string will work, but requires the additional step of checking to see if the contents of the two arrays of indices pointed to by the returned references are equivalent.
That'd work for the examples given, but could fail for a case like "CCCDDFFIII".