I think this is what you want:

@a = split //, 'xx110';
@b = split //, '001xx';
splice @a, ++$i, 0, $_ or $i++ for(@b);
print @a, "\n";
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Results: x0x0111x0xYou just have to read in each line of your files, then split the characters into an array. The splice line is sort of tricky. It inserts each element of @b into @a, at the 1st, 3rd, 5th ... position of @a. I hope this helps. There may be another and better way to merge arrays, but I cant think of one right now.