nindoja

Use strings or character arrays, your choice. Loop through each strand, comparing each base one by one. Then:

1) If the two bases are different, add the base to the diff_base string.
2) If the two bases are the same, and add a '0' to the diff_base string.

Then you can see where the differences are by outputting the diff_base string, and all non-zero values are differences.

Klipt

For a more thorough comparison I'd recommend edit distance:
although in this case the 'differences' will be a whole sequence of insertions, deletions, and substitutions, so I'm not sure how you'd output that ... it may be overkill for your project.