I have a small doubt regarding my program. Hope you will help me in solving that.



let the input seq is "ttttttttttagaaaagavtttggyttttttt";

here the input matches with $a only with the letters in bold : ttttttttttagaaaagavtttggyttttttt

i want to know what we can do to give input showing both matches and mismatches in the input.(mismatch shold me shown as a hiphen)
That means the output should be like this:
The given sequence matches with the pattern at - - - - - - - - - - agaaaagav- - -ggy - - - - - - -

Hope you will help me in solving out this.

Thanks in advance,