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

Example:

$a="agaaaagavvgglggy"
$b=<STDIN>;

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,
siri

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