When we give an input sequence , the tool should match with the pattern and give the matches and mismatches in the output.

i will give you 2 small examples. if you cant get it pls let me know.
i will try to give a clear idea.

example 1:

$a=APPLE; # let it be a pattern
$b=<STDIN>; # input sequence

suppose my input sequence ($b) is : MYAPPLES
Then the input ($b) will match with $a only from 3rd letter to 7th letter.( i.e APPLE)
i want to get out put as below:

The matching region is - - APPLE- (i.e mismatches should be shown as hiphen)

If the pattern is "MYAPPLE" and the input is "APPLEMY"

Then the output should be:

- -APPLE- -

i.e the first 2 hiphens represent gaps and last 2 hiphens represent mismatches.


Example2:
$a="agaaaagavvgglggy" # a pattern signature
$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.(mismatches in the seq should be shown as a hiphen)
That means the output should be like this:
The given sequence matches with the pattern at - - - - - - - - - - agaaaagav- - -ggy - - - - - -

You're probably looking for a diff algorithm.

http://search.cpan.org/~yappo/String...String/Diff.pm

Beyond that, you haven't specified the problem completely enough to come up with an actual answer. And it sounds like a homework problem to me.