1. You didn't show what you've tried so far
  2. You didn't define how many mismatches are permitted
  3. You didn't tell what's a "nucleotid"
  4. You didn't define what to do if there are less than 5 nucleotids on either side
  5. You expect us to work for free?

So to "solve" your problem in the most easy way, matching your description: 

my $s1='TCGAGTGGCCATGAACGTGCCAATTG';
my $s2='ATGATCCTG';
($s1,$s2) = ($s2,$s1) if length($s1) > length($s2);
my $len= length $s1;
print "Matches:\n";
for (my $i=0; $i+$len+10 <= length $s2; ++$i) {
    print substr($s2, $i, $len+10),"\n";
}

[download]

prints: 

Matches:
TCGAGTGGCCATGAACGTG
CGAGTGGCCATGAACGTGC
GAGTGGCCATGAACGTGCC
AGTGGCCATGAACGTGCCA
GTGGCCATGAACGTGCCAA
TGGCCATGAACGTGCCAAT
GGCCATGAACGTGCCAATT
GCCATGAACGTGCCAATTG

[download]

I didn't bother to put the number of mismatches. In most cases it will be length($s1) ;)

>
s$$([},&%#}/&/]+}%&{})*;#$&&s&&$^X.($'^"%]=\&(|?*{%
+.+=%;.#_}\&"^"-+%*).}%:##%}={~=~:.")&e&&s""`$''`"e

In reply to Re: Comparing 2 different-sized strings by Skeeve
in thread Comparing 2 different-sized strings by AdrianJ217

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