Like this?

#! perl -slw
use strict;
use Inline C => Config => BUILD_NOISY => 1;
use Inline C => <<'END_C',  NAME => 'dnacmp', CLEAN_AFTER_BUILD => 0;

void dnacmp( char *a, char *b ) {
    int n = 0;
    Inline_Stack_Vars;

    Inline_Stack_Reset;
    while( *a && *b ) {
        if( *a != *b ) {
            Inline_Stack_Push( sv_2mortal( newSVpvf( "%d:%c:%c", n, *a
+, *b ) ) );
        }
        a++; b++; n++;
    }
    Inline_Stack_Done;
    return;
}

SV *dnacmp2( char *a, char *b ) {
    SV *res = newSVpv( "", 0 );
    int n = 0;

    while( *a && *b ) {
        if( *a != *b )
            sv_catpvf( res, "%d:%c:%c ", n, *a, *b );
        ++a, ++b, ++n;
    }
    return res;
}

END_C
use Data::Dump qw[ pp ];

sub rndStr{ join'', @_[ map{ rand @_ } 1 .. shift ] }

our $N //= 10e3;
our $L //= 8;

my @seqs; $#seqs = $N-1;
$seqs[ $_ ] = rndStr( $L, qw[ A C G T ] ) for 0 .. $#seqs;

my %stats;
for my $i ( 0 .. $#seqs ) {
    for my $j ( $i+1 .. $#seqs ) {
        m[\d+:(.:.)] and ++$stats{ $1 } for dnacmp( @seqs[ $i, $j ] );
    }
}

pp \%stats;

__END__
C:\test>dnacmp -N=10 -L=40
{
  "A:C" => 102,
  "A:G" => 137,
  "A:T" => 113,
  "C:A" => 105,
  "C:G" => 125,
  "C:T" => 113,
  "G:A" => 112,
  "G:C" => 96,
  "G:T" => 110,
  "T:A" => 117,
  "T:C" => 84,
  "T:G" => 144,
}
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yup. i don't get the output though...is it a Data::Dump problem? here's my code:

#!/opt/local/bin/perl
use Inline C => Config => BUILD_NOISY => 1;
use Inline C => <<'END_C', NAME => 'dnacmp', CLEAN_AFTER_BUILD => 0;

void dnacmp( char *a, char *b ) {
    int n = 0;
    Inline_Stack_Vars;

    Inline_Stack_Reset;
    while( *a && *b ) {
        if( *a != *b ) {
            Inline_Stack_Push( sv_2mortal( newSVpvf( "%d:%c:%c", n, *a
+, *b ) ) );
        }
        a++; b++; n++;
    }
    Inline_Stack_Done;
    return;
}

SV *dnacmp2( char *a, char *b ) {
    SV *res = newSVpv( "", 0 );
    int n = 0;

    while( *a && *b ) {
        if( *a != *b )
            sv_catpvf( res, "%d>%c:%c ", n, *a, *b );
        ++a, ++b, ++n;
    }
    return res;
}
END_C

use Bio::Seq;
use Bio::DB::Sam;
use Data::Dump qw[ pp ];

my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );
my %stats;

for my $read (@allReads) {
    my ( $ref, $matches, $query ) = $read->padded_alignment;
    m[\d+:(.:.)] and ++$stats{ $1 } for dnacmp2( $ref, $query );
    print $read->qname, "\n", dnacmp2( $ref, $query ), "\n";
}
pp \%stats;
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