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#!/usr/bin/perl

# http://perlmonks.org/?node_id=1144405

use Algorithm::Diff qw(traverse_sequences);
use strict;
use warnings;

my $S=" MSATPLTQEQKKA";
my $T=" MNATLTQQTKA";

my @from = split //, shift // $S;
my @to = split //, shift // $T;

my $top = '';
my $bottom = '';

traverse_sequences( \@from, \@to,
  {
  MATCH     => sub {print $from[shift()]},
  MATCH     => sub {$top .= $from[shift()]; $bottom .= $to[pop()]},
  DISCARD_A => sub {$top .= $from[shift()]; $bottom .= ' '},
  DISCARD_B => sub {$top .= ' '; $bottom .= $to[pop()]},
  } );
print "$top\n$bottom\n";
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This outputs:

 MS ATPLTQEQK KA
 M NAT LTQ Q TKA
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These two sequences are aligned by common character.

Please show inputs and desired output when you ask for help.
Giving several test cases is always a good idea.