#!/usr/bin/perl

use strict;
use Algorithm::Diff qw/LCS/;

my @strings;

# fill @strings with your 300 elements of 3k characters each, then ...

for my $i ( 0 .. $#strings-1 ) {
    my @seq1 = split //, $strings[$i];
    for my $j ( $i+1 .. $#strings ) {
        my @seq2 = split //, $strings[$j];
        my @lcs = LCS( \@seq1, \@seq2 );
        print "LCS for $i :: $j is ", join( "",@lcs,"\n" );
    }
}