use Algorithm::Diff qw(diff sdiff LCS traverse_sequences); my @seq1= split //,"1 AGCTGATCGAGCTAGTACCCTAGCTC 26"; my @seq2 =split //,"15 AGCTGATCGAGCTAGTACCCTATCTC 40"; my @diffs = diff( \@seq1, \@seq2 ); foreach (@diffs) { foreach (@{$_}) { print join " " => @{$_},"\n"; } print "\n"; } #### + 1 5 - 2 - 25 G + 25 T - 30 2 + 30 4 - 31 6 + 31 0