@seqss = split ('',$seq);
$m=scalar @seqss;
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[$m-1];

would be better written as

@seqss = split ('',$seq);
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[-1];