map{$s1 =~ s/$_/[$_]/g} @a1;
map{$s2 =~ s/$_/[$_]/g} @a2;
map{$s3 =~ s/$_/[$_]/g} @a3;
map{$s4 =~ s/$_/[$_]/g} @a4;
print  join("\n",$s1,$s2,$s3,$s4)."\n";

gives;
CCC[ATCTG]TCCTT[ATTTG]CTG
AC[CCATC]TGTCCTTGGCCAT
[CCACC]A[GCACC]TGTC
C[CCAAC]ACCTGCTGCCT

Is this what you want? If not, Please give what is expected to happen 
+for the last 2 strings.

Hope this helps!
[download]