>perl -wMstrict -le
"my $seq =
   'AATCGGGTATGAAAAATTTTGCCGGCGTTTGCGATGAATATATTGCCGGAGAGA';
 ;;
 my $prime1 = 'ATGA';
 my $prime2 = 'TGCCG';
 ;;
 my @subseqs = $seq =~ m{ $prime1 (.*?) $prime2 }xmsg;
 printf qq{'$_' } for @subseqs;
"
'AAAATTT' 'ATATAT'