#!/usr/bin/perl --
use strict; use warnings; use Data::Dump;
$_ = 'G_I1E2_GTGGAG^303CTGgacgCCCTGC_I2E3_TACA';
my @matches = "";
while( m{
    ([ACTG]+)# $1 is upper
    |
    ([actg]+) # $2 is lower
}gxsm
      ){
    if( $1 ){
       $matches[-1] .= $1;
    }
    if( $2 ){
       push @matches, "";
    }

}
dd \@matches;
__END__
["GGTGGAGCTG", "CCCTGCTACA"]