Try the updated NEBcutter V3.0
This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and "submit". Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. Warning: your browser is not fully supported by NEBcutter. To achieve full functionality please use Netscape Navigator 4.0 or higher, or Microsoft Internet Explorer 4.0 or higher. What's new in V2.0 Citing NEBcutter