A new tool is launched for DNA restriction analysis, named gCut and you can download it by visiting this page: gcut.sourceforge.net
read the manual and the readme file (important) and try this program (its free).
well, its not the same in gCut you enter the restriction enzyme you want to work with and he will find the restriction sites in your sequence (must be in fasta format) and gives you all the fragments of dna that result. its really important , you have to see it.
you cant do it in a sequence with 10 million bp, gCut can analyse sequences with 100 million bp in few seconds and gives very precise results in fact the results are unquestionable. so give it look and tell me what you think.