Does this genome you sequenced have the prophage integrated? In which case you can just do careful analysis of phage genes vs host genes and identify the crossover points. Or are you looking for "putative" integration sites? Those can not really be determined a priori except for the known ones since phage evolve to use existing sequences as their integration site.
Thw genomes I am studying O157 isolates, the sequence is completed (closed) and have around 14-16 lambdoid phages interated, Those carriying shiga toxin genes is easy to determine the integration site because they are well known and I can identify by in silico PCR. But the others is dificult because I have no a reference genome pre-integration.
There is an entire array of e. coli genomes in the database, can you not identify genes or regions that have become unlinked due to the prophage insertion?