See our SD Java CloneDR, a tool for detecting exact and near-miss duplicate code in large Java systems.
The CloneDR will find code clones in spite of whitespace changes, line breaks, comment insertions deletions, modification of constants or identifiers, and in a number of cases, even replacement of one statement by another or a block of statements.
It shows where each set of clones is found, each individual clone, an abstraction of the clones having their shared commonality and parameterization of the abstraction to show how each clone instance can be derived from the abstraction.
It finds 10-20% clones in most Java systems.