some questions about dnadiff output

[binlangman]

dnadiff can provide detailed information on the differences between two genomes, especially the difference between two assemblies of the same organism. I have used two different tools(i.e. ABySS and Velvet) to assembly the same data set, and then I've compared the two assemblies by run the following commands: dnadiff /opt2/tools/readdepth/velvet/contigs.fa /opt2/tools/readdepth/abyss/asm-contigs.fa and dnadiff /opt2/tools/readdepth/abyss/asm-contigs.fa /opt2/tools/readdepth/velvet/contigs.fa. However, the two output files(i.e. out.report) are different. I think the output files should be same, because it only compares the two assemblies, and the output should be independent of the oder of contigs which were produced by different assembly tools, but the fact is not. Why? And I want to know what caused the difference of the outputs?

Thanks very much!