Surprisingly short barcode sequences are capable of distinguishing between species. Even 50-base barcodes can discriminate between >95% of species. The analysis is performed by adding sequence information from the 5' region of COI (A) and cytb (B) and calculating the probabilities.
Hajibabaei et al. BMC Biology 2007 5:24 doi:10.1186/1741-7007-5-24