One way of describing the separation of two sequences in flow space is by the hamming distance between them for relevant flows. Hamming distance is the number of flows in which the expected homopolymer length is different between the two sequences. For example, if two barcodes differ in 5 flows in flows 9-22, those two barcodes have hamming distance 5.

Hamming distance corresponds naturally to the ability to detect and correct errors. When two sequences have hamming distance 5, 2 errors can occur on one of the sequences and that sequence is still 3 errors away from the other sequence. Sequences separated by hamming distance 5 can tolerate 2 errors and still be classified correctly.