Fig. 4. Consensus sequences of the ALIEN DNA determined through multiple sequence alignment of read basecalls.

A An example subset of a multiple sequence alignment for test sequence 1 showing how the consensus sequence can be determined by combining multiple single-molecule reads. B The basecall probability at each sequence position displayed as a stacked bar plot colored by base identity. Sequencing accuracy for each strand is determined by alignment of the final consensus basecall to the central 22 nucleotides of the true sequence. Three bases were trimmed off each end to eliminate edge effects so that the measured sequencing accuracy is an estimate of bulk sequencing accuracy. Sequencing errors (mismatches, insertions, and deletions) are marked with a minus sign below the sequence position. Insertion and deletion errors are also shown as gaps in the true sequence and consensus sequence, respectively. Average per-base consensus accuracy is 81 ± 4% (s.e.m.). The per-base consensus accuracy for Test sequences 1-4 are: 78 ± 8% (N = 18 reads), 78 ± 8% (N = 21 reads), 67 ± 9% (N = 43 reads), and 83 ± 7% (N = 20 reads), respectively. Error bars are s.e.m.