Extended Data Figure 1.
FM Index alignment examples. (top) FM index alignment of a standard DNA sequence, where the size of each box represents the number of possible locations. (middle) FM alignment of a sequence where every position could be one of two bases. Base ambiguity is analogous to the k-mers we consider for every event. (bottom) Same as middle but alignments starting from all positions are found by filling in the gaps between ranges from previous alignments.