Indels in Alignments

An example of an insertion or deletion (indel) type of mismatch.

The image, as in the previous two slides, shows two sequences, A C A G A C dash G A and A C A T A C A G A, placed one above the other. They have identical nucleotides at seven of the nine positions, which are indicated by asterisks. At the seventh position, there is a missing nucleotide (indicated by a dash) in the top sequence compared to an A in the bottom sequence. This dash is labeled as an indel.

Because an indel is an addition or removal of a pair of DNA bases, an indel in an alignment will be represented by a gap (sometimes a dash) in the alignment.