Interpreting Alignments

A simple sequence alignment.

The image 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 out of nine positions, which are indicated by asterisks. At the fourth position, the top sequence has a G compared to a T in the lower sequence. The other mismatch is a missing nucleotide at the seventh position (indicated by a dash) in the top sequence compared to an A in the bottom sequence.

  • Each line is one DNA sequence, and each column is a position in the alignment.
  • An asterisk indicates that all the letters in that column match.