Fig. 1

An example of a protein family, its alignment with a gene, and read mapping positions of a read pair against the gene. The Pkinase model had annotation line of consensus structure. The line beginning with Pkinase is the consensus of the query model. Capital letters show positions of the most conservation. Dots (.) in this line represent insertions in the target gene sequence with respect to the model. The midline represents matches between the Pkinase model and the AT2G28930.1 gene sequence. A + represents positive score. The line beginning with AT2G28930.1 is the target gene sequence. Dashes (-) in this line represents deletions in the gene sequence with respect to the model. The bottom line indicates the posterior probability of each aligned residue. A 0 represents 0-5%, 1 represents 5-15%,..., 9 represents 85-95%, and * represents 95-100% posterior probability. The line starting with r ₁ and ending with r ₂ is read mapping regions on the gene sequence. A - indicates where the position of the read can be mapped to the gene sequence