Figure 3: Creation and characteristics of thermoalignments compared to local alignments and the number of mismatches.
From: ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
(a.1) Examples of full-length primer sequences. (a.2) The top-ranking BLASTn high-scoring segment pair (HSP) alignment for two off-target sequences (bottom strand) is processed into a (a.3) thermoalignment by end-filling (ungapped BLASTn) or removing gaps and end-filling (gapped BLASTn) the original BLASTn HSP alignment. (b) For 877 candidate primers outputted by the UOD module for the 24 kb region described in the text, the Tm was calculated for each top-ranking BLASTn HSP alignment and the corresponding thermoalignment. (c) Using the subset of thermoalignments formed from ungapped BLASTn HSPs (n = 169,404 alignments), the plot shows the relationship between the off-target Tm for thermoalignments compared to the total number of mismatches. (d) Using the same subset of data in (c) the plot shows the difference between the on-target Tm and the off-target Tm of thermoalignments compared to the total number of mismatches.
