The phrase "alignment regions" is correct and usable in written English.
It can be used in contexts related to biology, genetics, or any field where alignment of sequences or structures is discussed.
Example: "The researchers focused on the alignment regions of the DNA sequences to identify genetic variations."
Alternatives: "alignment zones" or "alignment areas".
All HT-based alignment tools use the same seed-and-extend strategy [ 11, 12], which proceeds by searching for candidate alignment regions (CARs), aligning each location, and reporting the best alignments.
We identified proteins with two or more non-overlapping alignment regions where each region aligned separately to smaller homologs.
Protein models were aligned using MUSCLE and low-quality alignment regions were removed by TrimAl (Edgar 2004; Capella-Gutierrez et al. 2009).
First, each gene-set was separately aligned using muscle 3.6 [ 33] and ambiguous alignment regions were removed using Gblocks (version 0.91b) [ 34] with no gaps allowed.
Amino acid replacements were calculated for all gap-free alignment regions of >100 residues and also for fully aligned sequences including gaps.
Channel protein sequences were aligned with the use of MUSCLE (Edgar, 2004), and low-quality alignment regions were removed by the TrimAl program (Capella-Gutiérrez et al., 2009).
For these N and Sb contents, the system will still be in the type-I band alignment region [12].
Further detailed examination was done of the alignment region immediately surrounding the PRE.
For a few subfamilies, some hits were restricted to a short alignment region with fuzzy limits.
Sequence divergence was calculated using the alignment region with sequence in all species compared.
(i) For the region based on Ptrio(n) < 0.05, the inverted alignment region was completely included within the forward alignment region, or >80% of the inverted region overlapped with the corresponding forward alignment region whereas the rest of the inverted region was aligned as gaps in the forward alignment.
