The phrase "alignment ends" is correct and usable in written English.
It can be used in contexts related to positioning, organization, or coordination, particularly in technical or design discussions.
Example: "The alignment ends of the components must be adjusted to ensure proper fit and function."
Alternatives: "alignment boundaries" or "alignment limits".
The new alignment ends a short distance east of the Cove Valley service plaza on the original segment.
The one-way street alignment ends at 11th Avenue South, but quickly begins again as US 30 / US 67 turn to the north onto northbound South Third Street and southbound South Fourth Street.
The one-way street alignment ends at 11th Avenue South, but quickly begins again as US 30 / US 67 turn to the north onto northbound S. Third Street and southbound South 4th Street.
The shift gives the number of possible insertions and deletions not considered at the alignment ends.
We searched a maximum of 400 bp on either side of the coding sequences to eliminate very thin alignment ends.
Not considering the special case of indels at the alignment ends would have classified this read as incorrectly mapped.
Once CCS reads are sorted, the pipeline uses Bowtie2's default alignment (end-to-end read alignment) to align reads to the corresponding reference sequence and outputs a set of alignments in SAM format.
Existing alleles were translation-aligned between start (alignment start) and stop (alignment end) codons, those containing a frameshift or stop codon were removed, and the modal consensus sequence was exported.
Likewise, the score of a best alignment ending in an unconserved (intergenic) region cannot be calculated from the score of a best alignment ending in a conserved region (intron) of the two sequences.
Given this fact, the score of a best alignment ending in a conserved (intronic) region cannot be calculated from the score of a best alignment ending in an unconserved (intergenic) region of the input genomic sequences.
Consequently, the score of a best alignment ending in the first (resp. last) position of the searched gene can only be calculated in the presence of the codon ATG (resp. TAA, TAG, TGA) in both sequences.
