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The DNA sequences were aligned based on the protein alignment.

Thereafter, the nucleotide sequences were aligned based on the protein sequence alignment profile using PAL2NAL [ 61].

Prank [ 80] was used to conduct codon alignment, in which two protein sequences were aligned first and then DNA sequences were aligned based on the corresponding protein alignments.

In subsequent imaging sessions, previously imaged regions were relocalized and precisely aligned based on the unique pattern of blood vessels, neuronal cell bodies, and their processes.

Sequences were aligned based on the amino acid sequence using the program Clustal-W [66].

The paired ends generated for each mapping parent were aligned based on the reference contig set.

Sequences were aligned based on the translated amino-acid sequences using ClustalW in DAMBE [ 44].

tRNA genes were manually aligned based on the previously defined secondary structures.

Template sequences were first aligned based on a multiple structural superposition and then the target sequence was aligned.

The sequences were aligned based on motif conservation by MAST (Motif Alignment Search Tool) [ 78].

The promoter sequences from 107 strains were determined and aligned based on YFP expression.