Up to this stage, the alignment consists of aligned representatives of NCIV clusters.
Contigs were aligned locally in both directions and clustered together if the alignment consisted of ≥20% of the total length of each contig and the sequence was ≥99% identical over the alignment.
A block is then defined as a region in the alignment consisting of at least 3 columns, in which the NorMD is above the threshold value of 0.2.
nAij and nBij are the number of sites in the alignment consist of codons i and j for gene A and gene B, respectively.
An ambiguous region of the alignment consisting mainly of short runs of C and/or T (positions 67 109), and two regions affected by transposon activity (690 771 and 1035 1119), were excluded from the analysis.
The longest Galinter alignment consists of 117 aligned NCIVs, and the results are visualized in Figure 3A and 3B.
This nucleotide alignment consisted of 1,915 unambiguously aligned sites, once gaps and ambiguously aligned regions were removed.
The alignment consists of 26 pairs of aligned ORFs, spanning one third of the protein interaction networks of VZV and KSHV.
The resulting alignment consists of 68 genes, 52 species and 15,554 unambiguously aligned positions.
Some of the reads match multiple positions in the genome, which we refer to as alignments (for paired end reads, an alignment consists of the positions where the two reads in the pair align with the genome).
