This 5' flank pattern is present in about 35% of the aligned sequences, and is not present in alignments of motifs outside of the HADB enrichment zone.
In alignments of 11 Streptococcus pneumoniae genomes, the aligned core varied by 1904 nucleotides out of ~1.59 M core nucleotides aligned for values of G between 1000 10 000.
Genomes were aligned using mauveAligner (Mauve version 2.1.1) [39], [39] with default parameters, which resulted in alignments of 116 genome segments.
Deletions were readily observed in alignments of 454-reads to the reference genome.
Beijing retained its characteristic willingness to adjust to changes in alignments of power and in the composition of foreign governments without passing a moral judgment".
The MSAs resulted in alignments of widely different lengths and quality (Table 2).
Finally, Shannon's entropy for each position in alignments of SVR and NR sequences was assessed.
Recently, two methods have been described that detect conserved RNA secondary structures in alignments of multiple genomes [58], [59].
Similar, but less steep, miRNA conservation profiles have been distinguished in alignments of multiple primate species [8].
The rate of amino acid substitution per site was estimated at each position in alignments of protein sequence from four Saccharomyces species for 3334 genes.
Ultraconserved elements were first defined as sequences at least 200 bp long that show perfect conservation in alignments of the human, mouse and rat reference genomes (perfect HMR conservation).
