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The higher level of nucleotide conservation of the North American PEDV strains in the E and M genes and greater genetic variability of N gene may be representative of geographic specificity rather than virulence.
Although the level of nucleotide conservation is quite variable among the different tRNAs (% differences: 0 6.9% nucleotide differences), the identified tRNA-like structures evolve faster than most canonical tRNAs (1.6 10.4% nucleotide differences).
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Indeed, trnG, trnK, trnN, trnM and trnE, which showed the highest levels of nucleotide conservation (%INUC ≥ 70), were all located on the α strand.
Because the host range of some bacteriophages is quite limited and, in many cases, each bacteriophage only attacks a single strain of bacterium [ 44], the prophage region itself may not demonstrate high levels of nucleotide conservation in the genome.
In addition, sequence comparison of SPS+A modules across multiple Drosophila species revealed elevated levels of nucleotide conservation in the regions between and adjacent to the paired S sites for several E spl -C gE spl -C5].
ALN, alignment name; %INUC, percent of identical nucleotides agenes on the L strand Nucleotide conservation was strongest on the H strand, with trnC, trnG and trnM, having the highest levels of nucleotide conservation (%INUC > 50), followed by TrnE, trnL2, trnQ, trnS2, trnV and trnY at 40 ≤ %INUC ≤ 50.
The difference in degree of nucleotide conservation between the IDR and the remainder of the molecule is highly significant (P<10−16), and indicates a dramatically higher level of divergence for the IDR-encoding portion of the mammalian TS transcript.
In addition, we repeated the above analyses using phyloP score as the measure of nucleotide conservation level (Additional file 4: Figure S3).
The pattern of nucleotide conservation was markedly α strand-biased.
CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos.
A plot of nucleotide conservation and intron occurrence was used to visually select promising loci.
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