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We further removed all positions for which Convoluta was not present (due to partial gene sequences), resulting in a final alignment of 11,959 positions.
The combined 16S, CaM and 18S alignment, totaling 2691 DNA base pairs (bp), was edited by eye and 53 bp corresponding to ambiguous regions within the 16S and 18S fragments were excluded, resulting in a final alignment of 2638 bp.
These were excluded resulting in a final alignment of 56 unique primate mtDNA genome haplotypes.
We obtained between 680 and 726 bp (Otus lettia ussuriensis and Aegolius acadicus, respectively) for the myoglobin intron-2 resulting in a final alignment of 749 bp.
Of these, 394 bp were excluded from the analyses due to alignment ambiguities in non-coding genes and saturation in the 3rd codon position of the mitochondrial ND2 locus, resulting in a final alignment of 5782 bp.
The alignment was then trimmed using trimAl (Capella-Gutiérrez et al. 2009) with gap threshold and conservation parameters both set at 0.5, resulting in a final alignment of 381,280 positions.
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In this case, a final alignment of 1,435 concatenated proteins (444,554 amino acids) was used in the analysis.
As discussed in Observation 1, a final alignment is generated by extending a seed from its end positions.
In the final step, a final alignment is chosen based on the the coverage of the alignment over the target sequence.
Sequences of CYTB and IRBP were edited and aligned in SeqScape v2.5 (Applied Biosystems), producing a final alignment of 1140 and 1276 bp, respectively.
A final alignment was created in which the POMGnT1 sequence was aligned with the sequence of the homology model.
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