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Figure 1a shows a DNA alignment of five sequences.
Figure 3C shows the averaged LOHA plots (101 bp sliding window) for the DNA alignment of all 406 sequence pairs, for 105 sequence pairs of G1 and 45 G2 sequence pairs.
The full coding DNA alignment of all LRRs from all the available GALA proteins (>400 sequences) was analyzed and none of the tests gave a significant evidence for positive selection, although parameter estimates hinted that this possibility could not be ruled out.
Each short diagonal represents the DNA alignment of two PRAME genes or pseudogenes.
Phylogenetic trees were reconstructed using DNA alignment of pre and post-therapy NS5A sequences corresponding to each patient in the study.
DOI: http://dx.doi.org/10.7554/eLife.01096.011 10.7554/eLiFigure96.012 Figure 4 figure supplement 3. DNA alignment of cpmrp –related ABC transporter sequences in C. populi.
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Concatenated DNA alignments of the 7 housekeeping genes were used for phylogenetic analysis.
Conservation of cassette exons was assessed by the analysis of DNA to DNA alignments of orthologous genes.
As indicated above, pairwise DNA alignments of flanking and intergenic pdm sequences did not show any evidence of collinearity.
In-frame DNA alignments of the gene sequences were made using the translated amino-acid sequence using BioEdit 7.0.9.0 [ 83] and ClustalW [ 84] and adjusted by eye.
Finally, we used INDELible to simulate DNA alignments of 250, 500 and 1000 bp on the previously mentioned multispecies coalescent trees.
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