Other clades are robustly supported throughout the alignment space, indicating that the exclusion of ambiguously-aligned regions can lead to a loss of phylogenetically valuable information.
The CICPs appear throughout the alignment and there is a dearth of correlation with predicted contacts in the disordered C-terminus region (Fig. 2C).
In contrast, the dog and rodent sequences contained multiple nucleotide insertions and /or deletions, resulting in multiple gap insertions throughout the alignment (Figure S1).
This step insures that the two subtrees are consistent throughout the alignment, however it does not guarantee that the subtree topologies are consistent.
Additionally, ITS2 sequence length was 474 bp in the outgroup Pleistodontes sp from F. glandifera and created indels throughout the alignment.
However we observe that several blocks of 2 4 conserved residues exist throughout the alignment of the LRR-domain between DcAFP and grass IRI-sequences.
Alignment of 154 cluster members, 1 for each species contained and ranging in length from 127 to 266 aa, with Clustal Omega (Sievers et al., 2011) showed good alignment throughout the length of the sequences with 28 identical and 27 similar positions distributed throughout the alignment with 9.69% overall identity (data not shown).
Sites 54, 394, 407, 132 and 448 for instance show a conserved polarity throughout the alignment, excepted for the Q6L8R2_RAPSA allele, which shows polarity change for the five sites.
Specifically, bowtie was run using default parameters of maximum number of mismatches (N) = 2, seed length (V) of 28, and maximum total of Phred quality scores at all mismatched positions throughout the alignment (E) = 70.
Comparison of secondary structure elements (α helices and β strands) with S. tuberosum AGPase SS shows a high percentage of sequence conservation throughout the alignment which suggests a similar functionality of this protein in both monocot and dicot.
