The phrase "alignment problematic" is not correct in standard written English.
It may be intended to describe a situation where alignment is an issue, but it lacks proper grammatical structure.
Example: "The alignment problematic in our project has caused several delays and misunderstandings."
Alternatives: "alignment issues" or "problematic alignment".
The mouse and rat sequences were not included as they additionally each contain two large non-homologous insertions which make alignments problematic.
Overall, lion LTRs are not identical between subtypes B and E, differing by 15% in nucleotide substitutions, comparable to that observed between FIV Fca subtypes A, B and C. Deep genetic divergence between FIV strains from different cat species made alignments problematic.
After removing genes for which mapping of positions in the data from the University of Washington to positions in the UCSC alignment was problematic, we were left with 891 genes and 20.3 Mb of resequenced data (Table 1).
Phylogenetic analyses excluded gap regions to avoid ambiguity in regions where alignment was problematic.
The reliance on a single multiple alignment is problematic, especially since transposon sequences can be very poorly conserved.
Molecular clock dating stands and falls with the accuracy with which genetic distances can be estimated [ 80]; thus we consider the removal of ambiguous (i.e. potentially non-homologous) sites from the alignment as problematic.
Gene models for which EST sequence alignment was problematic (e.g. the 2,268 excluded ESTs described above) were visually inspected, resulting in some cases in gene model mergers and/or refinements.
In particular, we found that pairwise alignments with LAGAN performed better than available multi-species alignments, because fewer regions were excluded and because placement of insertions and deletions in multi-species alignments is problematic.
These studies were, however, criticized on the basis that the alignments were problematic (Di Giulio 2007).
The set of clusters based on 30% similarity threshold were more divergent; consequently, for some large clusters alignments were problematic.
