Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences.
The tremendous diversity both within and between zebrafish strains [ 47,48], nearly a magnitude greater than that of human, combined with the duplicated genome and other species-specific differences can complicate alignment and overwhelm somatic mutation algorithms with false calls.
In addition, we removed markers where the local sequence divergence complicated the alignment of L er short reads to the reference sequence, since such regions can interfere with the allele frequency calculation ('Materials and methods').
We speculate that CREST fails at the BLAT alignment stage, because small novel sequences complicate the alignment results.
Many H chemical shifts are sensitive to pH, temperature, or salts, complicating spectral alignment and database matching.
Low complexity and repetitive regions are common in the human genome, which complicates the alignment of short sequencing reads.
The X. tropicalis sequence was not included in this analysis because its unique Otop family expansion complicates the alignment of non-coding sequences with other species' sequences.
As expected the average identity also drops slightly (2.8 2.9%) because with increased length of the assembled sequences, internal sequence variations accumulate and complicate the alignment of the extended contigs against the target genome.
In nine cases (one in the motif-free set and eight in the motif-containing set), the presence of indels not verified by ESTs or a high variability, both in the very 5' end of the gene sequences, complicated the local alignment.
As a result, age-based politics now greatly complicates political alignments based on class.
