From a technical perspective, accurate genotyping across MAP2K3 was complicated by nucleotide mismatches between homologous regions of MAP2K3 and two MAP2K3 segmental duplications (i.e. PSVs).
These microsatellites included 39 di-nucleotide, 10 trinucleotide, and 11 motif-complicated nucleotide.
These microsatellites included 99 di-nucleotide, 37 trinucleotide, 10 tetranucleotide, and 23 motif-complicated nucleotide (Table 1).
The resolution of these issues through molecular phylogenetic studies is, however, complicated by the high nucleotide substitution rate found in all tunicates so far analyzed, both at level of nuclear and mitochondrial (mt) genes (Singh et al. 2009; Tsagkogeorga et al. 2010; Rubinstein et al. 2013 and references therein).
Both of the above approaches are complicated by regions of unpaired nucleotides (loops and bulges) known to be present in many miRNA-target interactions [16].
The pattern observed for the Nc nucleotides is more complicated.
Search for cancer-predisposing single-nucleotide gene polymorphisms is complicated due to weakness of expected associations.
By using the inherent quenching of deoxyguanosine nucleotides in the amplicon, complicated probe designs involving internal quenching can be avoided.
After this region, there were several hundred additional nucleotides, composed primarily of complicated CA-rich repetitive sequences, in CR.
Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4%% of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome.
Microarray experiments that aim to elucidate gene expression differences between treatment and control groups usually involve reference or related designs in a small sample set and cross-hybridizations between gene spots with high nucleotide similarity complicate data interpretation.
