Probe design was classified as: "not recommended" when more than 300 matches of 16-mers were found in the genome.
All possible 5-mers were represented more than four times in the B. aphidicola reference genome, while 83 (or 2%) of all 6-mers were found less than four times.
Furthermore, more than 90% of all possible 5-mers were found four or more times in both the PhiX and the plasmid genomes, used for modelling Illumina and Roche/454 errors, respectively.
As nearly 75% of the 11-mers were found to be conserved between human and mouse 5'-UTRs (2935 out of 4009), we investigated if the interactions with conserved miRNAs were a function of uAUG sequence conservation.
Less than 30% of all possible 6-mers were present four or more times in these two genomes, while all possible 4-mers were found more than four times in the plasmid genome, and all but one in the PhiX genome (Table 2).
Homologue sequences to the 33-mer were found in rye and barley, but not in oats or other cereals [ 6].
Through comparing the predicted secondary structures of all the candidates, a conservative bulge-hairpin structure section (about 29 mer) was found, and then it was determined to be the binding motif to streptavidin.
Variable recognition of Gag 15-mers was found in both B*27/57 neg LTNP/EC and progressors.
If the key is absent, the reverse complement of the read is used to extend the seed if the end k-mers are found.
The 30-mer is found in numbers ranging from 42 to 75 in different Bordetella species, whereas the smaller 26 bp core is much more abundant (Fig. 8B).
There are a significant number of positions where, for a given 50-base sequence, one or more identical 50-mers are found elsewhere on the genome.
