Third, single nucleotide polymorphisms (SNPs) were tested, whereas multiple loci might be involved in the development of initial dependence symptoms.
The 5hmC-containing BTSAT4 candidate displays multiple loci amongst the genome, whereas the BTSAT6 sequence includes the RGL1 gene locus (5hmC Targets 2 and 3, Additional file 1: Table S1).
DROMPA can accept multiple mapped reads (reads mapped on multiple loci of the reference genome), whereas most available peak-calling programs can only accept uniquely mapped reads (reads mapped onto the reference genome only once).
Most conserved miRNAs exists as gene families and are therefore represented by multiple loci in Arabidopsis, rice and Populus whereas recently evolved/evolving miRNAs are found to have a single locus in the genome [ 24- 26].
In particular, 236 of these ESTs aligned with single loci on the L. japonicus genome, whereas the remaining 57 matched multiple loci (Supplementary Table S2).
These confounding effects can, in principle, be separated by examining multiple loci since demographic history modifies the genetic pattern of the whole genome whereas only certain loci are affected by selection [ 1].
Similarly, one of the two datasets with multiple individuals sampled per species is optimized for locus-by-locus gene tree inference (D p, 0 ), whereas the other is optimized for gene tree inference using multiple loci simultaneously (D p ).
Whereas 19 of 22 conserved Arabidopsis miRNA families were represented at multiple loci, only three (MIR158, MIR447 and MIR845) of 48 non-conserved miRNAs were members of multigene families (Figure 2B).
Of the 962 multiple loci, 324 and 409 were mapped onto the same or homeologous linkage groups, respectively, whereas 229 multiple loci were mapped onto other linkage groups (Table S4).
