Table 2. IpiRId’s kernels instantiation.

(D: distance; L: minimal length).

Kernel	Class	Instantiation parameters
U1|A10	Specific motifs inside	{motif,position}: {U,1}, {A,10}
K-merFreq	K-mer frequencies	N (number of k-mers) = 32 motifs
K-merPos	K-mer positions	N (number of k-mers) = 32 motifs
TE binding	Binding with targets	target: Transposable elements (TE)
CentroTelo	Specific positions	observation: centromer, telomeres
Histone	Specific positions	observation: H3K9me3, H3K27me3
Cluster	Clusters	K (number of neighbours) = 4
A-Myb	Promoters upstream	promoter: A-Myb; D = 40 kb
G-Quadruplex	G-quadruplex	D = 40 kb
CpG islands	CpG islands	L = 100; D = 20 kb
LINE|SINE|LTR	Transposons	TE: LINE, SINE, LTR; D = 40 kb
InvertRep	Inverted repeats	D = 40 kb