Table 1. Analysis for stimulatory and inhibitory motifs in Trypanosomatidae and vertebrate genomes.

	Organism	Frequency	Expected number	Observed number	rO/E
Stimulatory motif
RRCGYY	L. major	5.63.10−3	184500	197597	1.07
	T. cruzi	4.23.10−3	137439	105362	0.77
	T. brucei	3.31.10−3	87665	82685	0.94
	T. vivax	4.56.10−3	103513	70098	0.68
	Mouse	2.76.10−3	7607250	1490164	0.20
	Human	2.76.10−3	8875125	1665432	0.19
HRWCGTTN	L. major	5.04.10−4	16531	18555	1.12
	T. cruzi	6.92.10−4	22496	17819	0.79
	T. brucei	8.02.10−4	21258	18976	0.89
	T. vivax	6.47.10−4	14710	13428	0.91
	Mouse	8.50.10−4	2345140	309431	0.13
	Human	8.50.10−4	2735997	347034	0.13
Inhibitory motif
CCNDDNNGGG	L. major	1.19.10−3	39055	12726	0.33
	T. cruzi	6.51.10−4	21165	8478	0.40
	T. brucei	3.82.10−4	10118	7873	0.78
	T. vivax	7.65.10−4	17372	5267	0.30
	Mouse	2.55.10−4	703493	936758	1.33
	Human	2.55.10−4	820742	1183790	1.44
WKKVGGGG	L. major	6.48.10−4	21254	19451	0.92
	T. cruzi	4.17.10−4	13557	10625	0.78
	T. brucei	2.76.10−4	7312	9605	1.31
	T. vivax	4.71.10−4	10691	5305	0.50
	Mouse	2.00.10−4	552602	944031	1.71
	Human	2.00.10−4	644703	787326	1.22

Stimulatory motifs (RRCGYY for [purin-purin-C-G-pyrimidin-pyrimidin]; HRWCGTTN for [(notG)-purin-(A or T)-C-G-T-T-any base] and inhibitory motifs (WKKVGGGG for [(A or T)-(G or T)-(G or T)-(A or C or T)-G-G-G-G]; CCNDDNNGGG for [C-C-x-(notC)-(notC)-x-x-G-G-G], where × stands for any base) were searched in whole genomes. For each motif, the counted number was indicated as the observed number. The expected motif number was calculated as (motif frequency × genome size). The motif frequency corresponds to the product of frequency for each nucleotide, which is different from one genome to another (Table S1). The rO/E corresponds to the ratio between the observed number and the expected number of the motifs.