Table 2.

Distribution of the Most Abundant TF Binding Motifs (A) and Additional Motifs Analyzed (B) in Tomato and Potato

(A) TF Name	TF Binding Motif Degenerate Sequence	Solanum lycopersicum			S. tuberosum
		#Genome	#Mite	% in MITEa	#Genome	#Mite	% in MITEb
ABF3	ACACGTGT	5,627	717	12.74*	5,501	1,349	24.52*
ABI5	bgmCACGTGk	7,117	1,379	19.38*	9,749	3,024	31.02*
bZIP911	GrTGACGTGkmC	230	136	59.13*	100	5	5
FHY3	ywCACGCGCThw	522	134	25.67*	393	62	15.78*
MYB3	dGGTAGGTara	1,798	75	4.17	1,669	265	15.88*
OJ1058_F05.8	mCACGTGk	16,498	2,079	12.6*	18,626	5,716	30.69*
PIF3	dgCCACGTGr	2,320	513	22.11*	3,766	828	21.99*
PIF4	CACGTGsc	11,085	1,079	9.73*	11,650	1,903	16.33*
TCP15/TCP23	GGGCCCAC	4,651	1,499	32.23*	3,619	306	8.46*
(B) TF name	TF binding motif degenerate sequence	#Genome	#Mite	% in MITE	#Genome	#Mite	% in MITE
E2F	TTSSCGSSAA	2525	48	1.90	2069	57	2.75
Gbox	GCCACGT	32741	5882	17.97*	27804	4591	16.51*
Ibox	CTTATCC	80750	3128	3.87*	69964	8640	12.35*
MSA	GACCGTT	26610	326	1.23	16359	524	3.20
UP1	GGCCCA	112751	6376	5.65*	111904	4677	4.18

Note.—Asterisk denotes significant enrichment in the MITE fraction (Fisher’s exact test, P value < 0.05). Frequencies in the MITE fraction exceeding three times the MITE coverage are highlighted in red.

^aMITE coverage: 3.15%.

^bMITE coverage: 4.65%.