Table 3. Tetra-and penta-nucleotide pairs and the related messages with shortest distance ≤84 bp

M1	M2	Match (Expect)	p value	Up_dis	Dis	Factor 1	Factor 2
CCAA	GAAT	19 (12.9)	0.043	17	63	R/T	R/A/T
CAGTG	TCACG	2 (0.3)	0.042	33	73	A	A/T
ACCAA	TTAAA	10 (3.3)	0.0013	16	51	R/T	-
ACCAA	TAAAA	10 (4.1)	0.0075	18	50	R/T	A
ACCAA	TATTT	9 (4.0)	0.018	18	68	R/T	R/A
ACCAA	AATAT	8 (3.9)	0.038	18	64	R/T	R/A/T
TCAGT	ATATC	5 (2.0)	0.046	16	43	-	A
TCAGT	CACCA	3 (0.8)	0.045	5	34	-	R/A

Bonded motifs denote the positive regulatory ones in upstream regions. “Match” denotes the number of genes strongly matched by the motif pair. “Up_dis” denotes the average distances between M1 and the translation start site. “Dis” denotes the average shortest distances between M1 and M2. “Factor 1” and “Factor 2” denote the transcription factors binding to M1 and M2. “R”, “A” and “T” represent RAP1, ABF1 and TAF respectively. Table 4 has similar notes.

Table 4 Tetra- and penta-nucleotide pairs and the related messages with shortest distance ≤147 bp

M1	M2	Match (Expect)	p value	Up_dis	Dis	Factor 1	Factor 2
ACCAA	TGCTA	9 (3.5)	0.0083	29	99	R/T	A