Motifs	Sequence	References
Motif 1	CGTTTGATGTT	Riese et al. (1997) Cell 88:777
Tcf	GCTTTGATCTG	Halfon et al. (2000) Cell 103:63
	ACTTTGATCTC	Yu et al. (1998) EMBO J. 17:7021
	CCTTTGATCT	Yang et al. (2000) Development 127:3695
Motif 2	CACTTGA	Lee et al. (1997) JBC 272:17531
Tinman	CACTTGA	Lee et al. (1997) JBC 272:17531
	CACTTGA	Lee et al. (1997) JBC 272:17531
	CACTTGA	Gajewski et al. (1997) EMBO J. 16:515
	CACTTGA	Gajewski et al. (1997) EMBO J. 16:515
	CAATTAA	Halfon et al. (2000) Cell 103:63
	CACTTCA	Halfon et al. (2000) Cell 103:63
	CACTTAA	Halfon et al. (2000) Cell 103:63
	CACTTGG	Halfon et al. (2000) Cell 103:63
Motif 3	CATATG	Lee et al. (1997) JBC 272:17531
Twist	CATATG	Lee et al. (1997) JBC 272:17531
	CATATG	Yin et al. (1997) Development 124:4971
	CATGTG	Yin et al. (1997) Development 124:4971
	CATGTG	Yin et al. (1997) Development 124:4971
	CATATG	Yin et al. (1997) Development 124:4971
	CACATG	Cripps et al. Genes Dev. 12:422
	CAGATG	Halfon et al. (2000) Cell 103:63
	CATATG	Halfon et al. (2000) Cell 103:63
Motif 4	GCCCCGTC	Xu et al. (1998) Genes Dev. 12:2354
Mad	GACGAGAC	Xu et al. (1998) Genes Dev. 12:2354
	GCCGCCGA	Xu et al. (1998) Genes Dev. 12:2354
	GTCGCCGC	Xu et al. (1998) Genes Dev. 12:2354
	GCCGGTCT	Xu et al. (1998) Genes Dev. 12:2354
	GCCCTGGA	Xu et al. (1998) Genes Dev. 12:2354
	GCCGCTGT	Xu et al. (1998) Genes Dev. 12:2354
	GCCTCCCA	Xu et al. (1998) Genes Dev. 12:2354
	GGCCGGCA	Certel et al. (2000) Dev. 127:3173
	GCCGTCGC	Kim et al. (1997) Nature 388:304
	GCCGGCGC	Kim et al. (1997) Nature 388:304
	GCCGCCGT	Kim et al. (1997) Nature 388:304
	GACGCCAG	Kim et al. (1997) Nature 388:304
	GCCGTGGG	Kim et al. (1997) Nature 388:304
	GGCGTCAG	Szuts et al. (1998) Genes Dev. 12:2022
	GCCGCAGA	Halfon et al. (2000) Cell 103:63
	GCCGAACC	Halfon et al. (2000) Cell 103:63
	GCAGCCGC	Halfon et al. (2000) Cell 103:63
	GCCGCAGC	Halfon et al. (2000) Cell 103:63
	GTCGTCGC	Halfon et al. (2000) Cell 103:63
Motif 5	TCCGGAAGC	Halfon et al. (2000) Cell 103:63
Pnt	TCCGGATGC	Halfon et al. (2000) Cell 103:63
	TCCGGATCT	Halfon et al. (2000) Cell 103:63
	CATGGATGC	Halfon et al. (2000) Cell 103:63
	GGGGGAAGC	Xu et al. (2000) Cell 103:87
	CCAGGAAGT	Xu et al. (2000) Cell 103:87
	GGTGGATGC	Xu et al. (2000) Cell 103:87
	ACCGGATGC	Xu et al. (2000) Cell 103:87

Web Table 1. Sequences composing the position weight matrices (PWMs) for each of the five transcription factors used in the combinatorial model-based search for cis-regulatory elements.