Table 1.

Motif (Zld, TATA, and Inr) Searches of 25 Bcd-Dependent Promoters

Gene	Expression stage	Promoter peak	Distance to the nearest enhancer (bp)	Zld site	TATA box	Inr
hbP2	pre-MBT	narrow	52	GTACCTG—47bp—CTACCTG–5bp–TATATAAA—20bp———TCAGTCAGTC
gt	pre-MBT	narrow	4978	TATAAA—25bp———TCAGTT
slp1	pre-MBT	narrow	710	TATAAA—25bp———TCAGCT
knirps	pre-MBT	N/A	54	TATATATA—24bp———TCAGTT
eve	pre-MBT	N/A	1074	TATAAA—23bp———GCACAC
ftz	pre-MBT	narrow	3219	TATATA—24bp———TCATTC
odd	pre-MBT	N/A	2086	TCAGTT
Bsq25D	pre-MBT	narrow	32	CTACCTG—18bp—CAGGTAG–17bp—TATAAA—20bp———GCAGTT
run	pre-MBT	narrow	2448	TCAGTT
h	pre-MBT	narrow	3964	TAGGTAG——————93bp——————TCAGTC
OS	pre-MBT	N/A	4160	TCAGTT
Kr	MBT-zyg	narrow	856	TATA—24bp———TCAGTC
btd	MBT-zvP	N/A	2693	TCAGTC
hbn	MBT-zvq	N/A	872	TCAGTC
prd	MBT-zyg	N/A	2954	TTACCTG—————84bp——————TCAGTC
otd	MBT-zyg	N/A	4145	TCATTT
ems	MBT-zvq	narrow	6789	TTATTC
CG3502	MBT-zvq	N/A	577	* TATACCAGGTAA—13bp—TCAGTT
bowl	MBT-zvq	narrow	2927	TCAGTC
edl	MBT-zvq	narrow	850	TCAGTT
salm	MBT-zvq	narrow	10265	TCACTC
D	MBT-zvq	N/A	3669	TCAGTC
tsh	MBT-zvq	narrow	48038	TCAGTCAGTC
bancal	MBT-mat	narrow	4747	TTAGTT
cnc	MBT-mat	N/A	1987	TCAGTCAGTCAGTT

25 Bcd-dependent promoters were scanned for motifs (Zld site, TATA box, and Inr) within the window of −220 to +20 bp with respect to the TSS (See STAR Methods). The columns from left to right are: gene symbol, class of expression stage, initiation pattern (narrow/focused or widespread promoter peak), the distance to the nearest Bcd-dependent enhancer, and motifs with spacing in between. The sequences were aligned according to the position of the Inr in each promoter, which exactly overlaps or is in close proximity to the annotated TSS. Abbreviations: MBT – midblastula transition; zyg – zygotic; mat – maternal; N/A – data not available.

^*CG3502 has a combined TATA-Zld motif.