16 gap and pair-rule genes
52 CRMs - obtained by BLASTing CRMs from Schroeder et al., 2004 against the sequences in Additional file 1

Seq	Begin	End	Comment
btd	15884	17683	btd_head
ems	15933	17176	ems_dfd-abdb
ems	23359	23700	ems_dfd-wt
ems	12903	13206	ems_head
eve	14697	14794	eve_mas
eve	26693	27493	eve_stripe1
eve	18470	19132	eve_stripe2
eve	16259	16769	eve_stripe3_7
eve	24657	25258	eve_stripe4_6
eve	27400	28199	eve_stripe5
fkh	31103	32106	fkh_salivary
ftz	22294	23988	ftz_3prime_element
ftz	13912	15083	ftz_distal_enhancer
ftz	15749	16072	ftz_prox323
ftz	13582	13994	ftz_ps4_activator
ftz	18953	20070	ftz_zebra_element
gt	23559	24503	gt_berman
h	15165	16040	h_stripe1
h	10551	11631	h_stripe2_6
h	8603	9514	h_stripe3+4
h	14320	14883	h_stripe5
h	9078	10551	h_stripe7+
hb	23284	24004	hb_anterior_actv
hb	29481	30503	hb_central_stripe_and_posterior_actv
hkb	23162	23751	hkb_ventral_element_plus
kni	25084	25240	kni_223
kni	24209	25085	kni_kd
kni	25018	25084	kni_kni64_element
kr	19142	20372	Kr_AD2
kr	16003	17161	Kr_CD1
kr	17436	19142	Kr_CD2_AD1
oc	40300	40486	oc_head
oc	42557	44394	oc_otd_early_enhancer
prd	29694	32794	prd_A8_repressor
prd	24094	24894	prd_cc_repressor
prd	24894	25494	prd_P1_enhancer
prd	25794	26494	prd_Pstripe_enhancer
prd	26994	27394	prd_stripe1_enhancer
prd	27994	29694	prd_stripe2P_enhancer
prd	21454	23023	prd_zebra_enhancer
run	22989	25989	run_6_stripe
run	14908	19999	run_7_stripe
run	5570	7186	run_stripe1
run	8752	11066	run_stripe3
run	7186	8521	run_stripe5
run	5570	11155	run_stripe7
slp1	14600	15335	slp_ecto_stripes
slp1	16035	16656	slp1_head
slp1	17462	19015	slp1_meso_stripes
tll	15242	17701	tll_K2
tll	17701	20460	tll_P2
tll	19085	20460	tll_P3