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Table 3
New pCRMs from genome-wide eCIS-ANALYST (75 highest scoring predictions)
	CRM	Known element overlap	Arm	pCRM start	pCRM end	pCRM length	5' gene	pCRM relative position	3' gene	pCRM relative position	Conserved sites		Conserved site density		z score	Additional gap/pair-rule gene within 20 kb	pCRM relative position
											A	A+P	A	A+P

1	PCE8050	h stripes 3/4,6,7 [73]	3L	8,622,879	8,626,839	3,961	CG6486	+14646	h	-7829	36	62	9	16	20.1
2	PCE8051	kni upstream [74]	3L	20,614,714	20,617,020	2,307	kni	-813	CG13253	+20716	25	31	11	13	13.2
3	PCE8052	nub blastoderm	2L	12,604,311	12,606,913	2,603	CG15488	+1653	nub	-304	20	33	8	13	11.6
4	PCE8053	eve stripes 3/7 [75]	2R	5,035,493	5,037,290	1,798	CG12134	+3712	eve	-2433	21	24	12	13	11.5	Adam	+5901
5	PCE8054	hairy stripes 1,5 [73]	3L	8,628,846	8,631,011	2,166	CG6486	+20613	h	-3657	17	29	8	13	10.5
6	PCE8055	runt stripe 3 [76]	X	20,356,848	20,360,054	3,207	CG1338	-9192	run	-6801	17	34	5	11	10.3
7	PCE8056		X	20,323,964	20,326,397	2,434	CG11692	-12536	Cyp6v1	-4186	16	28	7	12	9.6
8	PCE8057	hb HZ1.4 [77]	3R	4,526,225	4,527,991	1,767	hb	-2670	CG8112	+1273	17	21	10	12	9.5
9	PCE8059	eve stripes 4/6 [78]	2R	5,044,597	5,046,030	1,434	eve	+4874	TER94	-3763	15	18	10	13	9.0	Adam	+15005
10	PCE8060	gt posterior [11]	X	2,186,709	2,189,069	2,361	gt	-974	tko	+11679	18	21	8	9	8.9
11	PCE8061		X	3,169,806	3,172,348	2,543	CG12535	-17954	CG14269	+21857	13	29	5	11	8.8
12	PCE8063	CE8021	3L	18,339,914	18,341,941	2,028	grim	-86621	rpr	+5341	16	20	8	10	8.5
13	PCE8064		3R	6,255,663	6,256,945	1,283	CG6345	-13879	Cyp12e1	-3594	13	17	10	13	8.4
14	PCE8065		3R	4,026,032	4,027,816	1,785	grn	-18853	CG7800	-15898	15	19	8	11	8.4
15	PCE8066		X	20,348,460	20,352,624	4,165	CG1338	-804	run	-14231	16	28	4	7	8.3
16	PCE8067	ftz upstream [23]	3R	2,682,314	2,684,591	2,278	Scr	-7972	ftz	-5455	15	22	7	10	8.3
17	PCE8068		X	18,701,007	18,702,700	1,694	CG32541	+39691	CG32541	+39691	12	22	7	13	8.2
18	PCE8069		2R	17,274,311	17,276,017	1,707	CG3380	-2521	dve	-11496	14	19	8	11	8.2
19	PCE8070		2L	7,616,050	7,618,366	2,317	CG6739	+15430	CG13792	+19862	14	23	6	10	8.1
20	PCE8071	sqz neurogenic	3R	14,999,463	15,001,552	2,090	sqz	+9504	CG14282	-1186	12	24	6	11	8.0	nos	+16485
21	PCE8072		X	5,674,422	5,676,386	1,965	CG3726	+16870	CG12728	-6597	11	24	6	12	7.8
22	PCE8073		2R	14,903,099	14,903,925	827	Toll-7	+12482	Obp56i	-27903	11	11	13	13	7.8
23	PCE8074		3R	23,192,304	23,192,750	447	CG13980	+8073	side	+40862	7	8	16	18	7.7
24	PCE8075		3R	10,762,920	10,764,750	1,831	CG3837	+18501	CG14861	-75759	13	19	7	10	7.6
25	PCE8076	eve stripe 2 [75]	2R	5,038,454	5,039,041	588	CG12134	+6673	eve	-682	8	10	14	17	7.6	Adam	+8862
26	PCE8077		2L	13,541,662	13,542,651	990	kuz	+9371	kuz	+9371	11	13	11	13	7.6
27	PCE8078		2L	14,424,056	14,425,158	1,103	BG:DS06238.4	-16773	BG:DS08340.1	+7810	12	13	11	12	7.6
28	PCE8080	odd stripes 3/6	2L	3,601,045	3,602,748	1,704	odd	-1728	Dot	-9112	12	19	7	11	7.5
29	PCE8081		3L	17,412,324	17,413,414	1,091	CG18265	+24035	CG7603	-1413	11	14	10	13	7.5
30	PCE8083		3L	14,121,556	14,123,127	1,572	Sox21b	-41352	D	+4373	12	17	8	11	7.3
31	PCE8084		2L	4,098,489	4,099,006	518	ed	+74542	ed	+74542	7	9	14	17	7.3
32	PCE8085		2R	12,253,766	12,255,302	1,537	CG10953	-23540	CG10950	-3625	13	15	8	10	7.2
33	PCE8086		3L	20,612,647	20,614,073	1,427	*kni*	+1254	CG13253	+23663	11	17	8	12	7.2
34	PCE8087		2R	3,391,037	3,391,561	525	CG30358	+10444	CG14755	-16724	7	9	13	17	7.2
35	PCE8088		3L	16,418,107	16,418,469	363	CG33158	+49435	argos	+14111	6	6	17	17	7.2
36	PCE8089		3R	12,368,159	12,368,687	529	CG11769	+28970	CG31448	-670	7	9	13	17	7.2	CG14889	-13735
37	PCE8091		3L	11,213,064	11,213,664	601	scylla	+3224	CG32083	+24695	8	9	13	15	7.1
38	PCE8092		2L	1,233,357	1,235,228	1,872	CG5156	+3715	CG5397	-6475	9	23	5	12	7.1
39	PCE8093		3L	15,688,222	15,691,204	2,983	comm	-10920	CG13445	-67172	13	22	4	7	7.0
40	PCE8094		2R	10,492,861	10,493,546	686	CG30472	-5321	CG12959	-26488	9	9	13	13	7.0
41	PCE8095		3R	23,894,562	23,895,459	898	CG12870	+31901	CG12870	+31901	10	11	11	12	7.0
42	PCE8096		3L	6,762,543	6,765,157	2,615	vvl	+12855	Prat2	+108336	13	20	5	8	6.9
43	PCE8097		3R	10,238,130	10,238,652	523	CG14846	-1983	CG14847	+4557	7	8	13	15	6.8
44	PCE8099		2L	18,305,051	18,306,251	1,201	Fas3	+6868	Fas3	+6868	10	14	8	12	6.7
45	PCE8100	eve early APR [79]	2R	5,042,174	5,042,884	711	eve	+2451	TER94	-6909	8	10	11	14	6.7	Adam	+12582
46	PCE8102	tll posterior [80]	3R	26,663,942	26,665,204	1,263	CG15544	+21005	tll	-2251	11	13	9	10	6.6
47	PCE8104	ems neurogenic [81]	3R	9,723,602	9,724,936	1,335	E5	-23682	ems	-2663	12	12	9	9	6.6
48	PCE8105		3R	17,817,909	17,818,791	883	Eip93F	+25598	Eip93F	+25598	9	11	10	12	6.6
49	PCE8106		3L	10,499,018	10,501,551	2,534	CG32062	+25485	CG32062	+25485	11	21	4	8	6.6
50	PCE8107		3L	4,612,891	4,614,005	1,115	CG13716	-161	CG13715	+1681	11	11	10	10	6.6
51	PCE8108		2L	14,403,771	14,404,937	1,167	CG15284	-4301	BG:DS06238.4	+2346	10	13	9	11	6.5
52	PCE8109		3R	7,941,601	7,942,426	826	CG31361	+17775	CG4702	+11512	9	10	11	12	6.5
53	PCE8110		2L	8,804,166	8,805,336	1,171	CG9468	-30684	SoxN	-12519	10	13	9	11	6.5
54	PCE8111		3L	8,612,337	8,613,016	680	CG6486	+4104	h	-21652	8	9	12	13	6.5
55	PCE8112		3L	4,377,989	4,379,208	1,220	CG7447	+13842	Syx17	-3984	11	12	9	10	6.5
56	PCE8113		2L	14,113,291	14,113,893	603	CG15292	-3974	CG31768	-6693	7	9	12	15	6.5
57	PCE8114		3L	3,997,600	3,998,923	1,324	CG14985	+13500	fd64A	-799	11	13	8	10	6.5
58	PCE8115	eve stripe 1 [79]	2R	5,046,559	5,047,297	739	eve	+6836	TER94	-2496	8	10	11	14	6.5	Adam	+16967
59	PCE8116		2R	16,921,501	16,922,240	740	CG13493	-11091	PpN58A	+4194	8	10	11	14	6.5
60	PCE8118		3R	14,822,848	14,823,484	637	*gukh*	+13085	*gukh*	+13085	8	8	13	13	6.4
61	PCE8119		3R	12,671,525	12,672,987	1,463	abd-A	-15737	CG10349	-32477	11	14	8	10	6.4
62	PCE8120		3L	10,492,688	10,495,539	2,852	CG32062	+19155	CG32062	+19155	10	23	4	8	6.4
63	PCE8121		2L	16,841,696	16,842,392	697	CG6012	-2193	CG31781	-5178	8	9	11	13	6.4
64	PCE8122		3L	6,885,832	6,887,436	1,605	Prat2	-11445	CG14820	-5022	11	15	7	9	6.4
65	PCE8123		2L	15,162,778	15,164,524	1,747	BG:DS03192.2	-6373	BG:DS07295.1	+59479	11	16	6	9	6.4
66	PCE8124		2R	6,888,483	6,889,700	1,218	CG12443	+13963	CG13192	-428	10	13	8	11	6.4
67	PCE8125		2L	20,466,022	20,467,708	1,687	CG2493	-32831	CG15476	+4184	10	17	6	10	6.4
68	PCE8126		3L	2,779,198	2,779,658	461	CG2083	+1101	CG2083	+1101	6	7	13	15	6.3
69	PCE8127		X	4,630,473	4,632,106	1,634	CG12681	+14179	CG15470	-3196	9	18	6	11	6.3
70	PCE8128		3R	27,713,381	27,715,087	1,707	heph	+35171	heph	+35171	10	17	6	10	6.3
71	PCE8130		3R	12,383,752	12,385,269	1,518	*CG14889*	+1858	*CG14889*	+1858	11	14	7	9	6.3
72	PCE8131		3R	21,329,716	21,331,058	1,343	CG5111	+8355	msi	-2351	8	17	6	13	6.3
73	PCE8132		3R	16,242,660	16,243,128	469	CG10881	+8657	CG17208	+20535	6	7	13	15	6.3
74	PCE8133		3R	24,120,296	24,122,240	1,945	CG12516	-668	larp	+19112	12	15	6	8	6.2
75	PCE8134		3L	8,733,754	8,734,394	641	CG32030	+8601	CG32030	+8601	7	9	11	14	6.2

Seventy-five top pCRMs, ranked by a z-score based on the number and density of conserved binding sites (see text for details). Site density columns list the number of conserved sites per kilobase (relative to the D. melanogaster sequence). The number and density of conserved sites are shown under two conditions - aligned sites only (A), or aligned + preserved sites (A+P) (see Materials and methods). The 5' and 3' gene columns correspond to the closest transcription (or annotation) start 5' and 3' of the pCRM. If a pCRM is within an intron, only the intron-containing gene is reported and its name is italicized. The names of genes with early anterior-posterior patterns are in bold. Early anterior-posterior genes that start within 20 kb of the pCRM (but are not the immediate annotation in the 5' or 3' direction) are also listed. Named enhancers without a reference are from this study.
Berman et al. Genome Biology 2004 5:R61 doi:10.1186/gb-2004-5-9-r61

Table 3