Table S12. Known motifs enriched in predicted enhancer regions.
Motifs are from Xie et al., Nature 2005					

Name	Consensus	Enhancer over-conservation	Enhancer enrichment	Promoter over-conservation	Promoter enrichment
AP-2ALPHA	SCYNNNGGC	1.00E-300	1.00E-300	4.66E-05	
STAT5A	AWTTCY	1.00E-300	5.80E-220	3.83E-177	6.16E-31
TEF-1	GRRATG	1.00E-300	4.33E-65	5.75E-36	
IY	AWTTTCC	1.04E-279	2.06E-50	5.09E-36	9.98E-18
FOXO1	RWAAACAA	1.08E-270	6.63E-53	1.03E-43	
HNF-3	TRTTTRYTYW	1.12E-247	4.51E-50	3.64E-21	
MEIS1	TGACAG	3.92E-221	4.25E-05	1.88E-56	
MYOD	RNCAGGTG	3.84E-215		1.25E-94	4.19E-05
NF-AT	WGGAAANW	1.57E-188	3.85E-60	7.83E-15	6.57E-24
TCF11	WNNATGAC	5.86E-181	5.69E-94	1.33E-31	
AP-1	CTGASTCA	9.09E-174	1.00E-300	2.31E-43	1.14E-05
SRY	KTWGTTT	3.09E-140	1.41E-10	2.05E-37	
AP-4	GCAGCTGNY	2.92E-123	5.07E-05	4.77E-48	
ER	RNNNTGACCT	6.28E-112	6.10E-15	3.00E-35	
GATA	WGATAR	1.43E-109			
PEA3	MGGAWGT	4.43E-105	3.71E-21	7.04E-282	6.15E-57
TCF-4	WTCAAAGS	7.02E-104	1.87E-11	1.71E-20	
AML1	ACCACA	1.76E-96	2.89E-48		
T3R	MNTGWCCT	2.48E-95	2.16E-27	9.79E-09	
TBP	TATAAATW	5.39E-80		4.88E-32	
NCX	GTAAKTNG	3.35E-74		2.10E-19	
SOX-5	ATTGTT	4.66E-74	4.02E-27	6.44E-17	
NKX6-2	WADTAAWTA	6.53E-74		7.96E-14	
DBP	GTDTGCT	1.21E-72	2.18E-07	1.09E-05	
NKX2-5	TYAAGTG	7.55E-72	4.13E-39		5.54E-12
CHX10	GCTAATTA	8.62E-70		1.17E-12	
HOXA4	CYAATTWT	2.12E-69		9.41E-14	6.20E-05
NF-1	TGGNNNNNNGCCAA	1.45E-56	2.85E-99	1.39E-09	
IRF1	AAGTGAA	1.23E-50	8.26E-19	9.56E-12	1.50E-14
NKX2-5	CWTAATTG	2.56E-50		4.83E-09	
ELF-1	RNWMBAGGAART	1.87E-40	7.83E-07	7.46E-16	3.63E-07
TCF-1(P)	GKCRGKTT	1.52E-36		2.04E-07	
STAT1	CANTTCCS	9.86E-34	6.14E-05	3.26E-140	3.80E-119
C/EBPBETA	KNTTGCNYAAY	9.27E-29	1.71E-32	1.12E-04	1.35E-04
OCTAMER	ATGCAAATNA	3.15E-28		1.21E-23	1.09E-09
CRX	KGRGATTANNNR	5.19E-28		2.22E-09	6.76E-04
CREB	TGACGTMA	3.24E-27	5.64E-14	6.38E-123	5.41E-249
STAT	TCCMAGAA	4.13E-27	6.70E-11	2.94E-08	8.08E-07
SF-1	TGRCCTTG	2.14E-25		5.11E-17	
YY1	GCCATNTT	2.37E-21		2.65E-133	
AREB6	WCAGGTGWNW	1.16E-17		3.38E-08	4.09E-10
NF-Y	YSATTGGYY	3.54E-17		1.00E-300	5.94E-209
PBX-1	WTGATTGNT	7.86E-16		6.41E-06	
RFX1	GTTRCYWNGYNAC	3.03E-15		5.23E-27	4.52E-09
C-REL	SGGRNTTTCC	1.63E-14		4.04E-11	
BACH2	SRTGAGTCANC	7.87E-14	1.56E-163	6.73E-09	
E4BP4	RTTACRTAAY	9.31E-14		7.43E-10	
TAL-1ALPHA/E47	AACAGATGKT	2.48E-12			
PU.1	WGAGGAAG	2.84E-12		1.37E-14	
POU3F2	ATTARCATAA	2.82E-10		1.42E-06	
POU1F1	ATGAATAAWT	1.59E-09	6.04E-06	1.19E-04	
RORALPHA2	TGACCTANWTW	2.93E-09			
P65	GGGRATTTCC	7.63E-09	3.37E-04	1.03E-09	5.33E-04
CAC-BP	GRGGSTGGG	4.39E-08			
HNF-6	HWAAATCAATAW	7.46E-08			
ELK-1	CCGGAART	1.27E-07		5.30E-165	1.00E-300
RP58	TCCAGATGTT	2.58E-07			
MEF-2	YTAAAWATAGCY	1.19E-05	2.42E-05	2.16E-04	5.26E-04
AHR	TNGCGTG	1.48E-05	3.31E-04		
MYB	GNCNGTT	2.03E-05		2.93E-19	
AREB6	ABWCAGGTRNR	2.52E-05			
IPF1	KGTCATTANNDC	3.98E-05			
ATF-1	TGACGTCARRG	4.76E-05	1.65E-06	6.91E-09	4.34E-30
BRN-2	YKNATTWYSNATG	1.24E-04			
MAZ	GGGGAGGG	1.78E-04	5.23E-06	4.87E-07	
LHX3	TTAATTAATT	3.50E-04			
LEF1	CTTTGA	1.02205884431E-310	4.34E-13	1.17E-66