Results of motif discovery tools on the
yeast transcriptional regulatory map

• Motif discovery tools were executed on the ChIP-chip data constructed by [Harbison, '04].
• We included only TFs that bound more than four promoters, and whose binding motifs have been reported in the literature. These "correct" motifs were downloaded from [MacIsaac, '06].
• Yeast promoter sequences (up to 600bp upstream the TSS) were downloaded from SGD.
• Each tool was run twice on each dataset - once with motif length 8, and once with motif length 10. The two top-scoring motifs from each run were compared to the correct motif using the PWM divergence measure of [Harbison, '04] (average Euclidean distance).
• Here we used a PWM divergence cutoff of 0.24, i.e., if the divergence between one of the 4 reported motifs and the correct motif is less than 0.24, the tool is said to successfully recover the motif ("Yes" in the "Success" column). All PWM divergence scores under 0.24 are shown in the "Top 4 motifs" column.

Benchmark	Organism	Target-set size	Promoter length	Correct motif	Program	Success	Time (secs.)	Top 4 motifs (two for length 8 and two for length 10)
ABF1_YPD	Yeast	267	601	ABF1 (MacIsaac et al. '06)	MEME	No	4211
					AlignACE	Yes	3389	ABF1 0.0488		ABF1 0.0438
					YMF	No	1213
					Amadeus	Yes	448	ABF1 0.1443	ABF1 0.1876	ABF1 0.155	ABF1 0.1577
					Weeder	Yes	2916	ABF1 0.2087	ABF1 0.2107
					Trawler	Yes	122		ABF1[ABF1_Fraenkel2] 0.1961
ACE2_YPD	Yeast	92	601	ACE2 (MacIsaac et al. '06)	MEME	No	590
					AlignACE	No	379
					YMF	No	841
					Amadeus	No	443
					Weeder	No	867
					Trawler	No	103
ADR1_HEAT	Yeast	14	601	ADR1 (MacIsaac et al. '06)	MEME	No	18
					AlignACE	No	78
					YMF	No	685
					Amadeus	Yes	318		ADR1 0.223
					Weeder	No	140
					Trawler	No	58
ADR1_SM	Yeast	5	601	ADR1 (MacIsaac et al. '06)	MEME	No	3
					AlignACE	No	34
					YMF	No	666
					Amadeus	No	223
					Weeder	No	52
					Trawler	No	57
ADR1_YPD	Yeast	35	601	ADR1 (MacIsaac et al. '06)	MEME	No	89
					AlignACE	No	139
					YMF	No	722
					Amadeus	No	367
					Weeder	No	309
					Trawler	No	78
AFT2_H2O2Hi	Yeast	61	601	AFT2 (MacIsaac et al. '06)	MEME	Yes	258	AFT2 0.2282
					AlignACE	Yes	323	AFT2 0.2399		AFT2 0.2341
					YMF	No	811
					Amadeus	Yes	416	AFT2 0.2398
					Weeder	Yes	583	AFT2 0.1392	AFT2 0.2204
					Trawler	No	88
AFT2_H2O2Lo	Yeast	114	601	AFT2 (MacIsaac et al. '06)	MEME	Yes	883	AFT2 0.1094
					AlignACE	Yes	862		AFT2 0.1326
					YMF	Yes	871		AFT2 0.224
					Amadeus	Yes	401	AFT2 0.1153		AFT2 0.1336	AFT2 0.0668
					Weeder	Yes	1070	AFT2 0.0969		AFT2 0.129	AFT2 0.1647
					Trawler	No	144
AFT2_YPD	Yeast	22	601	AFT2 (MacIsaac et al. '06)	MEME	No	40
					AlignACE	No	100
					YMF	No	693
					Amadeus	No	352
					Weeder	No	202
					Trawler	No	80
ASH1_BUT14	Yeast	51	601	ASH1 (MacIsaac et al. '06)	MEME	No	185
					AlignACE	Yes	198		ASH1 0.1967		ASH1 0.1577
					YMF	No	762
					Amadeus	Yes	414			ASH1 0.1311
					Weeder	No	494
					Trawler	No	119
AZF1_YPD	Yeast	21	601	AZF1 (MacIsaac et al. '06)	MEME	Yes	37	AZF1 0.1926
					AlignACE	Yes	37	AZF1 0.1956		AZF1 0.2293	AZF1 0.2172
					YMF	No	689
					Amadeus	No	384
					Weeder	No	219
					Trawler	Yes	80	AZF1[AZF1_Fraenkel2] 0.2049
BAS1_SM	Yeast	17	601	BAS1 (MacIsaac et al. '06)	MEME	Yes	26	BAS1 0.1931
					AlignACE	Yes	43		BAS1 0.1184
					YMF	Yes	684	BAS1 0.2204
					Amadeus	Yes	335	BAS1 0.1634			BAS1 0.2189
					Weeder	Yes	166	BAS1 0.1322	BAS1 0.1961	BAS1 0.1182
					Trawler	Yes	67		BAS1[BAS1_Fraenkel2] 0.1255
BAS1_YPD	Yeast	41	601	BAS1 (MacIsaac et al. '06)	MEME	Yes	137	BAS1 0.1159
					AlignACE	Yes	159				BAS1 0.1709
					YMF	Yes	741		BAS1 0.2159
					Amadeus	Yes	388	BAS1 0.1078		BAS1 0.178
					Weeder	Yes	375	BAS1 0.1185	BAS1 0.213	BAS1 0.1411	BAS1 0.164
					Trawler	Yes	124				BAS1[BAS1_Fraenkel2] 0.0838
CAD1_SM	Yeast	26	601	CAD1 (MacIsaac et al. '06)	MEME	Yes	50		CAD1 0.1309	CAD1 0.0917
					AlignACE	No	109
					YMF	Yes	706		CAD1 0.1353
					Amadeus	No	328
					Weeder	Yes	229	CAD1 0.1292	CAD1 0.1062	CAD1 0.1088	CAD1 0.1655
					Trawler	No	100
CAD1_YPD	Yeast	34	601	CAD1 (MacIsaac et al. '06)	MEME	Yes	88		CAD1 0.1074	CAD1 0.0893
					AlignACE	No	113
					YMF	No	745
					Amadeus	Yes	360	CAD1 0.0832		CAD1 0.0776
					Weeder	Yes	323	CAD1 0.1109	CAD1 0.0832	CAD1 0.1597	CAD1 0.0946
					Trawler	No	102
CBF1_SM	Yeast	280	601	CBF1 (MacIsaac et al. '06)	MEME	Yes	5333	CBF1 0.0189		CBF1 0.0522
					AlignACE	Yes	3268	CBF1 0.0267			CBF1 0.057
					YMF	Yes	1227	CBF1 0.0267	CBF1 0.2354	CBF1 0.0633	CBF1 0.1214
					Amadeus	Yes	274	CBF1 0.0338	CBF1 0.2178	CBF1 0.0267
					Weeder	Yes	3019	CBF1 0.0267	CBF1 0.0187	CBF1 0.0176	CBF1 0.0482
					Trawler	Yes	370	CBF1[CBF1_Fraenkel2] 0.1367
CBF1_YPD	Yeast	14	601	CBF1 (MacIsaac et al. '06)	MEME	Yes	17	CBF1 0.049		CBF1 0.0262
					AlignACE	Yes	58	CBF1 0.0571		CBF1 0.0754
					YMF	Yes	689	CBF1 0.0267		CBF1 0.0267
					Amadeus	Yes	309	CBF1 0.0604		CBF1 0.1055
					Weeder	Yes	126	CBF1 0.0353	CBF1 0.0267	CBF1 0.0652	CBF1 0.0543
					Trawler	Yes	70	CBF1[CBF1_Fraenkel2] 0.0609
CIN5_H2O2Hi	Yeast	81	601	CIN5 (MacIsaac et al. '06)	MEME	No	496
					AlignACE	Yes	397				CIN5 0.1801
					YMF	Yes	831	CIN5 0.168
					Amadeus	Yes	412	CIN5 0.165	CIN5 0.212	CIN5 0.1068
					Weeder	Yes	818	CIN5 0.1389	CIN5 0.1468	CIN5 0.1497	CIN5 0.1827
					Trawler	No	119
CIN5_H2O2Lo	Yeast	130	601	CIN5 (MacIsaac et al. '06)	MEME	No	929
					AlignACE	Yes	627				CIN5 0.1696
					YMF	No	917
					Amadeus	Yes	417	CIN5 0.1769		CIN5 0.1096
					Weeder	Yes	1345	CIN5 0.1269	CIN5 0.116	CIN5 0.127	CIN5 0.1885
					Trawler	No	131
CIN5_YPD	Yeast	153	601	CIN5 (MacIsaac et al. '06)	MEME	No	1251
					AlignACE	No	775
					YMF	No	971
					Amadeus	Yes	432	CIN5 0.1511		CIN5 0.0894
					Weeder	Yes	1658	CIN5 0.1291	CIN5 0.1122	CIN5 0.1181	CIN5 0.1354
					Trawler	Yes	149	CIN5[CIN5_Fraenkel2] 0.2069
DAL80_RAPA	Yeast	40	601	DAL80 (MacIsaac et al. '06)	MEME	No	91
					AlignACE	No	179
					YMF	No	725
					Amadeus	Yes	366	DAL80 0.1694
					Weeder	No	337
					Trawler	No	79
DAL80_YPD	Yeast	13	601	DAL80 (MacIsaac et al. '06)	MEME	Yes	11			DAL80 0.161
					AlignACE	No	30
					YMF	No	681
					Amadeus	Yes	335			DAL80 0.1879	DAL80 0.1496
					Weeder	No	133
					Trawler	No	58
DAL81_RAPA	Yeast	95	601	DAL81 (MacIsaac et al. '06)	MEME	No	498
					AlignACE	No	325
					YMF	No	844
					Amadeus	No	421
					Weeder	No	967
					Trawler	No	95
DAL81_YPD	Yeast	33	601	DAL81 (MacIsaac et al. '06)	MEME	No	68
					AlignACE	No	96
					YMF	No	727
					Amadeus	No	379
					Weeder	No	315
					Trawler	No	146
DAL82_RAPA	Yeast	56	601	DAL82 (MacIsaac et al. '06)	MEME	No	172
					AlignACE	No	168
					YMF	No	761
					Amadeus	No	411
					Weeder	Yes	555	DAL82 0.2017
					Trawler	No	111
DAL82_SM	Yeast	59	601	DAL82 (MacIsaac et al. '06)	MEME	No	267
					AlignACE	No	273
					YMF	No	773
					Amadeus	Yes	418	DAL82 0.2256
					Weeder	Yes	579	DAL82 0.2059
					Trawler	No	62
DAL82_YPD	Yeast	16	601	DAL82 (MacIsaac et al. '06)	MEME	No	21
					AlignACE	No	117
					YMF	No	686
					Amadeus	No	322
					Weeder	No	139
					Trawler	No	74
FKH1_YPD	Yeast	142	601	FKH1 (MacIsaac et al. '06)	MEME	Yes	1374	FKH1 0.05		FKH1 0.0499
					AlignACE	Yes	1229		FKH1 0.1074		FKH1 0.2022
					YMF	Yes	964	FKH1 0.1074
					Amadeus	Yes	449	FKH1 0.1608	FKH1 0.1494	FKH1 0.1064
					Weeder	Yes	1435	FKH1 0.0734	FKH1 0.134	FKH1 0.0849	FKH1 0.0775
					Trawler	Yes	119	FKH1[FKH1_Fraenkel2] 0.084
FKH2_H2O2Hi	Yeast	107	601	FKH2 (MacIsaac et al. '06)	MEME	Yes	778	FKH2 0.0818			FKH2 0.1774
					AlignACE	No	605
					YMF	Yes	900	FKH2 0.1299
					Amadeus	Yes	435	FKH2 0.1031		FKH2 0.0967
					Weeder	Yes	1017	FKH2 0.1952	FKH2 0.1994	FKH2 0.107	FKH2 0.1993
					Trawler	Yes	112		FKH2[FKH2_Fraenkel2] 0.1445
FKH2_H2O2Lo	Yeast	31	601	FKH2 (MacIsaac et al. '06)	MEME	Yes	69	FKH2 0.086			FKH2 0.1232
					AlignACE	Yes	99		FKH2 0.2199
					YMF	No	714
					Amadeus	Yes	334	FKH2 0.1655	FKH2 0.2008	FKH2 0.1358
					Weeder	Yes	267	FKH2 0.1222	FKH2 0.2007	FKH2 0.1138	FKH2 0.194
					Trawler	Yes	93		FKH2[FKH2_Fraenkel2] 0.073
FKH2_YPD	Yeast	122	601	FKH2 (MacIsaac et al. '06)	MEME	Yes	1001		FKH2 0.0984		FKH2 0.1169
					AlignACE	Yes	852				FKH2 0.2087
					YMF	Yes	918	FKH2 0.1299
					Amadeus	Yes	400	FKH2 0.0998		FKH2 0.1388
					Weeder	Yes	1160	FKH2 0.1813	FKH2 0.2009	FKH2 0.1072	FKH2 0.1896
					Trawler	Yes	146	FKH2[FKH2_Fraenkel2] 0.1052
GAL4_GAL	Yeast	41	601	GAL4 (MacIsaac et al. '06)	MEME	No	134
					AlignACE	Yes	163	GAL4 0.0901		GAL4 0.0917
					YMF	No	737
					Amadeus	Yes	371	GAL4 0.2074
					Weeder	No	394
					Trawler	No	60
GAL4_RAFF	Yeast	39	601	GAL4 (MacIsaac et al. '06)	MEME	No	125
					AlignACE	Yes	126	GAL4 0.1369		GAL4 0.1235
					YMF	No	726
					Amadeus	No	371
					Weeder	No	351
					Trawler	No	59
GAL4_YPD	Yeast	26	601	GAL4 (MacIsaac et al. '06)	MEME	No	48
					AlignACE	No	146
					YMF	No	700
					Amadeus	No	343
					Weeder	No	207
					Trawler	No	109
GAT1_RAPA	Yeast	27	601	GAT1 (MacIsaac et al. '06)	MEME	Yes	60	GAT1 0.2062
					AlignACE	Yes	53		GAT1 0.1943
					YMF	Yes	703	GAT1 0.067
					Amadeus	Yes	392				GAT1 0.2298
					Weeder	Yes	262	GAT1 0.224	GAT1 0.1156		GAT1 0.1338
					Trawler	Yes	100	GAT1[GAT1_Fraenkel2] 0.0796
GAT1_SM	Yeast	48	601	GAT1 (MacIsaac et al. '06)	MEME	No	166
					AlignACE	No	118
					YMF	No	752
					Amadeus	No	426
					Weeder	No	469
					Trawler	No	61
GAT1_YPD	Yeast	12	601	GAT1 (MacIsaac et al. '06)	MEME	No	12
					AlignACE	No	72
					YMF	No	686
					Amadeus	No	327
					Weeder	No	105
					Trawler	No	59
GCN4_RAPA	Yeast	161	601	GCN4 (MacIsaac et al. '06)	MEME	Yes	1865	GCN4 0.0651			GCN4 0.121
					AlignACE	Yes	1203		GCN4 0.0981		GCN4 0.1424
					YMF	Yes	973	GCN4 0.1403			GCN4 0.1629
					Amadeus	Yes	269	GCN4 0.1049		GCN4 0.08
					Weeder	Yes	1700	GCN4 0.1036	GCN4 0.0955	GCN4 0.0807	GCN4 0.1098
					Trawler	Yes	109	GCN4[GCN4_Fraenkel2] 0.1228
GCN4_SM	Yeast	190	601	GCN4 (MacIsaac et al. '06)	MEME	Yes	2426	GCN4 0.0684		GCN4 0.0579
					AlignACE	Yes	1819		GCN4 0.1247		GCN4 0.1002
					YMF	Yes	1034	GCN4 0.1537			GCN4 0.1629
					Amadeus	Yes	322	GCN4 0.072		GCN4 0.056
					Weeder	Yes	2026	GCN4 0.0825	GCN4 0.0724	GCN4 0.0698	GCN4 0.0838
					Trawler	Yes	177	GCN4[GCN4_Fraenkel2] 0.1343
GCN4_YPD	Yeast	75	601	GCN4 (MacIsaac et al. '06)	MEME	Yes	438	GCN4 0.0734			GCN4 0.1288
					AlignACE	Yes	310		GCN4 0.0904		GCN4 0.1339
					YMF	Yes	803	GCN4 0.1403		GCN4 0.1134
					Amadeus	Yes	303	GCN4 0.1098		GCN4 0.1073
					Weeder	Yes	722	GCN4 0.0797	GCN4 0.1015	GCN4 0.0915	GCN4 0.1151
					Trawler	Yes	90	GCN4[GCN4_Fraenkel2] 0.1062
GCR1_YPD	Yeast	15	601	GCR1 (MacIsaac et al. '06)	MEME	No	18
					AlignACE	Yes	77				GCR1 0.2121
					YMF	No	679
					Amadeus	No	295
					Weeder	No	139
					Trawler	No	80
GLN3_RAPA	Yeast	68	601	GLN3 (MacIsaac et al. '06)	MEME	Yes	332			GLN3 0.1878
					AlignACE	No	278
					YMF	Yes	792	GLN3 0.2155
					Amadeus	Yes	427	GLN3 0.1589		GLN3 0.202
					Weeder	Yes	688	GLN3 0.1975	GLN3 0.1874		GLN3 0.2207
					Trawler	Yes	99		GLN3[GLN3_Fraenkel2] 0.1692
GLN3_SM	Yeast	50	601	GLN3 (MacIsaac et al. '06)	MEME	No	178
					AlignACE	No	207
					YMF	No	756
					Amadeus	No	401
					Weeder	No	485
					Trawler	No	115
GLN3_YPD	Yeast	16	601	GLN3 (MacIsaac et al. '06)	MEME	No	21
					AlignACE	No	37
					YMF	No	683
					Amadeus	No	331
					Weeder	No	143
					Trawler	No	59
GZF3_H2O2Hi	Yeast	13	601	GZF3 (MacIsaac et al. '06)	MEME	No	16
					AlignACE	No	21
					YMF	No	677
					Amadeus	No	339
					Weeder	No	136
					Trawler	No	59
GZF3_RAPA	Yeast	39	601	GZF3 (MacIsaac et al. '06)	MEME	No	120
					AlignACE	No	251
					YMF	No	718
					Amadeus	No	343
					Weeder	Yes	287	GZF3 0.1912
					Trawler	No	76
GZF3_YPD	Yeast	7	601	GZF3 (MacIsaac et al. '06)	MEME	No	5
					AlignACE	No	18
					YMF	No	682
					Amadeus	Yes	243	GZF3 0.1847
					Weeder	No	66
					Trawler	No	58
HAC1_YPD	Yeast	15	601	HAC1 (MacIsaac et al. '06)	MEME	Yes	19	HAC1 0.1075			HAC1 0.0354
					AlignACE	Yes	76		HAC1 0.0707
					YMF	Yes	671	HAC1 0.1215
					Amadeus	Yes	337	HAC1 0.098		HAC1 0.0367
					Weeder	Yes	142	HAC1 0.056	HAC1 0.1035		HAC1 0.0689
					Trawler	Yes	67	HAC1[HAC1_Fraenkel2] 0.1046
HAP1_YPD	Yeast	150	601	HAP1 (MacIsaac et al. '06)	MEME	No	1525
					AlignACE	No	1300
					YMF	No	956
					Amadeus	Yes	420			HAP1 0.1731	HAP1 0.2122
					Weeder	No	1539
					Trawler	No	132
HAP2_RAPA	Yeast	42	601	HAP2 (MacIsaac et al. '06)	MEME	No	102
					AlignACE	No	138
					YMF	No	737
					Amadeus	No	408
					Weeder	Yes	418	HAP2 0.1515
					Trawler	No	82
HAP2_YPD	Yeast	21	601	HAP2 (MacIsaac et al. '06)	MEME	No	29
					AlignACE	No	59
					YMF	No	689
					Amadeus	No	391
					Weeder	No	206
					Trawler	No	64
HAP3_YPD	Yeast	30	601	HAP3 (MacIsaac et al. '06)	MEME	No	51
					AlignACE	Yes	59		HAP3 0.2048
					YMF	No	709
					Amadeus	Yes	375	HAP3 0.222	HAP3 0.0707	HAP3 0.2341	HAP3 0.1844
					Weeder	Yes	294	HAP3 0.0341
					Trawler	No	79
HAP4_H2O2Lo	Yeast	24	601	HAP4 (MacIsaac et al. '06)	MEME	No	36
					AlignACE	Yes	58			HAP4 0.218
					YMF	No	707
					Amadeus	No	350
					Weeder	No	250
					Trawler	Yes	69	HAP4[HAP4_Fraenkel2] 0.2037
HAP4_YPD	Yeast	77	601	HAP4 (MacIsaac et al. '06)	MEME	Yes	330				HAP4 0.1128
					AlignACE	No	332
					YMF	No	806
					Amadeus	Yes	395	HAP4 0.1103		HAP4 0.0727
					Weeder	Yes	650	HAP4 0.1274			HAP4 0.142
					Trawler	No	99
HAP5_SM	Yeast	39	601	HAP5 (MacIsaac et al. '06)	MEME	No	90
					AlignACE	No	131
					YMF	No	722
					Amadeus	No	416
					Weeder	No	395
					Trawler	No	72
HAP5_YPD	Yeast	12	601	HAP5 (MacIsaac et al. '06)	MEME	Yes	10			HAP5 0.0743
					AlignACE	No	28
					YMF	Yes	676				HAP5 0.2218
					Amadeus	Yes	339	HAP5 0.0958		HAP5 0.0208
					Weeder	Yes	119	HAP5 0.0488	HAP5 0.0751		HAP5 0.0219
					Trawler	Yes	88	HAP5[HAP5_Fraenkel2] 0.1749	HAP5[HAP5_Fraenkel2] 0.0219	HAP5[HAP5_Fraenkel2] 0.2236
HSF1_H2O2Hi	Yeast	125	601	HSF1 (MacIsaac et al. '06)	MEME	No	835
					AlignACE	Yes	520		HSF1 0.1874
					YMF	Yes	908	HSF1 0.1341
					Amadeus	Yes	450	HSF1 0.1701		HSF1 0.0906
					Weeder	Yes	1301	HSF1 0.1198	HSF1 0.1314	HSF1 0.0903	HSF1 0.1123
					Trawler	No	123
HSF1_H2O2Lo	Yeast	102	601	HSF1 (MacIsaac et al. '06)	MEME	Yes	574		HSF1 0.1054
					AlignACE	Yes	371		HSF1 0.1627
					YMF	Yes	883	HSF1 0.1341
					Amadeus	Yes	443	HSF1 0.1395		HSF1 0.1046
					Weeder	Yes	1015	HSF1 0.1185		HSF1 0.1009	HSF1 0.1304
					Trawler	Yes	93	HSF1[HSF1_Fraenkel2] 0.0983
HSF1_HEAT	Yeast	7	601	HSF1 (MacIsaac et al. '06)	MEME	No	3
					AlignACE	No	32
					YMF	No	665
					Amadeus	No	300
					Weeder	No	76
					Trawler	No	56
HSF1_YPD	Yeast	9	601	HSF1 (MacIsaac et al. '06)	MEME	No	6
					AlignACE	No	36
					YMF	No	669
					Amadeus	No	311
					Weeder	No	78
					Trawler	No	58
INO2_YPD	Yeast	48	601	INO2 (MacIsaac et al. '06)	MEME	Yes	129	INO2 0.0947		INO2 0.0708
					AlignACE	Yes	167		INO2 0.1067		INO2 0.1553
					YMF	Yes	758	INO2 0.1205
					Amadeus	Yes	381	INO2 0.1341		INO2 0.0651
					Weeder	Yes	471	INO2 0.0914	INO2 0.1055	INO2 0.1224	INO2 0.1228
					Trawler	Yes	112	INO2[INO2_Fraenkel2] 0.1647
INO4_YPD	Yeast	37	601	INO4 (MacIsaac et al. '06)	MEME	Yes	80	INO4 0.1026		INO4 0.0707
					AlignACE	Yes	76		INO4 0.1195
					YMF	Yes	726		INO4 0.0984
					Amadeus	Yes	358	INO4 0.0557		INO4 0.0517
					Weeder	Yes	365	INO4 0.0841	INO4 0.1009	INO4 0.0925	INO4 0.0603
					Trawler	Yes	113		INO4[INO4_Fraenkel2] 0.1649
LEU3_SM	Yeast	27	601	LEU3 (MacIsaac et al. '06)	MEME	Yes	43	LEU3 0.1421		LEU3 0.1203
					AlignACE	Yes	49		LEU3 0.1262		LEU3 0.1269
					YMF	Yes	705	LEU3 0.1287		LEU3 0.1284
					Amadeus	Yes	352	LEU3 0.1411		LEU3 0.1089
					Weeder	Yes	256	LEU3 0.0694	LEU3 0.0871	LEU3 0.0921	LEU3 0.0926
					Trawler	No	73
LEU3_YPD	Yeast	24	601	LEU3 (MacIsaac et al. '06)	MEME	Yes	34	LEU3 0.1786		LEU3 0.1333
					AlignACE	Yes	39		LEU3 0.1128		LEU3 0.0747
					YMF	Yes	703	LEU3 0.1323		LEU3 0.1284
					Amadeus	Yes	362	LEU3 0.2014		LEU3 0.1812
					Weeder	Yes	250	LEU3 0.105	LEU3 0.0618	LEU3 0.1479	LEU3 0.0906
					Trawler	No	73
MAC1_H2O2Hi	Yeast	18	601	MAC1 (MacIsaac et al. '06)	MEME	No	22
					AlignACE	No	52
					YMF	No	685
					Amadeus	No	346
					Weeder	No	176
					Trawler	No	109
MAC1_YPD	Yeast	42	601	MAC1 (MacIsaac et al. '06)	MEME	No	103
					AlignACE	No	107
					YMF	No	729
					Amadeus	No	378
					Weeder	No	381
					Trawler	No	94
MATA1_YPD	Yeast	6	601	MATA1 (MacIsaac et al. '06)	MEME	No	2
					AlignACE	No	28
					YMF	No	662
					Amadeus	No	262
					Weeder	No	56
					Trawler	Yes	70		MATA1[MATA1_Fraenkel2] 0.2311
MBP1_H2O2Hi	Yeast	137	601	MBP1 (MacIsaac et al. '06)	MEME	Yes	1026	MBP1 0.1115	MBP1 0.1423		MBP1 0.1069
					AlignACE	Yes	578	MBP1 0.0905			MBP1 0.0919
					YMF	Yes	938	MBP1 0.1073	MBP1 0.1808	MBP1 0.088	MBP1 0.088
					Amadeus	Yes	264	MBP1 0.089		MBP1 0.0949
					Weeder	Yes	1378	MBP1 0.0928	MBP1 0.0873	MBP1 0.0956	MBP1 0.0577
					Trawler	Yes	238	MBP1[MBP1_Fraenkel2] 0.098
MBP1_H2O2Lo	Yeast	61	601	MBP1 (MacIsaac et al. '06)	MEME	Yes	206	MBP1 0.0917		MBP1 0.0809
					AlignACE	Yes	112	MBP1 0.0947			MBP1 0.1209
					YMF	Yes	774	MBP1 0.1073	MBP1 0.1768	MBP1 0.088	MBP1 0.0947
					Amadeus	Yes	284	MBP1 0.0953		MBP1 0.0584
					Weeder	Yes	569	MBP1 0.0852	MBP1 0.0873	MBP1 0.0852	MBP1 0.0707
					Trawler	Yes	79	MBP1[MBP1_Fraenkel2] 0.0959
MBP1_YPD	Yeast	134	601	MBP1 (MacIsaac et al. '06)	MEME	Yes	989	MBP1 0.0912	MBP1 0.1017	MBP1 0.0918
					AlignACE	Yes	554		MBP1 0.0913
					YMF	Yes	933	MBP1 0.094			MBP1 0.088
					Amadeus	Yes	380	MBP1 0.1164		MBP1 0.1143	MBP1 0.1269
					Weeder	Yes	1329	MBP1 0.0742	MBP1 0.0793	MBP1 0.0714	MBP1 0.0575
					Trawler	Yes	130		MBP1[MBP1_Fraenkel2] 0.0946
MCM1_Alpha	Yeast	107	601	MCM1 (MacIsaac et al. '06)	MEME	Yes	630	MCM1 0.1937		MCM1 0.1123
					AlignACE	Yes	435	MCM1 0.0886		MCM1 0.1141
					YMF	Yes	893		MCM1 0.141
					Amadeus	Yes	439	MCM1 0.131		MCM1 0.1511	MCM1 0.1892
					Weeder	Yes	1045	MCM1 0.1127	MCM1 0.1315	MCM1 0.1355	MCM1 0.2169
					Trawler	Yes	141		MCM1[MCM1_Fraenkel2] 0.1198
MCM1_YPD	Yeast	77	601	MCM1 (MacIsaac et al. '06)	MEME	Yes	339				MCM1 0.195
					AlignACE	Yes	233	MCM1 0.0989		MCM1 0.0828
					YMF	No	827
					Amadeus	Yes	410	MCM1 0.0984		MCM1 0.1622	MCM1 0.2198
					Weeder	Yes	752	MCM1 0.1869	MCM1 0.1486	MCM1 0.104	MCM1 0.1988
					Trawler	No	87
MET28_YPD	Yeast	17	601	MET28 (MacIsaac et al. '06)	MEME	No	20
					AlignACE	No	55
					YMF	No	681
					Amadeus	Yes	315		MET28 0.2116
					Weeder	No	153
					Trawler	No	59
MET31_SM	Yeast	14	601	MET31 (MacIsaac et al. '06)	MEME	No	14
					AlignACE	No	50
					YMF	No	690
					Amadeus	No	329
					Weeder	No	130
					Trawler	No	70
MET31_YPD	Yeast	24	601	MET31 (MacIsaac et al. '06)	MEME	Yes	34	MET31 0.1246
					AlignACE	Yes	53		MET31 0.1174
					YMF	No	698
					Amadeus	Yes	358		MET31 0.233		MET31 0.1452
					Weeder	Yes	216	MET31 0.1461		MET31 0.1255
					Trawler	Yes	93			MET31[MET31_Fraenkel2] 0.1576
MET32_SM	Yeast	41	601	MET32 (MacIsaac et al. '06)	MEME	No	97
					AlignACE	No	115
					YMF	No	733
					Amadeus	Yes	336		MET32 0.2158		MET32 0.111
					Weeder	No	400
					Trawler	No	95
MET32_YPD	Yeast	51	601	MET32 (MacIsaac et al. '06)	MEME	No	147
					AlignACE	No	174
					YMF	No	754
					Amadeus	No	397
					Weeder	No	515
					Trawler	No	84
MET4_SM	Yeast	28	601	MET4 (MacIsaac et al. '06)	MEME	No	45
					AlignACE	No	70
					YMF	No	705
					Amadeus	Yes	389				MET4 0.1533
					Weeder	Yes	276		MET4 0.1095
					Trawler	No	94
MET4_YPD	Yeast	10	601	MET4 (MacIsaac et al. '06)	MEME	No	7
					AlignACE	No	38
					YMF	No	696
					Amadeus	Yes	301			MET4 0.0896
					Weeder	No	93
					Trawler	Yes	82			MET4[MET4_Fraenkel2] 0.0475
MIG1_YPD	Yeast	22	601	MIG1 (MacIsaac et al. '06)	MEME	No	30
					AlignACE	No	46
					YMF	No	695
					Amadeus	No	334
					Weeder	No	175
					Trawler	No	101
MOT3_H2O2Hi	Yeast	12	601	MOT3 (MacIsaac et al. '06)	MEME	No	9
					AlignACE	Yes	51				MOT3 0.2387
					YMF	No	676
					Amadeus	No	318
					Weeder	No	105
					Trawler	No	75
MOT3_H2O2Lo	Yeast	5	601	MOT3 (MacIsaac et al. '06)	MEME	No	2
					AlignACE	No	21
					YMF	No	658
					Amadeus	No	265
					Weeder	No	49
					Trawler	No	57
MOT3_SM	Yeast	16	601	MOT3 (MacIsaac et al. '06)	MEME	Yes	16	MOT3 0.1747
					AlignACE	Yes	42	MOT3 0.2118			MOT3 0.1951
					YMF	Yes	696		MOT3 0.161
					Amadeus	No	338
					Weeder	Yes	156	MOT3 0.1485	MOT3 0.1978	MOT3 0.1468	MOT3 0.2013
					Trawler	No	92
MOT3_YPD	Yeast	8	601	MOT3 (MacIsaac et al. '06)	MEME	Yes	4	MOT3 0.1189
					AlignACE	No	20
					YMF	No	662
					Amadeus	Yes	293		MOT3 0.1533
					Weeder	No	86
					Trawler	No	69
MSN2_Acid	Yeast	31	601	MSN2 (MacIsaac et al. '06)	MEME	No	53
					AlignACE	No	78
					YMF	No	710
					Amadeus	Yes	377		MSN2 0.2293
					Weeder	No	294
					Trawler	No	132
MSN2_H2O2Hi	Yeast	79	601	MSN2 (MacIsaac et al. '06)	MEME	Yes	353	MSN2 0.0941		MSN2 0.2104	MSN2 0.0875
					AlignACE	Yes	317		MSN2 0.0609		MSN2 0.0922
					YMF	Yes	820	MSN2 0.0825		MSN2 0.1623
					Amadeus	Yes	424		MSN2 0.0816		MSN2 0.1508
					Weeder	Yes	778	MSN2 0.1095	MSN2 0.1667
					Trawler	No	98
MSN2_H2O2Lo	Yeast	47	601	MSN2 (MacIsaac et al. '06)	MEME	Yes	125		MSN2 0.0818
					AlignACE	Yes	119		MSN2 0.0719
					YMF	Yes	742		MSN2 0.0725		MSN2 0.1553
					Amadeus	Yes	391			MSN2 0.1387
					Weeder	Yes	440			MSN2 0.1335
					Trawler	Yes	84			MSN2[MSN2_Fraenkel2] 0.1033
MSN2_RAPA	Yeast	51	601	MSN2 (MacIsaac et al. '06)	MEME	No	143
					AlignACE	No	143
					YMF	No	765
					Amadeus	No	426
					Weeder	No	488
					Trawler	No	82
MSN4_Acid	Yeast	6	601	MSN4 (MacIsaac et al. '06)	MEME	Yes	3		MSN4 0.0905	MSN4 0.1178
					AlignACE	No	21
					YMF	No	666
					Amadeus	Yes	273	MSN4 0.1255	MSN4 0.1406
					Weeder	Yes	49		MSN4 0.1148		MSN4 0.2001
					Trawler	No	56
MSN4_H2O2Hi	Yeast	71	601	MSN4 (MacIsaac et al. '06)	MEME	Yes	288		MSN4 0.1709
					AlignACE	No	240
					YMF	Yes	790	MSN4 0.1851		MSN4 0.1598
					Amadeus	No	423
					Weeder	Yes	707		MSN4 0.2124
					Trawler	Yes	102	MSN4[MSN4_Fraenkel2] 0.0904
MSN4_H2O2Lo	Yeast	19	601	MSN4 (MacIsaac et al. '06)	MEME	Yes	24		MSN4 0.2218
					AlignACE	No	55
					YMF	Yes	682				MSN4 0.1738
					Amadeus	No	343
					Weeder	No	177
					Trawler	No	99
MSN4_RAPA	Yeast	57	601	MSN4 (MacIsaac et al. '06)	MEME	Yes	178				MSN4 0.0986
					AlignACE	No	169
					YMF	No	781
					Amadeus	No	432
					Weeder	No	565
					Trawler	No	73
MSN4_YPD	Yeast	57	601	MSN4 (MacIsaac et al. '06)	MEME	No	219
					AlignACE	No	441
					YMF	No	763
					Amadeus	No	394
					Weeder	No	471
					Trawler	No	100
NRG1_H2O2Hi	Yeast	128	601	NRG1 (MacIsaac et al. '06)	MEME	Yes	1105	NRG1 0.0732			NRG1 0.0646
					AlignACE	Yes	810		NRG1 0.0984		NRG1 0.1314
					YMF	Yes	905		NRG1 0.1285
					Amadeus	Yes	403	NRG1 0.1041		NRG1 0.0664
					Weeder	Yes	1341	NRG1 0.0879		NRG1 0.1174
					Trawler	Yes	212		NRG1[NRG1_Fraenkel2] 0.0739
NRG1_H2O2Lo	Yeast	47	601	NRG1 (MacIsaac et al. '06)	MEME	No	158
					AlignACE	No	162
					YMF	No	745
					Amadeus	No	390
					Weeder	No	439
					Trawler	No	91
NRG1_YPD	Yeast	73	601	NRG1 (MacIsaac et al. '06)	MEME	No	404
					AlignACE	No	362
					YMF	No	797
					Amadeus	No	453
					Weeder	No	687
					Trawler	No	115
PDR1_H2O2Lo	Yeast	8	601	PDR1 (MacIsaac et al. '06)	MEME	No	5
					AlignACE	No	22
					YMF	No	671
					Amadeus	No	263
					Weeder	No	77
					Trawler	No	59
PDR1_YPD	Yeast	87	601	PDR1 (MacIsaac et al. '06)	MEME	No	523
					AlignACE	No	570
					YMF	No	824
					Amadeus	No	364
					Weeder	No	738
					Trawler	No	113
PDR3_YPD	Yeast	21	601	PDR3 (MacIsaac et al. '06)	MEME	No	28
					AlignACE	No	71
					YMF	Yes	688	PDR3 0.0362
					Amadeus	No	347
					Weeder	No	199
					Trawler	No	73
PHO2_H2O2Hi	Yeast	16	601	PHO2 (MacIsaac et al. '06)	MEME	No	17
					AlignACE	No	50
					YMF	No	678
					Amadeus	No	332
					Weeder	No	154
					Trawler	No	80
PHO2_SM	Yeast	26	601	PHO2 (MacIsaac et al. '06)	MEME	No	41
					AlignACE	No	41
					YMF	No	699
					Amadeus	Yes	358				PHO2 0.2268
					Weeder	No	269
					Trawler	No	71
PHO2_YPD	Yeast	33	601	PHO2 (MacIsaac et al. '06)	MEME	No	65
					AlignACE	No	69
					YMF	No	733
					Amadeus	No	371
					Weeder	Yes	337		PHO2 0.1443	PHO2 0.1585	PHO2 0.2194
					Trawler	No	78
PHO4_Pi-	Yeast	31	601	PHO4 (MacIsaac et al. '06)	MEME	Yes	53	PHO4 0.0689		PHO4 0.0368
					AlignACE	Yes	102	PHO4 0.084		PHO4 0.0793
					YMF	Yes	710	PHO4 0.0294			PHO4 0.0686
					Amadeus	Yes	326	PHO4 0.0772		PHO4 0.0642
					Weeder	Yes	263	PHO4 0.0445	PHO4 0.0448	PHO4 0.0633	PHO4 0.0692
					Trawler	Yes	85	PHO4[PHO4_Fraenkel2] 0.0748
PHO4_YPD	Yeast	72	601	PHO4 (MacIsaac et al. '06)	MEME	No	297
					AlignACE	No	227
					YMF	No	805
					Amadeus	No	400
					Weeder	No	678
					Trawler	No	102
PUT3_H2O2Lo	Yeast	90	601	PUT3 (MacIsaac et al. '06)	MEME	No	452
					AlignACE	No	341
					YMF	No	828
					Amadeus	No	388
					Weeder	No	896
					Trawler	No	111
PUT3_SM	Yeast	29	601	PUT3 (MacIsaac et al. '06)	MEME	No	49
					AlignACE	No	106
					YMF	No	702
					Amadeus	Yes	367				PUT3 0.1601
					Weeder	No	278
					Trawler	Yes	72	PUT3[PUT3_Fraenkel2] 0.2087
PUT3_YPD	Yeast	11	601	PUT3 (MacIsaac et al. '06)	MEME	Yes	9	PUT3 0.1436
					AlignACE	No	41
					YMF	Yes	675	PUT3 0.1211
					Amadeus	Yes	326		PUT3 0.1474
					Weeder	Yes	112	PUT3 0.0504
					Trawler	No	162
RAP1_YPD	Yeast	169	601	RAP1 (MacIsaac et al. '06)	MEME	Yes	1546	RAP1 0.1107		RAP1 0.1022
					AlignACE	Yes	1042	RAP1 0.1188		RAP1 0.0855
					YMF	Yes	1013	RAP1 0.1754	RAP1 0.1503	RAP1 0.2034	RAP1 0.1744
					Amadeus	Yes	411	RAP1 0.1061		RAP1 0.1164
					Weeder	Yes	1681	RAP1 0.1805	RAP1 0.1422	RAP1 0.1387	RAP1 0.1273
					Trawler	Yes	154	RAP1[RAP1_Fraenkel2] 0.1034
RCS1_H2O2Hi	Yeast	52	601	RCS1 (MacIsaac et al. '06)	MEME	Yes	151	RCS1 0.1398			RCS1 0.1202
					AlignACE	Yes	163	RCS1 0.1768			RCS1 0.1588
					YMF	Yes	751	RCS1 0.1802	RCS1 0.2265
					Amadeus	Yes	360	RCS1 0.1007		RCS1 0.1322
					Weeder	Yes	468	RCS1 0.1582	RCS1 0.162	RCS1 0.1675	RCS1 0.1633
					Trawler	Yes	95	RCS1[RCS1_Fraenkel2] 0.1261
RCS1_H2O2Lo	Yeast	261	601	RCS1 (MacIsaac et al. '06)	MEME	No	3570
					AlignACE	No	2029
					YMF	No	1195
					Amadeus	No	325
					Weeder	No	2838
					Trawler	No	165
RCS1_SM	Yeast	24	601	RCS1 (MacIsaac et al. '06)	MEME	Yes	37	RCS1 0.1583
					AlignACE	No	51
					YMF	Yes	697		RCS1 0.1768
					Amadeus	Yes	370			RCS1 0.2266
					Weeder	No	226
					Trawler	No	58
RCS1_YPD	Yeast	30	601	RCS1 (MacIsaac et al. '06)	MEME	Yes	49	RCS1 0.1772			RCS1 0.2376
					AlignACE	No	67
					YMF	No	715
					Amadeus	No	374
					Weeder	No	273
					Trawler	No	95
RDS1_H2O2Hi	Yeast	46	601	RDS1 (MacIsaac et al. '06)	MEME	Yes	118	RDS1 0.0264	RDS1 0.1684		RDS1 0.0728
					AlignACE	Yes	108		RDS1 0.0073
					YMF	Yes	749	RDS1 6.2		RDS1 6.2	RDS1 0.0837
					Amadeus	Yes	366	RDS1 0.1152		RDS1 0.0896
					Weeder	Yes	422	RDS1 6.2	RDS1 0.028	RDS1 0.0099	RDS1 6.2
					Trawler	Yes	76	RDS1[RDS1_Fraenkel2] 0.0651
REB1_H2O2Hi	Yeast	59	601	REB1 (MacIsaac et al. '06)	MEME	Yes	189	REB1 0.0244		REB1 0.0328
					AlignACE	Yes	175	REB1 0.0536		REB1 0.035
					YMF	Yes	775	REB1 0.0536	REB1 0.1051	REB1 0.0916	REB1 0.1051
					Amadeus	Yes	453	REB1 0.0884		REB1 0.034
					Weeder	Yes	564	REB1 0.0514	REB1 0.0736	REB1 0.0464	REB1 0.0554
					Trawler	Yes	90	REB1[REB1_Fraenkel2] 0.0581
REB1_YPD	Yeast	146	601	REB1 (MacIsaac et al. '06)	MEME	Yes	1155	REB1 0.0459		REB1 0.0415
					AlignACE	Yes	747	REB1 0.0675		REB1 0.0478
					YMF	Yes	956	REB1 0.0536	REB1 0.1051	REB1 0.0976	REB1 0.1545
					Amadeus	Yes	413	REB1 0.0404		REB1 0.0443
					Weeder	Yes	1437	REB1 0.0433	REB1 0.0638	REB1 0.0398	REB1 0.0685
					Trawler	Yes	132	REB1[REB1_Fraenkel2] 0.0401
RIM101_H2O2Hi	Yeast	16	601	RIM101 (MacIsaac et al. '06)	MEME	Yes	17	RIM101 0.2225			RIM101 0.2225
					AlignACE	No	26
					YMF	Yes	682				RIM101 0.2256
					Amadeus	No	353
					Weeder	No	160
					Trawler	No	76
RIM101_YPD	Yeast	7	601	RIM101 (MacIsaac et al. '06)	MEME	No	3
					AlignACE	No	25
					YMF	Yes	660			RIM101 0.2251
					Amadeus	No	237
					Weeder	No	71
					Trawler	No	58
RLM1_YPD	Yeast	60	601	RLM1 (MacIsaac et al. '06)	MEME	No	199
					AlignACE	No	167
					YMF	No	780
					Amadeus	No	422
					Weeder	No	621
					Trawler	No	75
ROX1_H2O2Hi	Yeast	57	601	ROX1 (MacIsaac et al. '06)	MEME	No	181
					AlignACE	No	200
					YMF	No	762
					Amadeus	No	391
					Weeder	No	525
					Trawler	No	98
ROX1_H2O2Lo	Yeast	6	601	ROX1 (MacIsaac et al. '06)	MEME	No	3
					AlignACE	No	28
					YMF	No	662
					Amadeus	No	279
					Weeder	No	61
					Trawler	No	57
ROX1_YPD	Yeast	68	601	ROX1 (MacIsaac et al. '06)	MEME	No	265
					AlignACE	No	217
					YMF	No	803
					Amadeus	No	410
					Weeder	No	663
					Trawler	No	97
RPH1_H2O2Hi	Yeast	29	601	RPH1 (MacIsaac et al. '06)	MEME	No	49
					AlignACE	No	104
					YMF	No	700
					Amadeus	No	353
					Weeder	No	233
					Trawler	No	88
RPH1_SM	Yeast	14	601	RPH1 (MacIsaac et al. '06)	MEME	No	14
					AlignACE	No	66
					YMF	No	677
					Amadeus	No	327
					Weeder	No	138
					Trawler	No	58
RPH1_YPD	Yeast	8	601	RPH1 (MacIsaac et al. '06)	MEME	No	4
					AlignACE	No	12
					YMF	No	661
					Amadeus	No	317
					Weeder	No	85
					Trawler	No	87
RPN4_H2O2Hi	Yeast	13	601	RPN4 (MacIsaac et al. '06)	MEME	Yes	10	RPN4 0.1522		RPN4 0.1317
					AlignACE	Yes	64		RPN4 0.1665
					YMF	Yes	672		RPN4 0.1255
					Amadeus	No	301
					Weeder	Yes	107		RPN4 0.1194	RPN4 0.1681
					Trawler	Yes	109	RPN4[RPN4_Fraenkel2] 0.1049
RPN4_H2O2Lo	Yeast	100	601	RPN4 (MacIsaac et al. '06)	MEME	Yes	547	RPN4 0.0253		RPN4 0.0418
					AlignACE	Yes	325	RPN4 0.0339		RPN4 0.0438
					YMF	Yes	907	RPN4 0.0883	RPN4 0.1887	RPN4 0.0965
					Amadeus	Yes	367	RPN4 0.0398		RPN4 0.0585
					Weeder	Yes	1010	RPN4 0.061	RPN4 0.0732	RPN4 0.087	RPN4 0.0736
					Trawler	No	123
RPN4_YPD	Yeast	39	601	RPN4 (MacIsaac et al. '06)	MEME	No	90
					AlignACE	No	88
					YMF	No	728
					Amadeus	No	385
					Weeder	No	382
					Trawler	No	77
RTG3_H2O2Hi	Yeast	37	601	RTG3 (MacIsaac et al. '06)	MEME	No	80
					AlignACE	No	120
					YMF	No	736
					Amadeus	Yes	388			RTG3 0.216
					Weeder	Yes	350				RTG3 0.0944
					Trawler	No	75
RTG3_H2O2Lo	Yeast	10	601	RTG3 (MacIsaac et al. '06)	MEME	No	7
					AlignACE	No	38
					YMF	No	668
					Amadeus	No	232
					Weeder	No	89
					Trawler	No	119
RTG3_RAPA	Yeast	54	601	RTG3 (MacIsaac et al. '06)	MEME	No	158
					AlignACE	No	142
					YMF	No	766
					Amadeus	Yes	421			RTG3 0.1301
					Weeder	No	524
					Trawler	Yes	147			RTG3[RTG3_Fraenkel2] 0.2317	RTG3[RTG3_Fraenkel2] 0.1718
RTG3_SM	Yeast	32	601	RTG3 (MacIsaac et al. '06)	MEME	No	56
					AlignACE	No	96
					YMF	No	707
					Amadeus	No	372
					Weeder	No	303
					Trawler	No	97
RTG3_YPD	Yeast	15	601	RTG3 (MacIsaac et al. '06)	MEME	No	16
					AlignACE	No	20
					YMF	No	676
					Amadeus	No	329
					Weeder	No	150
					Trawler	No	99
SIP4_SM	Yeast	21	601	SIP4 (MacIsaac et al. '06)	MEME	Yes	27				SIP4 0.1758
					AlignACE	Yes	41	SIP4 0.1769		SIP4 0.1589
					YMF	No	692
					Amadeus	Yes	356				SIP4 0.205
					Weeder	Yes	200		SIP4 0.2208		SIP4 0.2345
					Trawler	No	58
SIP4_YPD	Yeast	10	601	SIP4 (MacIsaac et al. '06)	MEME	No	7
					AlignACE	No	34
					YMF	No	666
					Amadeus	No	288
					Weeder	No	102
					Trawler	No	64
SKN7_H2O2Hi	Yeast	103	601	SKN7 (MacIsaac et al. '06)	MEME	Yes	588	SKN7 0.1947		SKN7 0.1697
					AlignACE	Yes	419				SKN7 0.2082
					YMF	No	870
					Amadeus	Yes	406	SKN7 0.1732		SKN7 0.1552
					Weeder	No	1041
					Trawler	No	136
SKN7_H2O2Lo	Yeast	190	601	SKN7 (MacIsaac et al. '06)	MEME	Yes	1932			SKN7 0.2343
					AlignACE	Yes	1258		SKN7 0.2052		SKN7 0.2085
					YMF	No	1046
					Amadeus	Yes	408	SKN7 0.2297		SKN7 0.1738
					Weeder	No	2032
					Trawler	No	234
SKN7_HEAT	Yeast	12	601	SKN7 (MacIsaac et al. '06)	MEME	Yes	10			SKN7 0.2252
					AlignACE	Yes	45	SKN7 0.2256			SKN7 0.2292
					YMF	No	669
					Amadeus	Yes	338			SKN7 0.2142
					Weeder	Yes	109		SKN7 0.2182
					Trawler	Yes	71	SKN7[SKN7_Fraenkel2] 0.2387
SKN7_YPD	Yeast	69	601	SKN7 (MacIsaac et al. '06)	MEME	Yes	275			SKN7 0.2232
					AlignACE	No	277
					YMF	No	787
					Amadeus	Yes	435			SKN7 0.1643
					Weeder	No	661
					Trawler	No	183
SKO1_YPD	Yeast	18	601	SKO1 (MacIsaac et al. '06)	MEME	Yes	22		SKO1 0.0953
					AlignACE	No	59
					YMF	No	683
					Amadeus	Yes	374	SKO1 0.1339		SKO1 0.1288
					Weeder	Yes	163	SKO1 0.1438	SKO1 0.186	SKO1 0.1285
					Trawler	Yes	91	SKO1[SKO1_Fraenkel2] 0.1514
SMP1_YPD	Yeast	91	601	SMP1 (MacIsaac et al. '06)	MEME	No	465
					AlignACE	No	381
					YMF	No	830
					Amadeus	No	412
					Weeder	No	890
					Trawler	No	124
STB5_YPD	Yeast	50	601	STB5 (MacIsaac et al. '06)	MEME	No	143
					AlignACE	No	162
					YMF	Yes	748		STB5 0.1831
					Amadeus	Yes	400	STB5 0.188		STB5 0.1626
					Weeder	No	483
					Trawler	Yes	72		STB5[STB5_Fraenkel2] 0.1686
STE12_Alpha	Yeast	125	601	STE12 (MacIsaac et al. '06)	MEME	Yes	853	STE12 0.103		STE12 0.2227
					AlignACE	Yes	514		STE12 0.1163		STE12 0.2301
					YMF	Yes	916	STE12 0.1164
					Amadeus	Yes	430	STE12 0.0962		STE12 0.1165
					Weeder	Yes	1260	STE12 0.1282	STE12 0.1157	STE12 0.1392	STE12 0.1005
					Trawler	Yes	132			STE12[STE12_Fraenkel2] 0.0797
STE12_BUT14	Yeast	135	601	STE12 (MacIsaac et al. '06)	MEME	Yes	1007	STE12 0.1162			STE12 0.2336
					AlignACE	Yes	720		STE12 0.2106		STE12 0.2313
					YMF	Yes	964	STE12 0.1164
					Amadeus	Yes	452		STE12 0.0987	STE12 0.0768
					Weeder	Yes	1433	STE12 0.1485	STE12 0.0861	STE12 0.0801
					Trawler	Yes	119		STE12[STE12_Fraenkel2] 0.0666
STE12_BUT90	Yeast	105	601	STE12 (MacIsaac et al. '06)	MEME	Yes	605		STE12 0.0953
					AlignACE	No	486
					YMF	Yes	878		STE12 0.1174		STE12 0.1869
					Amadeus	Yes	421	STE12 0.0957		STE12 0.1064
					Weeder	Yes	1046	STE12 0.0955	STE12 0.0924	STE12 0.0707	STE12 0.0807
					Trawler	No	212
STE12_YPD	Yeast	63	601	STE12 (MacIsaac et al. '06)	MEME	Yes	216	STE12 0.0933		STE12 0.2183	STE12 0.0921
					AlignACE	Yes	157	STE12 0.1163
					YMF	Yes	786		STE12 0.1164
					Amadeus	Yes	438	STE12 0.0827		STE12 0.0866
					Weeder	Yes	614	STE12 0.1045	STE12 0.0972	STE12 0.0986	STE12 0.1133
					Trawler	Yes	117			STE12[STE12_Fraenkel2] 0.0803
STP1_SM	Yeast	71	601	STP1 (MacIsaac et al. '06)	MEME	No	284
					AlignACE	No	212
					YMF	No	798
					Amadeus	No	403
					Weeder	No	700
					Trawler	No	69
STP1_YPD	Yeast	14	601	STP1 (MacIsaac et al. '06)	MEME	Yes	13	STP1 0.1147
					AlignACE	Yes	34	STP1 0.1021			STP1 0.157
					YMF	Yes	678		STP1 0.1973		STP1 0.2345
					Amadeus	Yes	335				STP1 0.204
					Weeder	Yes	144			STP1 0.1986
					Trawler	Yes	94	STP1[STP1_Fraenkel2] 0.2203
SUM1_YPD	Yeast	60	601	SUM1 (MacIsaac et al. '06)	MEME	Yes	241		SUM1 0.1357		SUM1 0.0795
					AlignACE	Yes	139		SUM1 0.1001		SUM1 0.086
					YMF	No	781
					Amadeus	Yes	410	SUM1 0.1212		SUM1 0.1354
					Weeder	Yes	562	SUM1 0.1582	SUM1 0.1989	SUM1 0.1816	SUM1 0.2237
					Trawler	Yes	163	SUM1[SUM1_Fraenkel2] 0.1979	SUM1[SUM1_Fraenkel2] 0.1205
SUT1_YPD	Yeast	69	601	SUT1 (MacIsaac et al. '06)	MEME	No	272
					AlignACE	Yes	212				SUT1 0.2061
					YMF	No	790
					Amadeus	Yes	425	SUT1 0.234		SUT1 0.2388
					Weeder	Yes	731			SUT1 0.2323
					Trawler	No	507
SWI4_YPD	Yeast	161	601	SWI4 (MacIsaac et al. '06)	MEME	Yes	1395	SWI4 0.112			SWI4 0.1047
					AlignACE	Yes	870				SWI4 0.166
					YMF	No	982
					Amadeus	Yes	397	SWI4 0.1413		SWI4 0.1019
					Weeder	Yes	1667	SWI4 0.1414		SWI4 0.1047
					Trawler	Yes	149	SWI4[SWI4_Fraenkel2] 0.2181
SWI5_YPD	Yeast	120	601	SWI5 (MacIsaac et al. '06)	MEME	No	793
					AlignACE	No	511
					YMF	No	893
					Amadeus	Yes	407	SWI5 0.2283
					Weeder	No	1197
					Trawler	No	181
SWI6_YPD	Yeast	158	601	SWI6 (MacIsaac et al. '06)	MEME	Yes	1347	SWI6 0.1056			SWI6 0.1138
					AlignACE	Yes	780		SWI6 0.1543
					YMF	Yes	987	SWI6 0.1141		SWI6 0.1141
					Amadeus	Yes	373	SWI6 0.1122		SWI6 0.0895
					Weeder	Yes	1620	SWI6 0.0962	SWI6 0.1097	SWI6 0.1141	SWI6 0.0917
					Trawler	Yes	196	SWI6[SWI6_Fraenkel2] 0.1672
TEC1_Alpha	Yeast	43	601	TEC1 (MacIsaac et al. '06)	MEME	No	109
					AlignACE	No	91
					YMF	No	739
					Amadeus	No	370
					Weeder	No	434
					Trawler	No	77
TEC1_BUT14	Yeast	38	601	TEC1 (MacIsaac et al. '06)	MEME	Yes	83			TEC1 0.0801
					AlignACE	No	120
					YMF	No	721
					Amadeus	Yes	361	TEC1 0.1196
					Weeder	No	361
					Trawler	No	179
TEC1_YPD	Yeast	42	601	TEC1 (MacIsaac et al. '06)	MEME	No	101
					AlignACE	Yes	117				TEC1 0.2145
					YMF	No	731
					Amadeus	No	358
					Weeder	Yes	390			TEC1 0.1322
					Trawler	No	74
TYE7_YPD	Yeast	60	601	TYE7 (MacIsaac et al. '06)	MEME	Yes	278	TYE7 0.1243		TYE7 0.0929
					AlignACE	Yes	231	TYE7 0.1102			TYE7 0.0932
					YMF	Yes	786	TYE7 0.1176
					Amadeus	Yes	337	TYE7 0.1143		TYE7 0.0659
					Weeder	Yes	572	TYE7 0.104	TYE7 0.1073	TYE7 0.1292	TYE7 0.104
					Trawler	Yes	104		TYE7[TYE7_Fraenkel2] 0.066
UGA3_RAPA	Yeast	32	601	UGA3 (MacIsaac et al. '06)	MEME	No	53
					AlignACE	No	136
					YMF	No	706
					Amadeus	No	341
					Weeder	No	251
					Trawler	No	87
UGA3_SM	Yeast	12	601	UGA3 (MacIsaac et al. '06)	MEME	No	10
					AlignACE	No	26
					YMF	No	672
					Amadeus	No	313
					Weeder	No	118
					Trawler	No	63
UGA3_YPD	Yeast	5	601	UGA3 (MacIsaac et al. '06)	MEME	No	2
					AlignACE	No	22
					YMF	No	655
					Amadeus	No	254
					Weeder	No	49
					Trawler	No	57
UME6_H2O2Hi	Yeast	104	601	UME6 (MacIsaac et al. '06)	MEME	Yes	578	UME6 0.0722		UME6 0.0666
					AlignACE	Yes	254	UME6 0.0801		UME6 0.0658
					YMF	Yes	883	UME6 0.1061	UME6 0.1178	UME6 0.1251
					Amadeus	Yes	339	UME6 0.0601		UME6 0.0616
					Weeder	Yes	1006	UME6 0.0726	UME6 0.0883	UME6 0.0692	UME6 0.0891
					Trawler	Yes	116	UME6[UME6_Fraenkel2] 0.1591
UME6_YPD	Yeast	133	601	UME6 (MacIsaac et al. '06)	MEME	Yes	960	UME6 0.0706		UME6 0.0676
					AlignACE	Yes	433	UME6 0.0781		UME6 0.0629
					YMF	Yes	932	UME6 0.1061	UME6 0.1178	UME6 0.1387
					Amadeus	Yes	368	UME6 0.0748		UME6 0.0596
					Weeder	Yes	1373	UME6 0.0719	UME6 0.0944	UME6 0.0747	UME6 0.0932
					Trawler	Yes	156	UME6[UME6_Fraenkel2] 0.0997
XBP1_H2O2Lo	Yeast	77	601	XBP1 (MacIsaac et al. '06)	MEME	Yes	335	XBP1 0.2129		XBP1 0.1994
					AlignACE	No	405
					YMF	No	801
					Amadeus	Yes	432		XBP1 0.1798
					Weeder	Yes	673			XBP1 0.2051
					Trawler	No	132
YAP1_H2O2Hi	Yeast	7	601	YAP1 (MacIsaac et al. '06)	MEME	No	4
					AlignACE	No	30
					YMF	No	669
					Amadeus	No	266
					Weeder	No	52
					Trawler	No	57
YAP1_H2O2Lo	Yeast	38	601	YAP1 (MacIsaac et al. '06)	MEME	Yes	84	YAP1 0.1593		YAP1 0.1448
					AlignACE	Yes	116				YAP1 0.153
					YMF	Yes	721		YAP1 0.1822
					Amadeus	Yes	377	YAP1 0.1987		YAP1 0.1261
					Weeder	Yes	376	YAP1 0.1017	YAP1 0.1343	YAP1 0.137	YAP1 0.1413
					Trawler	Yes	83		YAP1[YAP1_Fraenkel2] 0.131
YAP1_YPD	Yeast	72	601	YAP1 (MacIsaac et al. '06)	MEME	Yes	293			YAP1 0.1304
					AlignACE	No	250
					YMF	No	797
					Amadeus	Yes	417	YAP1 0.109		YAP1 0.1472
					Weeder	Yes	709	YAP1 0.0985	YAP1 0.1879	YAP1 0.2022	YAP1 0.1417
					Trawler	No	109
YAP3_YPD	Yeast	18	601	YAP3 (MacIsaac et al. '06)	MEME	No	22
					AlignACE	No	47
					YMF	No	690
					Amadeus	No	330
					Weeder	No	169
					Trawler	No	86
YAP6_H2O2Hi	Yeast	90	601	YAP6 (MacIsaac et al. '06)	MEME	No	459
					AlignACE	No	339
					YMF	No	835
					Amadeus	Yes	419			YAP6 0.1257
					Weeder	No	841
					Trawler	No	84
YAP6_H2O2Lo	Yeast	60	601	YAP6 (MacIsaac et al. '06)	MEME	No	200
					AlignACE	No	143
					YMF	Yes	773		YAP6 0.1594
					Amadeus	No	437
					Weeder	Yes	587	YAP6 0.1788	YAP6 0.1573		YAP6 0.1597
					Trawler	No	94
YAP6_YPD	Yeast	93	601	YAP6 (MacIsaac et al. '06)	MEME	No	483
					AlignACE	No	336
					YMF	No	836
					Amadeus	No	423
					Weeder	No	926
					Trawler	No	128
YAP7_H2O2Hi	Yeast	141	601	YAP7 (MacIsaac et al. '06)	MEME	Yes	1078	YAP7 0.0803			YAP7 0.1022
					AlignACE	Yes	720		YAP7 0.1858		YAP7 0.1485
					YMF	Yes	943	YAP7 0.1488			YAP7 0.2086
					Amadeus	Yes	448	YAP7 0.0717		YAP7 0.1411
					Weeder	Yes	1440	YAP7 0.1326	YAP7 0.1082	YAP7 0.148	YAP7 0.1521
					Trawler	Yes	135		YAP7[YAP7_Fraenkel2] 0.1105
YAP7_H2O2Lo	Yeast	152	601	YAP7 (MacIsaac et al. '06)	MEME	Yes	1252	YAP7 0.1207		YAP7 0.1118
					AlignACE	Yes	813		YAP7 0.2028		YAP7 0.1614
					YMF	Yes	964	YAP7 0.1488			YAP7 0.2086
					Amadeus	Yes	412	YAP7 0.082		YAP7 0.1321
					Weeder	Yes	1572	YAP7 0.1283	YAP7 0.107	YAP7 0.087	YAP7 0.1472
					Trawler	Yes	140	YAP7[YAP7_Fraenkel2] 0.0973
YHP1_YPD	Yeast	20	601	YHP1 (MacIsaac et al. '06)	MEME	No	25
					AlignACE	No	60
					YMF	No	686
					Amadeus	Yes	374			YHP1 0.2247
					Weeder	No	224
					Trawler	No	58
YOX1_YPD	Yeast	43	601	YOX1 (MacIsaac et al. '06)	MEME	Yes	101				YOX1 0.1996
					AlignACE	No	69
					YMF	No	781
					Amadeus	Yes	407			YOX1 0.1943	YOX1 0.0878
					Weeder	Yes	411	YOX1 0.1549	YOX1 0.0839		YOX1 0.1545
					Trawler	No	73
ZAP1_YPD	Yeast	22	601	ZAP1 (MacIsaac et al. '06)	MEME	Yes	28	ZAP1 0.2131		ZAP1 0.1897
					AlignACE	No	95
					YMF	No	705
					Amadeus	Yes	313			ZAP1 0.144
					Weeder	Yes	163	ZAP1 0.2318	ZAP1 0.1483	ZAP1 0.1938	ZAP1 0.195
					Trawler	No	103