Data set	nTP	nFP	nFN	nTN	sTP	sFP	sFN		nSn	nPPV	nSp	nPC	nCC	sSn	sPPV	sASP
dm01g	8	64	117	5811	1	8	6		0.064	0.1111111	0.9891064	0.042328	0.0696603	0.1428571	0.1111111	0.1269841
dm02r	0	40	49	1911	0	6	5		0	0	0.9794977	0	-0.0226397	0	0	0
dm03m	17	72	87	5824	2	9	7		0.1634615	0.1910112	0.9877883	0.0965909	0.163292	0.2222222	0.1818182	0.2020202
dm04g	0	80	135	7785	0	10	9		0	0	0.9898284	0	-0.0131674	0	0	0
dm05g	0	64	160	7276	0	8	14		0	0	0.9912807	0	-0.0136972	0	0	0
dm06r	7	9	91	2893	1	1	6		0.0714286	0.4375	0.9968987	0.0654206	0.1667617	0.1428571	0.5	0.3214286
dm07m	0	32	0	4468	0	4	0		NaN	0	0.9928889	0	NaN	NaN	0	NaN
dm08m	0	56	0	5944	0	7	0		NaN	0	0.9906667	0	NaN	NaN	0	NaN
hm01g	0	0	236	35764	0	0	16		0	NaN	1	0	NaN	0	NaN	NaN
hm02r	0	0	257	8743	0	0	11		0	NaN	1	0	NaN	0	NaN	NaN
hm03r	0	0	408	14592	0	0	15		0	NaN	1	0	NaN	0	NaN	NaN
hm04m	0	64	168	25768	0	8	11		0	0	0.9975225	0	-0.004006	0	0	0
hm05r	0	24	193	2783	0	3	11		0	0	0.9914499	0	-0.0235476	0	0	0
hm06g	34	2	41	4423	4	0	5		0.4533333	0.9444444	0.999548	0.4415584	0.6508162	0.4444444	1	0.7222222
hm07m	0	32	127	4841	0	4	6		0	0	0.9934332	0	-0.0129565	0	0	0
hm08m	60	20	130	7290	7	2	6		0.3157895	0.75	0.997264	0.2857143	0.4788584	0.5384615	0.7777778	0.6581197
hm09g	4	20	156	14820	0	3	10		0.025	0.1666667	0.9986523	0.0222222	0.060792	0	0	0
hm10m	2	22	87	2889	0	3	11		0.0224719	0.0833333	0.9924425	0.018018	0.0284053	0	0	0
hm11g	8	56	261	7675	1	7	18		0.0297398	0.125	0.9927564	0.0246154	0.0455211	0.0526316	0.125	0.0888158
hm12r	5	25	65	905	0	3	5		0.0714286	0.1666667	0.9731183	0.0526316	0.0666286	0	0	0
hm13r	0	0	164	5836	0	0	9		0	NaN	1	0	NaN	0	NaN	NaN
hm14r	0	32	82	1886	0	4	4		0	0	0.983316	0	-0.026366	0	0	0
hm15r	0	0	90	7910	0	0	4		0	NaN	1	0	NaN	0	NaN	NaN
hm16g	0	0	164	20836	0	0	7		0	NaN	1	0	NaN	0	NaN	NaN
hm17g	70	8	75	5347	8	1	2		0.4827586	0.8974359	0.9985061	0.4575163	0.6521097	0.8	0.8888889	0.8444444
hm18m	0	0	88	14912	0	0	7		0	NaN	1	0	NaN	0	NaN	NaN
hm19g	0	24	87	2389	0	3	4		0	0	0.9900539	0	-0.0186944	0	0	0
hm20r	221	243	1085	68451	26	30	50		0.169219	0.4762931	0.9964626	0.1426727	0.2762748	0.3421053	0.4642857	0.4031955
hm21g	16	32	77	4875	2	4	5		0.172043	0.3333333	0.9934787	0.128	0.2293473	0.2857143	0.3333333	0.3095238
hm22m	28	22	78	2872	3	5	2		0.2641509	0.56	0.9923981	0.21875	0.3699785	0.6	0.375	0.4875
hm23r	3	21	140	1836	0	3	5		0.020979	0.125	0.9886914	0.0182927	0.0228835	0	0	0
hm24m	28	12	64	3896	4	1	4		0.3043478	0.7	0.9969294	0.2692308	0.4538997	0.5	0.8	0.65
hm25g	0	0	70	930	0	0	5		0	NaN	1	0	NaN	0	NaN	NaN
hm26m	8	32	239	8721	0	5	10		0.0323887	0.2	0.9963441	0.0286738	0.0705701	0	0	0
mus01r	8	8	77	1407	1	1	5		0.0941176	0.5	0.9943463	0.0860215	0.1991026	0.1666667	0.5	0.3333333
mus02r	8	48	224	8720	0	7	12		0.0344828	0.1428571	0.9945255	0.0285714	0.0584597	0	0	0
mus03g	14	34	128	2324	2	4	7		0.0985915	0.2916667	0.985581	0.0795455	0.141973	0.2222222	0.3333333	0.2777778
mus04m	14	74	250	6662	1	15	13		0.0530303	0.1590909	0.9890143	0.0414201	0.0718902	0.0714286	0.0625	0.0669643
mus05r	16	40	72	1872	2	5	4		0.1818182	0.2857143	0.9790795	0.125	0.200029	0.3333333	0.2857143	0.3095238
mus06g	0	34	67	1399	0	5	5		0	0	0.9762736	0	-0.0329296	0	0	0
mus07g	8	32	92	5868	1	4	3		0.08	0.2	0.9945763	0.0606061	0.1173204	0.25	0.2	0.225
mus08m	0	56	41	4403	0	7	3		0	0	0.9874411	0	-0.0107642	0	0	0
mus09r	0	28	41	931	0	4	2		0	0	0.9708029	0	-0.0350936	0	0	0
mus10g	61	104	162	12673	6	13	9		0.2735426	0.369697	0.9918604	0.1865443	0.3078455	0.4	0.3157895	0.3578947
mus11m	51	29	160	5760	7	3	8		0.2417062	0.6375	0.9949905	0.2125	0.3801275	0.4666667	0.7	0.5833333
mus12m	8	18	137	1337	0	4	7		0.0551724	0.3076923	0.9867159	0.0490798	0.0948442	0	0	0
yst01g	7	33	115	8845	1	4	6		0.057377	0.175	0.9962829	0.0451613	0.0932833	0.1428571	0.2	0.1714286
yst02g	19	23	89	1869	3	3	2		0.1759259	0.452381	0.9878436	0.1450382	0.2581514	0.6	0.5	0.55
yst03m	42	18	105	3835	6	4	12		0.2857143	0.7	0.9953283	0.2545455	0.4350174	0.3333333	0.6	0.4666667
yst04r	13	27	94	5866	2	3	4		0.1214953	0.325	0.9954183	0.0970149	0.1901394	0.3333333	0.4	0.3666667
yst05r	22	0	50	1428	2	0	2		0.3055556	1	1	0.3055556	0.5433404	0.5	1	0.75
yst06g	40	0	120	3340	5	0	2		0.25	1	1	0.25	0.491253	0.7142857	1	0.8571429
yst07m	0	24	0	2976	0	3	0		NaN	0	0.992	0	NaN	NaN	0	NaN
yst08r	70	40	209	10681	7	4	7		0.2508961	0.6363636	0.996269	0.2194357	0.3905679	0.5	0.6363636	0.5681818
yst09g	52	21	163	15764	5	2	8		0.2418605	0.7123288	0.9986696	0.220339	0.4109439	0.3846154	0.7142857	0.5494505
yst10m	0	24	0	4976	0	3	0		NaN	0	0.9952	0	NaN	NaN	0	NaN
Fly	32	417	639	41912	4	53	47		0.04769	0.0712695	0.9901486	0.0294118	0.0461357	0.0784314	0.0701754	0.0743034
Human	487	691	4632	281190	55	89	243		0.0951358	0.4134126	0.9975486	0.083821	0.191872	0.1845638	0.3819444	0.2832541
Mouse	188	505	1451	53356	20	72	78		0.1147041	0.2712843	0.990624	0.0876866	0.1605781	0.2040816	0.2173913	0.2107365
Yeast	265	210	945	59580	31	26	43		0.2190083	0.5578947	0.9964877	0.1866197	0.3418471	0.4189189	0.5438596	0.4813893
Total	972	1823	7667	436038	110	240	411		0.112513	0.3477639	0.9958366	0.0929077	0.1892296	0.2111324	0.3142857	0.2627091
WordSpy results.
	nTP	nFP	nFN	nTN	sTP	sFP	sFN		nSn	nPPV	nSp	nPC	nCC	sSn	sPPV	sASP
WordSpy	972	1823	7667	436038	110	240	411		0.112513	0.3477639	0.9958366	0.0929077	0.1892296	0.2111324	0.3142857	0.2627091
Weeder	748	1748	7915	438089	84	207	438		0.0863442	0.2996795	0.9960258	0.0718471	0.1523904	0.1609195	0.2886598	0.2247897
RSA	345	1891	8318	437946	38	275	484		0.0398245	0.1542934	0.9957007	0.032689	0.0694201	0.0727969	0.1214058	0.0971013
YMF	554	3492	8109	436345	63	462	459		0.0639501	0.1369254	0.9920607	0.045578	0.0815315	0.1206897	0.12	0.1203448
Consensus	178	1394	8485	438443	21	137	501		0.0205472	0.1132316	0.9968306	0.0176991	0.0404697	0.0402299	0.1329114	0.0865706
AlignACE	477	3789	8186	436048	46	329	476		0.0550618	0.1118143	0.9913854	0.0383071	0.0658602	0.0881226	0.1226667	0.1053946
MEME	581	4836	8082	435001	58	358	464		0.0670668	0.1072549	0.989005	0.0430402	0.0706485	0.1111111	0.1394231	0.1252671
MotifSampler	520	4344	8143	435493	51	452	471		0.0600254	0.1069079	0.9901236	0.0399785	0.0666396	0.0977011	0.1013917	0.0995464
ANN-Spec	754	7799	7909	432038	81	874	441		0.0870368	0.0881562	0.9822684	0.0458025	NaN	0.1551724	0.0848168	0.1199946
Improbizer	594	7942	8069	431895	64	701	458		0.0685675	0.0695876	0.9819433	0.0357724	NaN	0.1226054	0.0836601	0.1031327
MITRA	272	4092	8391	435745	26	385	496		0.0313979	0.0623281	0.9906966	0.021325	0.0309787	0.0498084	0.0632603	0.0565344
GLAM	223	5619	8440	434218	24	473	498		0.0257417	0.0381719	0.9872248	0.0156141	NaN	0.045977	0.0482897	0.0471334
SeSiMCMC	530	13813	8133	426024	42	517	480		0.0611797	0.0369518	0.9685952	0.0235807	0.0493712	0.0804598	0.0751342	0.077797
QuickScore	151	4856	8512	434981	17	897	505		0.0174305	0.0301578	0.9889595	0.0111695	0.0083704	0.032567	0.0185996	0.0255833
results of 14 programs.