Metazoan benchmark results

Results of motif discovery tools on the
compendium of metazoan TF and miRNA target sets

Benchmark setup:

Motif discovery tools were executed on the compendium we constructed.
For each TF, the position weight matrix (one or more) from Transfac (release 10.2) was taken as the correct motif. Similary, the 8-long seed from miRBase (release 10.0) was considered as the correct motif of the correcposing miRNA.
Human, mouse, fly (D. melanogaster) and worm (C. elegans) promoter sequences (from 1000 bases upstream to 200 bases downstream of the TSS) were downloaded from Ensembl (v42-44). Human and mouse full-length 3' UTRs were downloaded from Ensembl (v45). All sequences are repeat- (and, in the case of promoters, exon-) masked.
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 Trasnfac/miRBase 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.

Back to the Amadeus supplementary results page.

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)

CREB_Zhang Human 2338 1201 M00039, M00113, M00177, M00178, M00916, M00917 (Transfac) MEME No did not finish

AlignACE No did not finish

YMF No 9719

Amadeus Yes 797 CREB[M00113] 0.0938
CREB[M00039] 0.1172
CREB[M00178] 0.132
CREB[M00917] 0.1383
CREB[M00916] 0.1495
CREB[M00177] 0.156 CREB[M00039] 0.1132
CREB[M00178] 0.1272
CREB[M00917] 0.158
CREB[M00916] 0.1581
CREB[M00177] 0.1624
CREB[M00113] 0.19

Weeder Yes 50984 CREB[M00039] 0.212

Trawler No 224

E2F4_Cam Human 201 1201 M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac) MEME No 3008

AlignACE No 7726

YMF No 1478

Amadeus Yes 606 E2F[M00516] 0.1272
E2F[M00920] 0.1356
E2F-1[M00938] 0.14
E2F[M00919] 0.1466
E2F-1[M00940] 0.1509
E2F[M00050] 0.1755
E2F[M01114] 0.2164 E2F[M00920] 0.133
E2F[M00919] 0.1374
E2F[M00516] 0.1378
E2F[M00050] 0.1579
E2F-1[M00940] 0.1617
E2F[M01114] 0.2046
E2F-1[M00938] 0.2158

Weeder Yes 4048 E2F[M00050] 0.1131
E2F-1[M00940] 0.1175
E2F[M00919] 0.1441
E2F[M00516] 0.1465
E2F-1[M00938] 0.1519
E2F[M01114] 0.1574
E2F[M00920] 0.1647 E2F[M00050] 0.1055
E2F[M00516] 0.1415
E2F-1[M00938] 0.1898
E2F[M00920] 0.192
E2F[M00919] 0.2026
E2F-1[M00940] 0.2162
E2F[M01114] 0.2307 E2F[M00050] 0.1304
E2F[M00516] 0.1683
E2F[M01114] 0.192
E2F-1[M00940] 0.192
E2F[M00919] 0.2267
E2F[M00920] 0.2357 E2F[M00050] 0.1008
E2F[M00516] 0.1464
E2F[M00920] 0.1917
E2F[M00919] 0.2008
E2F-1[M00938] 0.2141
E2F-1[M00940] 0.218

Trawler Yes 903 E2F[M00050] 0.0927
E2F[M00516] 0.1075
E2F[M00920] 0.1187
E2F[M00919] 0.1307
E2F-1[M00940] 0.1355
E2F-1[M00938] 0.1496
E2F[M01114] 0.1763

E2F_Ren Human 79 1201 M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac) MEME No 454

AlignACE No 991

YMF No 987

Amadeus Yes 569 E2F[M00050] 0.0715
E2F-1[M00940] 0.083
E2F[M00516] 0.1115
E2F[M00920] 0.1348
E2F[M00919] 0.1351
E2F[M01114] 0.1514
E2F-1[M00938] 0.1704 E2F[M00050] 0.084
E2F[M00516] 0.1215
E2F-1[M00940] 0.1245
E2F[M00920] 0.1314
E2F[M00919] 0.1401
E2F-1[M00938] 0.1593
E2F[M01114] 0.1806

Weeder Yes 1652 E2F[M00050] 0.0925
E2F-1[M00940] 0.1103
E2F[M00516] 0.1181
E2F[M01114] 0.1292
E2F[M00919] 0.1403
E2F-1[M00938] 0.1504
E2F[M00920] 0.1505 E2F[M00050] 0.0929
E2F-1[M00940] 0.1579
E2F[M00516] 0.1728
E2F[M00919] 0.1763
E2F[M01114] 0.1902
E2F[M00920] 0.1929
E2F-1[M00938] 0.2027 E2F-1[M00940] 0.163
E2F[M00919] 0.1759
E2F[M00516] 0.1768
E2F[M00920] 0.183
E2F[M01114] 0.1931
E2F[M00050] 0.2056
E2F-1[M00938] 0.2296 E2F[M01114] 0.2007
E2F[M00919] 0.2308
E2F-1[M00940] 0.2371

Trawler Yes 505 E2F[M00919] 0.1719
E2F[M00920] 0.175
E2F[M00516] 0.1827
E2F-1[M00938] 0.1842
E2F[M01114] 0.1957
E2F-1[M00940] 0.2013

ERa_Kwon Human 496 1201 M00191, M00511, M00959 (Transfac) MEME No 22576

AlignACE No 55504

YMF No 3211

Amadeus No 602

Weeder No 9515

Trawler No 787

ETS1_Hollenhorst Human 1192 1201 M00032, M00074, M00339, M00743, M00771, M00971, M01078 (Transfac) MEME No 142233

AlignACE No did not finish

YMF Yes 5608 c-Ets-1[M00743] 0.2068 c-Ets-1[M00743] 0.2068

Amadeus Yes 634 c-Ets-1[M01078] 0.1695
Ets[M00971] 0.1722
ETS[M00771] 0.1925
c-Ets-1(p54)[M00032] 0.1943
c-Ets-1(p54)[M00074] 0.2073
c-Ets-1[M00339] 0.2082

Weeder Yes 25568 c-Ets-1[M00743] 0.1372
c-Ets-1(p54)[M00032] 0.1599
c-Ets-1[M01078] 0.1662
ETS[M00771] 0.1976
c-Ets-1[M00339] 0.2106
Ets[M00971] 0.2107
c-Ets-1(p54)[M00074] 0.2197 c-Ets-1[M00743] 0.1985
c-Ets-1(p54)[M00032] 0.2057
Ets[M00971] 0.2106
c-Ets-1[M01078] 0.2365 c-Ets-1[M00743] 0.1754
c-Ets-1[M01078] 0.1804
c-Ets-1(p54)[M00032] 0.1851
Ets[M00971] 0.1898
ETS[M00771] 0.2196
c-Ets-1[M00339] 0.2309
c-Ets-1(p54)[M00074] 0.2331

Trawler No 952

Foxp3_Marson Mouse 1060 1201 M00992 (Transfac) MEME No 107530

AlignACE No 243474

YMF No 6612

Amadeus No 924

Weeder No 20024

Trawler No 1022

GATA_Pauli Elegans 1342 1201 M00075, M00076, M00077, M00126, M00127, M00128, M00203, M00346, M00347, M00348, M00349, M00350, M00351, M00462, M00632, M00789 (Transfac) MEME No 174931

AlignACE No did not finish

YMF Yes 9120 GATA-2[M00348] 0.1699
GATA-1[M00347] 0.1834
GATA-X[M00203] 0.1958
GATA-1[M00346] 0.1977
GATA-1[M00128] 0.2056
[M00789] 0.2269
GATA-1[M00126] 0.2356

Amadeus Yes 720 GATA-2[M00348] 0.156
GATA-1[M00346] 0.1729
GATA-1[M00347] 0.1857
GATA-X[M00203] 0.1977
GATA-1[M00128] 0.2104
[M00789] 0.2131
GATA-3[M00350] 0.2136 GATA-X[M00203] 0.1587
GATA-2[M00348] 0.1719
[M00789] 0.1833
GATA-1[M00347] 0.1941
GATA-1[M00346] 0.2194
GATA-1[M00126] 0.237
GATA-3[M00350] 0.2386
GATA-1[M00128] 0.2391 [M00789] 0.2035
GATA-X[M00203] 0.2095

Weeder No 25075

Trawler No 1199

HCC-G1S_Whitfield Human 266 1201 M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac) MEME No 5955

AlignACE No 16223

YMF No 2048

Amadeus Yes 768 E2F[M01114] 0.1124
E2F[M00050] 0.1427
E2F[M00516] 0.1625
E2F-1[M00940] 0.1631
E2F[M00919] 0.1803
E2F[M00920] 0.1922
E2F-1[M00938] 0.2163 E2F[M00050] 0.1131
E2F[M00516] 0.1303
E2F-1[M00938] 0.1441
E2F[M00919] 0.1502
E2F[M00920] 0.1602
E2F-1[M00940] 0.2109

Weeder Yes 5108 E2F-1[M00940] 0.1164
E2F[M00050] 0.1215
E2F[M00516] 0.1441
E2F[M00919] 0.155
E2F[M01114] 0.1572
E2F-1[M00938] 0.1579
E2F[M00920] 0.1622 E2F[M00516] 0.1798
E2F[M00050] 0.2008
E2F[M00920] 0.2205
E2F-1[M00940] 0.2257
E2F[M00919] 0.2298 E2F[M00050] 0.1246
E2F[M00516] 0.1599
E2F[M00920] 0.1633
E2F[M00919] 0.1702
E2F-1[M00940] 0.1774
E2F-1[M00938] 0.1795
E2F[M01114] 0.2341 E2F[M00516] 0.1174
E2F[M00050] 0.1296
E2F-1[M00940] 0.1705
E2F[M00919] 0.1825
E2F[M00920] 0.1862
E2F-1[M00938] 0.2281

Trawler Yes 1254 E2F[M00050] 0.0818
E2F[M00516] 0.0922
E2F[M00919] 0.0997
E2F[M00920] 0.112
E2F-1[M00940] 0.1259
E2F[M01114] 0.1445
E2F-1[M00938] 0.1654 E2F[M00050] 0.0682
E2F[M00516] 0.1677
E2F-1[M00940] 0.1681
E2F[M00919] 0.1881
E2F-1[M00938] 0.2022
E2F[M01114] 0.2046
E2F[M00920] 0.2061 E2F[M01114] 0.1912
E2F[M00516] 0.2077
E2F[M00050] 0.2208
E2F-1[M00940] 0.2349
E2F[M00920] 0.237

HCC-G2M_Whitfield Human 344 1201 M00185, M00287, M00775 (Transfac) MEME No 10631

AlignACE No 28319

YMF No 2506

Amadeus Yes 731 NF-Y[M00775] 0.1569
NF-Y[M00287] 0.1653
NF-Y[M00185] 0.2234

Weeder No 6642

Trawler No 1506

HNF1a_Odom Human 206 1201 M00132, M00206, M00790, M01011 (Transfac) MEME No 3141

AlignACE Yes 9483 HNF1[M01011] 0.2084

YMF No 1669

Amadeus Yes 643 HNF-1[M00790] 0.1185
HNF-1[M00132] 0.1378
HNF1[M01011] 0.1761
HNF-1[M00206] 0.2191 HNF-1[M00132] 0.106
HNF-1[M00790] 0.1513
HNF1[M01011] 0.168
HNF-1[M00206] 0.1883

Weeder No 4047

Trawler Yes 394 HNF-1[M00132] 0.1522
HNF-1[M00790] 0.191
HNF1[M01011] 0.208
HNF-1[M00206] 0.2085

HNF4a_Odom Human 1475 1201 M00134, M00411, M00638, M00764, M01031 (Transfac) MEME No did not finish

AlignACE No did not finish

YMF No 7720

Amadeus No 882

Weeder No 31799

Trawler No 1321

HNF6_Odom Human 212 1201 M00639 (Transfac) MEME No 3357

AlignACE No 8898

YMF No 1656

Amadeus Yes 573 HNF-6[M00639] 0.2135

Weeder No 4182

Trawler No 516

HSF1_Page Human 328 1201 M00146, M01023 (Transfac) MEME No 9552

AlignACE No 24705

YMF No 2480

Amadeus No 625

Weeder No 6371

Trawler No 1261

HSF_Machin Fly 183 1201 M00163, M00164, M00165, M00166 (Transfac) MEME No 2442

AlignACE No 5204

YMF No 1630

Amadeus No 466

Weeder No 4302

Trawler Yes 451 HSF[M00166] 0.2062
HSF[M00165] 0.215

ImmuneResponse_GO_Hs Human 586 1201 M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac) MEME No 32504

AlignACE Yes 82457 IRF-1[M00062] 0.1785
IRF-2[M00063] 0.1988 IRF[M00972] 0.1492
IRF1[M00747] 0.1669
IRF[M00772] 0.1807
ISRE[M00258] 0.1824
IRF-1[M00062] 0.1847
IRF-2[M00063] 0.2007 IRF[M00772] 0.205
IRF-7[M00453] 0.2162
IRF-1[M00062] 0.2337

YMF Yes 3597 IRF1[M00747] 0.155
ISRE[M00258] 0.1583
IRF-1[M00062] 0.1586
IRF[M00972] 0.1714
IRF-2[M00063] 0.1842
IRF[M00772] 0.1986 ISRE[M00258] 0.2017
IRF[M00772] 0.2068
IRF[M00972] 0.2247

Amadeus Yes 737 NF-kappaB[M00052] 0.1937
c-Rel[M00053] 0.2301 NF-kappaB[M00052] 0.1824
c-Rel[M00053] 0.219

Weeder No 10786

Trawler No 1594

ImmuneResponse_GO_Mm Mouse 329 1201 M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac) MEME No 10668

AlignACE Yes 20605 IRF[M00972] 0.1409
IRF1[M00747] 0.1498
IRF[M00772] 0.1591
ISRE[M00258] 0.163
IRF-1[M00062] 0.2136
IRF-7[M00453] 0.2155
IRF-2[M00063] 0.2178

YMF Yes 2572 IRF1[M00747] 0.1697
IRF-2[M00063] 0.1786
ISRE[M00258] 0.2064
IRF-1[M00062] 0.2144
IRF[M00972] 0.2255

Amadeus Yes 660 c-Rel[M00053] 0.186
NF-kappaB[M00052] 0.1963
NF-kappaB[M00774] 0.2086 IRF[M00972] 0.1818
IRF1[M00747] 0.1944
IRF[M00772] 0.1969
ISRE[M00258] 0.2137
IRF-1[M00062] 0.2353
IRF-2[M00063] 0.2372 NF-kappaB[M00052] 0.2244
NF-kappaB[M00194] 0.2357

Weeder No 6071

Trawler No 814

MEF2_Blais Mouse 25 1201 M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac) MEME No 61

AlignACE No 111

YMF No 774

Amadeus No 567

Weeder No 525

Trawler No 251

MEF2_Sandmann Fly 208 1201 M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac) MEME No 3333

AlignACE No 6075

YMF No 1833

Amadeus No 533

Weeder No 4890

Trawler No 699

MSL1_Legube Fly 116 1201 M00488 (Transfac) MEME Yes 925 DREF[M00488] 0.1149 DREF[M00488] 0.1212

AlignACE No 1960

YMF Yes 1324 DREF[M00488] 0.1125 DREF[M00488] 0.1578

Amadeus Yes 413 DREF[M00488] 0.1689 DREF[M00488] 0.1433

Weeder No 2653

Trawler Yes 350 DREF[M00488] 0.1455

Myc_Oryan Fly 714 1201 M00118, M00119, M00123, M00322, M00615, M00799, M01034 (Transfac) MEME No 51069

AlignACE Yes 78419 c-Myc:Max[M00615] 0.2375

YMF No 4133

Amadeus Yes 506 Myc[M00799] 0.1976
c-Myc:Max[M00123] 0.2085
c-Myc:Max[M00322] 0.2195 Myc[M00799] 0.1206
c-Myc:Max[M00615] 0.2263
Max[M00119] 0.2398

Weeder No 17511

Trawler No 1392

MyoD_Blais Mouse 102 1201 M00001, M00184, M00929 (Transfac) MEME No 711

AlignACE Yes 1831 MyoD[M00929] 0.2214

YMF No 1224

Amadeus Yes 557 MyoD[M00001] 0.1928
MyoD[M00184] 0.1998
MyoD[M00929] 0.2103 MyoD[M00184] 0.1587
MyoD[M00929] 0.1593
MyoD[M00001] 0.1956

Weeder Yes 2045 MyoD[M00184] 0.1819
MyoD[M00001] 0.2209 MyoD[M00929] 0.1715
MyoD[M00001] 0.1771
MyoD[M00184] 0.1777

Trawler Yes 245 MyoD[M00929] 0.1798
MyoD[M00184] 0.1925
MyoD[M00001] 0.2388

MyoD_Cao Mouse 102 1201 M00001, M00184, M00929 (Transfac) MEME No 713

AlignACE Yes 1973 MyoD[M00929] 0.2294

YMF No 1263

Amadeus Yes 570 MyoD[M00184] 0.1465
MyoD[M00929] 0.1546
MyoD[M00001] 0.1576 MyoD[M00184] 0.1238
MyoD[M00001] 0.2045
MyoD[M00929] 0.2127

Weeder Yes 2069 MyoD[M00184] 0.1631
MyoD[M00929] 0.1976
MyoD[M00001] 0.2004 MyoD[M00929] 0.1999
MyoD[M00184] 0.205
MyoD[M00001] 0.2355 MyoD[M00184] 0.1697
MyoD[M00001] 0.1854
MyoD[M00929] 0.2167

Trawler Yes 280 MyoD[M00184] 0.1923
MyoD[M00929] 0.2146 MyoD[M00184] 0.2155

MyoG_Cao Mouse 78 1201 M00712 (Transfac) MEME No 443

AlignACE No 1049

YMF No 1080

Amadeus Yes 561 myogenin[M00712] 0.1616 myogenin[M00712] 0.1389 myogenin[M00712] 0.2343

Weeder Yes 1626 myogenin[M00712] 0.111 myogenin[M00712] 0.1442

Trawler Yes 224 myogenin[M00712] 0.1403

Myogenin_Blais Mouse 106 1201 M00712 (Transfac) MEME No 768

AlignACE No 1890

YMF No 1220

Amadeus Yes 597 myogenin[M00712] 0.1161 myogenin[M00712] 0.1279

Weeder Yes 2189 myogenin[M00712] 0.1211 myogenin[M00712] 0.1158 myogenin[M00712] 0.1978 myogenin[M00712] 0.1033

Trawler Yes 360 myogenin[M00712] 0.1939 myogenin[M00712] 0.1333 myogenin[M00712] 0.2235 myogenin[M00712] 0.1822

NFkB_Schreiber Human 270 1201 M00052, M00053, M00194, M00774 (Transfac) MEME No 6000

AlignACE No 16432

YMF No 2091

Amadeus Yes 631 NF-kappaB[M00052] 0.1171
c-Rel[M00053] 0.1645
NF-kappaB[M00774] 0.1722
NF-kappaB[M00194] 0.2193 NF-kappaB[M00194] 0.2
NF-kappaB[M00774] 0.2364 c-Rel[M00053] 0.1482
NF-kappaB[M00774] 0.1487
NF-kappaB[M00052] 0.1626
NF-kappaB[M00194] 0.1955

Weeder Yes 5208 NF-kappaB[M00194] 0.2237

Trawler Yes 840 c-Rel[M00053] 0.1203
NF-kappaB[M00052] 0.1263
NF-kappaB[M00774] 0.1542
NF-kappaB[M00194] 0.174 NF-kappaB[M00052] 0.0945
NF-kappaB[M00774] 0.1371
NF-kappaB[M00194] 0.1541
c-Rel[M00053] 0.1568

Nanog_Boyer Human 714 1201 M01123 (Transfac) MEME No 48155

AlignACE No 116195

YMF No 4286

Amadeus No 702

Weeder No 15147

Trawler No 1173

Nrf1_Cam Human 674 1201 M00652 (Transfac) MEME Yes 43467 Nrf-1[M00652] 0.0524 Nrf-1[M00652] 0.079

AlignACE Yes 99183 Nrf-1[M00652] 0.0674 Nrf-1[M00652] 0.0785

YMF Yes 3559 Nrf-1[M00652] 0.0651 Nrf-1[M00652] 0.1613 Nrf-1[M00652] 0.1134 Nrf-1[M00652] 0.1162

Amadeus Yes 568 Nrf-1[M00652] 0.0833 Nrf-1[M00652] 0.105

Weeder Yes 14046 Nrf-1[M00652] 0.0944 Nrf-1[M00652] 0.0832 Nrf-1[M00652] 0.0946 Nrf-1[M00652] 0.0876

Trawler Yes 1054 Nrf-1[M00652] 0.1059 Nrf-1[M00652] 0.0914

Oct4_Boyer Human 241 1201 M00795, M01124, M01125 (Transfac) MEME No 4559

AlignACE No 13084

YMF Yes 1931 Octamer[M00795] 0.2323

Amadeus Yes 569 Octamer[M00795] 0.2226

Weeder No 4863

Trawler No 497

SRF_Cooper Human 172 1201 M00152, M00186, M00810, M00922, M01007 (Transfac) MEME No 2053

AlignACE No 6178

YMF Yes 1552 SRF[M00152] 0.1515
SRF[M01007] 0.161
SRF[M00810] 0.1886
SRF[M00922] 0.1979
SRF[M00186] 0.2004

Amadeus Yes 548 SRF[M01007] 0.2282
SRF[M00152] 0.2309 SRF[M01007] 0.1057
SRF[M00810] 0.1242
SRF[M00922] 0.1344
SRF[M00152] 0.1368
SRF[M00186] 0.1417

Weeder Yes 3365 SRF[M00152] 0.2371 SRF[M01007] 0.0869
SRF[M00152] 0.1035
SRF[M00810] 0.1087
SRF[M00186] 0.1147
SRF[M00922] 0.1173

Trawler Yes 463 SRF[M00152] 0.1574
SRF[M00810] 0.1615
SRF[M00922] 0.1672
SRF[M01007] 0.1684
SRF[M00186] 0.186 SRF[M00152] 0.0626
SRF[M00186] 0.1091
SRF[M00810] 0.1238
SRF[M00922] 0.1292
SRF[M01007] 0.1477

Sox2_Boyer Human 575 1201 M01014, M01125 (Transfac) MEME No 31204

AlignACE No 74186

YMF No 3530

Amadeus No 645

Weeder No 13387

Trawler No 844

YY1_XiRen Human 713 1201 M00059, M00069, M00793, M01035, jMA0095 (Transfac) MEME No 48261

AlignACE Yes 108689 YY1[jMA0095] 0.1087
YY1[M00793] 0.1303
YY1[M00069] 0.1815
YY1[M01035] 0.2142 YY1[jMA0095] 0.1105
YY1[M00793] 0.1356
YY1[M00069] 0.1848
YY1[M01035] 0.2201

YMF Yes 3620 YY1[M00069] 0.1254
YY1[jMA0095] 0.1418
YY1[M00793] 0.1555
YY1[M01035] 0.2057 YY1[jMA0095] 0.1656
YY1[M00069] 0.1997
YY1[M00793] 0.2174

Amadeus Yes 460 YY1[jMA0095] 0.1517
YY1[M01035] 0.1769
YY1[M00069] 0.1789
YY1[M00059] 0.2313 YY1[M00793] 0.1004
YY1[jMA0095] 0.1309
YY1[M01035] 0.1567
YY1[M00069] 0.1627
YY1[M00059] 0.2359

Weeder Yes 14037 YY1[jMA0095] 0.2131 YY1[M00793] 0.1386
YY1[jMA0095] 0.1449
YY1[M00069] 0.1961
YY1[M01035] 0.2045 YY1[jMA0095] 0.1104
YY1[M00793] 0.1154
YY1[M00069] 0.1666
YY1[M01035] 0.1957 YY1[jMA0095] 0.0979
YY1[M00793] 0.1293
YY1[M00069] 0.1962
YY1[M01035] 0.2246

Trawler Yes 1472 YY1[M00793] 0.0955
YY1[jMA0095] 0.1185
YY1[M00069] 0.164
YY1[M01035] 0.1733
YY1[M00059] 0.2128 YY1[jMA0095] 0.1142
YY1[M00793] 0.1271
YY1[M00069] 0.1574
YY1[M01035] 0.1907
YY1[M00059] 0.2366

let7_Brueckner Human 177 10001 MIMAT0000062 (miRBase) MEME No 1077

AlignACE No 5092

YMF No 1897

Amadeus No 861

Weeder No 2953

Trawler No 607

let7_Johnson Human 182 10001 MIMAT0000062 (miRBase) MEME No 1331

AlignACE No 8145

YMF No 2142

Amadeus Yes 992 hsa-let-7a[MIMAT0000062] 0.2142 hsa-let-7a[MIMAT0000062] 0.1705

Weeder Yes 3203 hsa-let-7a[MIMAT0000062] 0.0636 hsa-let-7a[MIMAT0000062] 0.1495

Trawler Yes 664 hsa-let-7a[MIMAT0000062] 0.1404 hsa-let-7a[MIMAT0000062] 0.0825

miR106b_Linsley Human 88 10001 MIMAT0000680 (miRBase) MEME Yes 460 hsa-miR-106b[MIMAT0000680] 0.0342 hsa-miR-106b[MIMAT0000680] 0.0609

AlignACE No 2114

YMF Yes 1377 hsa-miR-106b[MIMAT0000680] 0.0

Amadeus Yes 739 hsa-miR-106b[MIMAT0000680] 0.1072 hsa-miR-106b[MIMAT0000680] 0.0677

Weeder Yes 1705 hsa-miR-106b[MIMAT0000680] 0.0799 hsa-miR-106b[MIMAT0000680] 0.065 hsa-miR-106b[MIMAT0000680] 0.0592 hsa-miR-106b[MIMAT0000680] 0.0392

Trawler Yes 505 hsa-miR-106b[MIMAT0000680] 0.0312 hsa-miR-106b[MIMAT0000680] 0.0 hsa-miR-106b[MIMAT0000680] 0.1216

miR124_Lim Human 116 10001 MIMAT0000422 (miRBase) MEME Yes 598 hsa-miR-124a[MIMAT0000422] 0.019 hsa-miR-124a[MIMAT0000422] 0.0803

AlignACE No 3101

YMF Yes 1607 hsa-miR-124a[MIMAT0000422] 0.0

Amadeus Yes 665 hsa-miR-124a[MIMAT0000422] 0.0333 hsa-miR-124a[MIMAT0000422] 0.1624

Weeder Yes 2074 hsa-miR-124a[MIMAT0000422] 0.0774 hsa-miR-124a[MIMAT0000422] 0.0523 hsa-miR-124a[MIMAT0000422] 0.0542 hsa-miR-124a[MIMAT0000422] 0.0686

Trawler Yes 357 hsa-miR-124a[MIMAT0000422] 0.147 hsa-miR-124a[MIMAT0000422] 0.0905

miR155_Rodriguez Mouse 95 10001 MIMAT0000165 (miRBase) MEME No 322

AlignACE No 1311

YMF No 1129

Amadeus Yes 513 mmu-miR-155[MIMAT0000165] 0.2316 mmu-miR-155[MIMAT0000165] 0.1015

Weeder No 1376

Trawler Yes 297 mmu-miR-155[MIMAT0000165] 0.1231

miR16_Linsley Human 90 10001 MIMAT0000069 (miRBase) MEME Yes 520 hsa-miR-16[MIMAT0000069] 0.0928 hsa-miR-16[MIMAT0000069] 0.1074

AlignACE No 2557

YMF No 1534

Amadeus Yes 706 hsa-miR-16[MIMAT0000069] 0.0971 hsa-miR-16[MIMAT0000069] 0.1063

Weeder Yes 1934 hsa-miR-16[MIMAT0000069] 0.0906 hsa-miR-16[MIMAT0000069] 0.0711 hsa-miR-16[MIMAT0000069] 0.074 hsa-miR-16[MIMAT0000069] 0.0672

Trawler Yes 415 hsa-miR-16[MIMAT0000069] 0.1512 hsa-miR-16[MIMAT0000069] 0.0505 hsa-miR-16[MIMAT0000069] 0.156

miR1_Lim Human 65 10001 MIMAT0000416 (miRBase) MEME Yes 255 hsa-miR-1[MIMAT0000416] 0.0884

AlignACE No 1360

YMF No 1197

Amadeus Yes 673 hsa-miR-1[MIMAT0000416] 0.1121 hsa-miR-1[MIMAT0000416] 0.1157

Weeder Yes 1141 hsa-miR-1[MIMAT0000416] 0.0603 hsa-miR-1[MIMAT0000416] 0.0577 hsa-miR-1[MIMAT0000416] 0.0882 hsa-miR-1[MIMAT0000416] 0.0349

Trawler Yes 292 hsa-miR-1[MIMAT0000416] 0.1581 hsa-miR-1[MIMAT0000416] 0.1037 hsa-miR-1[MIMAT0000416] 0.0643

miR34_Chang Human 89 10001 MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase) MEME No 379

AlignACE No 2118

YMF Yes 1390 hsa-miR-34a[MIMAT0000255] 0.1428

Amadeus No 740

Weeder No 1486

Trawler No 330

miR34_He Human 367 10001 MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase) MEME Yes 6415 hsa-miR-34b[MIMAT0000685] 0.0030
hsa-miR-34c[MIMAT0000686] 0.0030
hsa-miR-34a[MIMAT0000255] 0.1274

AlignACE No 32662

YMF No 3080

Amadeus Yes 802 hsa-miR-34b[MIMAT0000685] 0.0839
hsa-miR-34c[MIMAT0000686] 0.1295
hsa-miR-34a[MIMAT0000255] 0.1295 hsa-miR-34b[MIMAT0000685] 0.1065
hsa-miR-34a[MIMAT0000255] 0.1188
hsa-miR-34c[MIMAT0000686] 0.1418

Weeder Yes 7817 hsa-miR-34a[MIMAT0000255] 0.085
hsa-miR-34c[MIMAT0000686] 0.1589
hsa-miR-34b[MIMAT0000685] 0.17 hsa-miR-34a[MIMAT0000255] 0.0391
hsa-miR-34c[MIMAT0000686] 0.1419
hsa-miR-34b[MIMAT0000685] 0.2338 hsa-miR-34c[MIMAT0000686] 0.0626
hsa-miR-34a[MIMAT0000255] 0.0626
hsa-miR-34b[MIMAT0000685] 0.0632 hsa-miR-34b[MIMAT0000685] 0.0401
hsa-miR-34c[MIMAT0000686] 0.0508
hsa-miR-34a[MIMAT0000255] 0.0508

Trawler No 800

miR373_Lim Human 43 10001 MIMAT0000726 (miRBase) MEME Yes 95 hsa-miR-373[MIMAT0000726] 0.1396

AlignACE No 353

YMF Yes 944 hsa-miR-373[MIMAT0000726] 0.0714

Amadeus Yes 588 hsa-miR-373[MIMAT0000726] 0.0 hsa-miR-373[MIMAT0000726] 0.0166

Weeder Yes 608 hsa-miR-373[MIMAT0000726] 0.1321 hsa-miR-373[MIMAT0000726] 0.2076 hsa-miR-373[MIMAT0000726] 0.2132 hsa-miR-373[MIMAT0000726] 0.2218

Trawler No 238

p53_Kannan Human 38 1201 M00034, M00272, M00761 (Transfac) MEME No 122

AlignACE No 300

YMF No 852

Amadeus No 501

Weeder Yes 684 p53[M00034] 0.2153

Trawler No 99

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)
CREB_Zhang	Human	2338	1201	M00039, M00113, M00177, M00178, M00916, M00917 (Transfac)	MEME	No	did not finish
					AlignACE	No	did not finish
					YMF	No	9719
					Amadeus	Yes	797		CREB[M00113] 0.0938 CREB[M00039] 0.1172 CREB[M00178] 0.132 CREB[M00917] 0.1383 CREB[M00916] 0.1495 CREB[M00177] 0.156		CREB[M00039] 0.1132 CREB[M00178] 0.1272 CREB[M00917] 0.158 CREB[M00916] 0.1581 CREB[M00177] 0.1624 CREB[M00113] 0.19
					Weeder	Yes	50984		CREB[M00039] 0.212
					Trawler	No	224
E2F4_Cam	Human	201	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	MEME	No	3008
					AlignACE	No	7726
					YMF	No	1478
					Amadeus	Yes	606	E2F[M00516] 0.1272 E2F[M00920] 0.1356 E2F-1[M00938] 0.14 E2F[M00919] 0.1466 E2F-1[M00940] 0.1509 E2F[M00050] 0.1755 E2F[M01114] 0.2164		E2F[M00920] 0.133 E2F[M00919] 0.1374 E2F[M00516] 0.1378 E2F[M00050] 0.1579 E2F-1[M00940] 0.1617 E2F[M01114] 0.2046 E2F-1[M00938] 0.2158
					Weeder	Yes	4048	E2F[M00050] 0.1131 E2F-1[M00940] 0.1175 E2F[M00919] 0.1441 E2F[M00516] 0.1465 E2F-1[M00938] 0.1519 E2F[M01114] 0.1574 E2F[M00920] 0.1647	E2F[M00050] 0.1055 E2F[M00516] 0.1415 E2F-1[M00938] 0.1898 E2F[M00920] 0.192 E2F[M00919] 0.2026 E2F-1[M00940] 0.2162 E2F[M01114] 0.2307	E2F[M00050] 0.1304 E2F[M00516] 0.1683 E2F[M01114] 0.192 E2F-1[M00940] 0.192 E2F[M00919] 0.2267 E2F[M00920] 0.2357	E2F[M00050] 0.1008 E2F[M00516] 0.1464 E2F[M00920] 0.1917 E2F[M00919] 0.2008 E2F-1[M00938] 0.2141 E2F-1[M00940] 0.218
					Trawler	Yes	903	E2F[M00050] 0.0927 E2F[M00516] 0.1075 E2F[M00920] 0.1187 E2F[M00919] 0.1307 E2F-1[M00940] 0.1355 E2F-1[M00938] 0.1496 E2F[M01114] 0.1763
E2F_Ren	Human	79	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	MEME	No	454
					AlignACE	No	991
					YMF	No	987
					Amadeus	Yes	569	E2F[M00050] 0.0715 E2F-1[M00940] 0.083 E2F[M00516] 0.1115 E2F[M00920] 0.1348 E2F[M00919] 0.1351 E2F[M01114] 0.1514 E2F-1[M00938] 0.1704		E2F[M00050] 0.084 E2F[M00516] 0.1215 E2F-1[M00940] 0.1245 E2F[M00920] 0.1314 E2F[M00919] 0.1401 E2F-1[M00938] 0.1593 E2F[M01114] 0.1806
					Weeder	Yes	1652	E2F[M00050] 0.0925 E2F-1[M00940] 0.1103 E2F[M00516] 0.1181 E2F[M01114] 0.1292 E2F[M00919] 0.1403 E2F-1[M00938] 0.1504 E2F[M00920] 0.1505	E2F[M00050] 0.0929 E2F-1[M00940] 0.1579 E2F[M00516] 0.1728 E2F[M00919] 0.1763 E2F[M01114] 0.1902 E2F[M00920] 0.1929 E2F-1[M00938] 0.2027	E2F-1[M00940] 0.163 E2F[M00919] 0.1759 E2F[M00516] 0.1768 E2F[M00920] 0.183 E2F[M01114] 0.1931 E2F[M00050] 0.2056 E2F-1[M00938] 0.2296	E2F[M01114] 0.2007 E2F[M00919] 0.2308 E2F-1[M00940] 0.2371
					Trawler	Yes	505		E2F[M00919] 0.1719 E2F[M00920] 0.175 E2F[M00516] 0.1827 E2F-1[M00938] 0.1842 E2F[M01114] 0.1957 E2F-1[M00940] 0.2013
ERa_Kwon	Human	496	1201	M00191, M00511, M00959 (Transfac)	MEME	No	22576
					AlignACE	No	55504
					YMF	No	3211
					Amadeus	No	602
					Weeder	No	9515
					Trawler	No	787
ETS1_Hollenhorst	Human	1192	1201	M00032, M00074, M00339, M00743, M00771, M00971, M01078 (Transfac)	MEME	No	142233
					AlignACE	No	did not finish
					YMF	Yes	5608	c-Ets-1[M00743] 0.2068	c-Ets-1[M00743] 0.2068
					Amadeus	Yes	634			c-Ets-1[M01078] 0.1695 Ets[M00971] 0.1722 ETS[M00771] 0.1925 c-Ets-1(p54)[M00032] 0.1943 c-Ets-1(p54)[M00074] 0.2073 c-Ets-1[M00339] 0.2082
					Weeder	Yes	25568	c-Ets-1[M00743] 0.1372 c-Ets-1(p54)[M00032] 0.1599 c-Ets-1[M01078] 0.1662 ETS[M00771] 0.1976 c-Ets-1[M00339] 0.2106 Ets[M00971] 0.2107 c-Ets-1(p54)[M00074] 0.2197	c-Ets-1[M00743] 0.1985 c-Ets-1(p54)[M00032] 0.2057 Ets[M00971] 0.2106 c-Ets-1[M01078] 0.2365	c-Ets-1[M00743] 0.1754 c-Ets-1[M01078] 0.1804 c-Ets-1(p54)[M00032] 0.1851 Ets[M00971] 0.1898 ETS[M00771] 0.2196 c-Ets-1[M00339] 0.2309 c-Ets-1(p54)[M00074] 0.2331
					Trawler	No	952
Foxp3_Marson	Mouse	1060	1201	M00992 (Transfac)	MEME	No	107530
					AlignACE	No	243474
					YMF	No	6612
					Amadeus	No	924
					Weeder	No	20024
					Trawler	No	1022
GATA_Pauli	Elegans	1342	1201	M00075, M00076, M00077, M00126, M00127, M00128, M00203, M00346, M00347, M00348, M00349, M00350, M00351, M00462, M00632, M00789 (Transfac)	MEME	No	174931
					AlignACE	No	did not finish
					YMF	Yes	9120	GATA-2[M00348] 0.1699 GATA-1[M00347] 0.1834 GATA-X[M00203] 0.1958 GATA-1[M00346] 0.1977 GATA-1[M00128] 0.2056 [M00789] 0.2269 GATA-1[M00126] 0.2356
					Amadeus	Yes	720	GATA-2[M00348] 0.156 GATA-1[M00346] 0.1729 GATA-1[M00347] 0.1857 GATA-X[M00203] 0.1977 GATA-1[M00128] 0.2104 [M00789] 0.2131 GATA-3[M00350] 0.2136		GATA-X[M00203] 0.1587 GATA-2[M00348] 0.1719 [M00789] 0.1833 GATA-1[M00347] 0.1941 GATA-1[M00346] 0.2194 GATA-1[M00126] 0.237 GATA-3[M00350] 0.2386 GATA-1[M00128] 0.2391	[M00789] 0.2035 GATA-X[M00203] 0.2095
					Weeder	No	25075
					Trawler	No	1199
HCC-G1S_Whitfield	Human	266	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	MEME	No	5955
					AlignACE	No	16223
					YMF	No	2048
					Amadeus	Yes	768	E2F[M01114] 0.1124 E2F[M00050] 0.1427 E2F[M00516] 0.1625 E2F-1[M00940] 0.1631 E2F[M00919] 0.1803 E2F[M00920] 0.1922 E2F-1[M00938] 0.2163		E2F[M00050] 0.1131 E2F[M00516] 0.1303 E2F-1[M00938] 0.1441 E2F[M00919] 0.1502 E2F[M00920] 0.1602 E2F-1[M00940] 0.2109
					Weeder	Yes	5108	E2F-1[M00940] 0.1164 E2F[M00050] 0.1215 E2F[M00516] 0.1441 E2F[M00919] 0.155 E2F[M01114] 0.1572 E2F-1[M00938] 0.1579 E2F[M00920] 0.1622	E2F[M00516] 0.1798 E2F[M00050] 0.2008 E2F[M00920] 0.2205 E2F-1[M00940] 0.2257 E2F[M00919] 0.2298	E2F[M00050] 0.1246 E2F[M00516] 0.1599 E2F[M00920] 0.1633 E2F[M00919] 0.1702 E2F-1[M00940] 0.1774 E2F-1[M00938] 0.1795 E2F[M01114] 0.2341	E2F[M00516] 0.1174 E2F[M00050] 0.1296 E2F-1[M00940] 0.1705 E2F[M00919] 0.1825 E2F[M00920] 0.1862 E2F-1[M00938] 0.2281
					Trawler	Yes	1254		E2F[M00050] 0.0818 E2F[M00516] 0.0922 E2F[M00919] 0.0997 E2F[M00920] 0.112 E2F-1[M00940] 0.1259 E2F[M01114] 0.1445 E2F-1[M00938] 0.1654	E2F[M00050] 0.0682 E2F[M00516] 0.1677 E2F-1[M00940] 0.1681 E2F[M00919] 0.1881 E2F-1[M00938] 0.2022 E2F[M01114] 0.2046 E2F[M00920] 0.2061	E2F[M01114] 0.1912 E2F[M00516] 0.2077 E2F[M00050] 0.2208 E2F-1[M00940] 0.2349 E2F[M00920] 0.237
HCC-G2M_Whitfield	Human	344	1201	M00185, M00287, M00775 (Transfac)	MEME	No	10631
					AlignACE	No	28319
					YMF	No	2506
					Amadeus	Yes	731			NF-Y[M00775] 0.1569 NF-Y[M00287] 0.1653 NF-Y[M00185] 0.2234
					Weeder	No	6642
					Trawler	No	1506
HNF1a_Odom	Human	206	1201	M00132, M00206, M00790, M01011 (Transfac)	MEME	No	3141
					AlignACE	Yes	9483				HNF1[M01011] 0.2084
					YMF	No	1669
					Amadeus	Yes	643	HNF-1[M00790] 0.1185 HNF-1[M00132] 0.1378 HNF1[M01011] 0.1761 HNF-1[M00206] 0.2191		HNF-1[M00132] 0.106 HNF-1[M00790] 0.1513 HNF1[M01011] 0.168 HNF-1[M00206] 0.1883
					Weeder	No	4047
					Trawler	Yes	394	HNF-1[M00132] 0.1522 HNF-1[M00790] 0.191 HNF1[M01011] 0.208 HNF-1[M00206] 0.2085
HNF4a_Odom	Human	1475	1201	M00134, M00411, M00638, M00764, M01031 (Transfac)	MEME	No	did not finish
					AlignACE	No	did not finish
					YMF	No	7720
					Amadeus	No	882
					Weeder	No	31799
					Trawler	No	1321
HNF6_Odom	Human	212	1201	M00639 (Transfac)	MEME	No	3357
					AlignACE	No	8898
					YMF	No	1656
					Amadeus	Yes	573		HNF-6[M00639] 0.2135
					Weeder	No	4182
					Trawler	No	516
HSF1_Page	Human	328	1201	M00146, M01023 (Transfac)	MEME	No	9552
					AlignACE	No	24705
					YMF	No	2480
					Amadeus	No	625
					Weeder	No	6371
					Trawler	No	1261
HSF_Machin	Fly	183	1201	M00163, M00164, M00165, M00166 (Transfac)	MEME	No	2442
					AlignACE	No	5204
					YMF	No	1630
					Amadeus	No	466
					Weeder	No	4302
					Trawler	Yes	451				HSF[M00166] 0.2062 HSF[M00165] 0.215
ImmuneResponse_GO_Hs	Human	586	1201	M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac)	MEME	No	32504
					AlignACE	Yes	82457	IRF-1[M00062] 0.1785 IRF-2[M00063] 0.1988		IRF[M00972] 0.1492 IRF1[M00747] 0.1669 IRF[M00772] 0.1807 ISRE[M00258] 0.1824 IRF-1[M00062] 0.1847 IRF-2[M00063] 0.2007	IRF[M00772] 0.205 IRF-7[M00453] 0.2162 IRF-1[M00062] 0.2337
					YMF	Yes	3597	IRF1[M00747] 0.155 ISRE[M00258] 0.1583 IRF-1[M00062] 0.1586 IRF[M00972] 0.1714 IRF-2[M00063] 0.1842 IRF[M00772] 0.1986	ISRE[M00258] 0.2017 IRF[M00772] 0.2068 IRF[M00972] 0.2247
					Amadeus	Yes	737	NF-kappaB[M00052] 0.1937 c-Rel[M00053] 0.2301		NF-kappaB[M00052] 0.1824 c-Rel[M00053] 0.219
					Weeder	No	10786
					Trawler	No	1594
ImmuneResponse_GO_Mm	Mouse	329	1201	M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac)	MEME	No	10668
					AlignACE	Yes	20605				IRF[M00972] 0.1409 IRF1[M00747] 0.1498 IRF[M00772] 0.1591 ISRE[M00258] 0.163 IRF-1[M00062] 0.2136 IRF-7[M00453] 0.2155 IRF-2[M00063] 0.2178
					YMF	Yes	2572		IRF1[M00747] 0.1697 IRF-2[M00063] 0.1786 ISRE[M00258] 0.2064 IRF-1[M00062] 0.2144 IRF[M00972] 0.2255
					Amadeus	Yes	660	c-Rel[M00053] 0.186 NF-kappaB[M00052] 0.1963 NF-kappaB[M00774] 0.2086		IRF[M00972] 0.1818 IRF1[M00747] 0.1944 IRF[M00772] 0.1969 ISRE[M00258] 0.2137 IRF-1[M00062] 0.2353 IRF-2[M00063] 0.2372	NF-kappaB[M00052] 0.2244 NF-kappaB[M00194] 0.2357
					Weeder	No	6071
					Trawler	No	814
MEF2_Blais	Mouse	25	1201	M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac)	MEME	No	61
					AlignACE	No	111
					YMF	No	774
					Amadeus	No	567
					Weeder	No	525
					Trawler	No	251
MEF2_Sandmann	Fly	208	1201	M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac)	MEME	No	3333
					AlignACE	No	6075
					YMF	No	1833
					Amadeus	No	533
					Weeder	No	4890
					Trawler	No	699
MSL1_Legube	Fly	116	1201	M00488 (Transfac)	MEME	Yes	925	DREF[M00488] 0.1149			DREF[M00488] 0.1212
					AlignACE	No	1960
					YMF	Yes	1324	DREF[M00488] 0.1125		DREF[M00488] 0.1578
					Amadeus	Yes	413	DREF[M00488] 0.1689		DREF[M00488] 0.1433
					Weeder	No	2653
					Trawler	Yes	350		DREF[M00488] 0.1455
Myc_Oryan	Fly	714	1201	M00118, M00119, M00123, M00322, M00615, M00799, M01034 (Transfac)	MEME	No	51069
					AlignACE	Yes	78419			c-Myc:Max[M00615] 0.2375
					YMF	No	4133
					Amadeus	Yes	506		Myc[M00799] 0.1976 c-Myc:Max[M00123] 0.2085 c-Myc:Max[M00322] 0.2195		Myc[M00799] 0.1206 c-Myc:Max[M00615] 0.2263 Max[M00119] 0.2398
					Weeder	No	17511
					Trawler	No	1392
MyoD_Blais	Mouse	102	1201	M00001, M00184, M00929 (Transfac)	MEME	No	711
					AlignACE	Yes	1831				MyoD[M00929] 0.2214
					YMF	No	1224
					Amadeus	Yes	557	MyoD[M00001] 0.1928 MyoD[M00184] 0.1998 MyoD[M00929] 0.2103		MyoD[M00184] 0.1587 MyoD[M00929] 0.1593 MyoD[M00001] 0.1956
					Weeder	Yes	2045		MyoD[M00184] 0.1819 MyoD[M00001] 0.2209	MyoD[M00929] 0.1715 MyoD[M00001] 0.1771 MyoD[M00184] 0.1777
					Trawler	Yes	245		MyoD[M00929] 0.1798 MyoD[M00184] 0.1925 MyoD[M00001] 0.2388
MyoD_Cao	Mouse	102	1201	M00001, M00184, M00929 (Transfac)	MEME	No	713
					AlignACE	Yes	1973				MyoD[M00929] 0.2294
					YMF	No	1263
					Amadeus	Yes	570	MyoD[M00184] 0.1465 MyoD[M00929] 0.1546 MyoD[M00001] 0.1576		MyoD[M00184] 0.1238 MyoD[M00001] 0.2045 MyoD[M00929] 0.2127
					Weeder	Yes	2069	MyoD[M00184] 0.1631 MyoD[M00929] 0.1976 MyoD[M00001] 0.2004		MyoD[M00929] 0.1999 MyoD[M00184] 0.205 MyoD[M00001] 0.2355	MyoD[M00184] 0.1697 MyoD[M00001] 0.1854 MyoD[M00929] 0.2167
					Trawler	Yes	280	MyoD[M00184] 0.1923 MyoD[M00929] 0.2146		MyoD[M00184] 0.2155
MyoG_Cao	Mouse	78	1201	M00712 (Transfac)	MEME	No	443
					AlignACE	No	1049
					YMF	No	1080
					Amadeus	Yes	561	myogenin[M00712] 0.1616		myogenin[M00712] 0.1389	myogenin[M00712] 0.2343
					Weeder	Yes	1626	myogenin[M00712] 0.111	myogenin[M00712] 0.1442
					Trawler	Yes	224		myogenin[M00712] 0.1403
Myogenin_Blais	Mouse	106	1201	M00712 (Transfac)	MEME	No	768
					AlignACE	No	1890
					YMF	No	1220
					Amadeus	Yes	597	myogenin[M00712] 0.1161		myogenin[M00712] 0.1279
					Weeder	Yes	2189	myogenin[M00712] 0.1211	myogenin[M00712] 0.1158	myogenin[M00712] 0.1978	myogenin[M00712] 0.1033
					Trawler	Yes	360	myogenin[M00712] 0.1939	myogenin[M00712] 0.1333	myogenin[M00712] 0.2235	myogenin[M00712] 0.1822
NFkB_Schreiber	Human	270	1201	M00052, M00053, M00194, M00774 (Transfac)	MEME	No	6000
					AlignACE	No	16432
					YMF	No	2091
					Amadeus	Yes	631	NF-kappaB[M00052] 0.1171 c-Rel[M00053] 0.1645 NF-kappaB[M00774] 0.1722 NF-kappaB[M00194] 0.2193	NF-kappaB[M00194] 0.2 NF-kappaB[M00774] 0.2364	c-Rel[M00053] 0.1482 NF-kappaB[M00774] 0.1487 NF-kappaB[M00052] 0.1626 NF-kappaB[M00194] 0.1955
					Weeder	Yes	5208				NF-kappaB[M00194] 0.2237
					Trawler	Yes	840		c-Rel[M00053] 0.1203 NF-kappaB[M00052] 0.1263 NF-kappaB[M00774] 0.1542 NF-kappaB[M00194] 0.174		NF-kappaB[M00052] 0.0945 NF-kappaB[M00774] 0.1371 NF-kappaB[M00194] 0.1541 c-Rel[M00053] 0.1568
Nanog_Boyer	Human	714	1201	M01123 (Transfac)	MEME	No	48155
					AlignACE	No	116195
					YMF	No	4286
					Amadeus	No	702
					Weeder	No	15147
					Trawler	No	1173
Nrf1_Cam	Human	674	1201	M00652 (Transfac)	MEME	Yes	43467	Nrf-1[M00652] 0.0524		Nrf-1[M00652] 0.079
					AlignACE	Yes	99183	Nrf-1[M00652] 0.0674		Nrf-1[M00652] 0.0785
					YMF	Yes	3559	Nrf-1[M00652] 0.0651	Nrf-1[M00652] 0.1613	Nrf-1[M00652] 0.1134	Nrf-1[M00652] 0.1162
					Amadeus	Yes	568	Nrf-1[M00652] 0.0833		Nrf-1[M00652] 0.105
					Weeder	Yes	14046	Nrf-1[M00652] 0.0944	Nrf-1[M00652] 0.0832	Nrf-1[M00652] 0.0946	Nrf-1[M00652] 0.0876
					Trawler	Yes	1054	Nrf-1[M00652] 0.1059	Nrf-1[M00652] 0.0914
Oct4_Boyer	Human	241	1201	M00795, M01124, M01125 (Transfac)	MEME	No	4559
					AlignACE	No	13084
					YMF	Yes	1931	Octamer[M00795] 0.2323
					Amadeus	Yes	569				Octamer[M00795] 0.2226
					Weeder	No	4863
					Trawler	No	497
SRF_Cooper	Human	172	1201	M00152, M00186, M00810, M00922, M01007 (Transfac)	MEME	No	2053
					AlignACE	No	6178
					YMF	Yes	1552				SRF[M00152] 0.1515 SRF[M01007] 0.161 SRF[M00810] 0.1886 SRF[M00922] 0.1979 SRF[M00186] 0.2004
					Amadeus	Yes	548	SRF[M01007] 0.2282 SRF[M00152] 0.2309		SRF[M01007] 0.1057 SRF[M00810] 0.1242 SRF[M00922] 0.1344 SRF[M00152] 0.1368 SRF[M00186] 0.1417
					Weeder	Yes	3365	SRF[M00152] 0.2371	SRF[M01007] 0.0869 SRF[M00152] 0.1035 SRF[M00810] 0.1087 SRF[M00186] 0.1147 SRF[M00922] 0.1173
					Trawler	Yes	463		SRF[M00152] 0.1574 SRF[M00810] 0.1615 SRF[M00922] 0.1672 SRF[M01007] 0.1684 SRF[M00186] 0.186		SRF[M00152] 0.0626 SRF[M00186] 0.1091 SRF[M00810] 0.1238 SRF[M00922] 0.1292 SRF[M01007] 0.1477
Sox2_Boyer	Human	575	1201	M01014, M01125 (Transfac)	MEME	No	31204
					AlignACE	No	74186
					YMF	No	3530
					Amadeus	No	645
					Weeder	No	13387
					Trawler	No	844
YY1_XiRen	Human	713	1201	M00059, M00069, M00793, M01035, jMA0095 (Transfac)	MEME	No	48261
					AlignACE	Yes	108689	YY1[jMA0095] 0.1087 YY1[M00793] 0.1303 YY1[M00069] 0.1815 YY1[M01035] 0.2142		YY1[jMA0095] 0.1105 YY1[M00793] 0.1356 YY1[M00069] 0.1848 YY1[M01035] 0.2201
					YMF	Yes	3620	YY1[M00069] 0.1254 YY1[jMA0095] 0.1418 YY1[M00793] 0.1555 YY1[M01035] 0.2057		YY1[jMA0095] 0.1656 YY1[M00069] 0.1997 YY1[M00793] 0.2174
					Amadeus	Yes	460	YY1[jMA0095] 0.1517 YY1[M01035] 0.1769 YY1[M00069] 0.1789 YY1[M00059] 0.2313		YY1[M00793] 0.1004 YY1[jMA0095] 0.1309 YY1[M01035] 0.1567 YY1[M00069] 0.1627 YY1[M00059] 0.2359
					Weeder	Yes	14037	YY1[jMA0095] 0.2131	YY1[M00793] 0.1386 YY1[jMA0095] 0.1449 YY1[M00069] 0.1961 YY1[M01035] 0.2045	YY1[jMA0095] 0.1104 YY1[M00793] 0.1154 YY1[M00069] 0.1666 YY1[M01035] 0.1957	YY1[jMA0095] 0.0979 YY1[M00793] 0.1293 YY1[M00069] 0.1962 YY1[M01035] 0.2246
					Trawler	Yes	1472	YY1[M00793] 0.0955 YY1[jMA0095] 0.1185 YY1[M00069] 0.164 YY1[M01035] 0.1733 YY1[M00059] 0.2128	YY1[jMA0095] 0.1142 YY1[M00793] 0.1271 YY1[M00069] 0.1574 YY1[M01035] 0.1907 YY1[M00059] 0.2366
let7_Brueckner	Human	177	10001	MIMAT0000062 (miRBase)	MEME	No	1077
					AlignACE	No	5092
					YMF	No	1897
					Amadeus	No	861
					Weeder	No	2953
					Trawler	No	607
let7_Johnson	Human	182	10001	MIMAT0000062 (miRBase)	MEME	No	1331
					AlignACE	No	8145
					YMF	No	2142
					Amadeus	Yes	992	hsa-let-7a[MIMAT0000062] 0.2142		hsa-let-7a[MIMAT0000062] 0.1705
					Weeder	Yes	3203	hsa-let-7a[MIMAT0000062] 0.0636		hsa-let-7a[MIMAT0000062] 0.1495
					Trawler	Yes	664	hsa-let-7a[MIMAT0000062] 0.1404			hsa-let-7a[MIMAT0000062] 0.0825
miR106b_Linsley	Human	88	10001	MIMAT0000680 (miRBase)	MEME	Yes	460	hsa-miR-106b[MIMAT0000680] 0.0342		hsa-miR-106b[MIMAT0000680] 0.0609
					AlignACE	No	2114
					YMF	Yes	1377		hsa-miR-106b[MIMAT0000680] 0.0
					Amadeus	Yes	739	hsa-miR-106b[MIMAT0000680] 0.1072		hsa-miR-106b[MIMAT0000680] 0.0677
					Weeder	Yes	1705	hsa-miR-106b[MIMAT0000680] 0.0799	hsa-miR-106b[MIMAT0000680] 0.065	hsa-miR-106b[MIMAT0000680] 0.0592	hsa-miR-106b[MIMAT0000680] 0.0392
					Trawler	Yes	505	hsa-miR-106b[MIMAT0000680] 0.0312	hsa-miR-106b[MIMAT0000680] 0.0	hsa-miR-106b[MIMAT0000680] 0.1216
miR124_Lim	Human	116	10001	MIMAT0000422 (miRBase)	MEME	Yes	598	hsa-miR-124a[MIMAT0000422] 0.019		hsa-miR-124a[MIMAT0000422] 0.0803
					AlignACE	No	3101
					YMF	Yes	1607	hsa-miR-124a[MIMAT0000422] 0.0
					Amadeus	Yes	665	hsa-miR-124a[MIMAT0000422] 0.0333		hsa-miR-124a[MIMAT0000422] 0.1624
					Weeder	Yes	2074	hsa-miR-124a[MIMAT0000422] 0.0774	hsa-miR-124a[MIMAT0000422] 0.0523	hsa-miR-124a[MIMAT0000422] 0.0542	hsa-miR-124a[MIMAT0000422] 0.0686
					Trawler	Yes	357	hsa-miR-124a[MIMAT0000422] 0.147	hsa-miR-124a[MIMAT0000422] 0.0905
miR155_Rodriguez	Mouse	95	10001	MIMAT0000165 (miRBase)	MEME	No	322
					AlignACE	No	1311
					YMF	No	1129
					Amadeus	Yes	513	mmu-miR-155[MIMAT0000165] 0.2316		mmu-miR-155[MIMAT0000165] 0.1015
					Weeder	No	1376
					Trawler	Yes	297	mmu-miR-155[MIMAT0000165] 0.1231
miR16_Linsley	Human	90	10001	MIMAT0000069 (miRBase)	MEME	Yes	520	hsa-miR-16[MIMAT0000069] 0.0928		hsa-miR-16[MIMAT0000069] 0.1074
					AlignACE	No	2557
					YMF	No	1534
					Amadeus	Yes	706	hsa-miR-16[MIMAT0000069] 0.0971		hsa-miR-16[MIMAT0000069] 0.1063
					Weeder	Yes	1934	hsa-miR-16[MIMAT0000069] 0.0906	hsa-miR-16[MIMAT0000069] 0.0711	hsa-miR-16[MIMAT0000069] 0.074	hsa-miR-16[MIMAT0000069] 0.0672
					Trawler	Yes	415	hsa-miR-16[MIMAT0000069] 0.1512	hsa-miR-16[MIMAT0000069] 0.0505	hsa-miR-16[MIMAT0000069] 0.156
miR1_Lim	Human	65	10001	MIMAT0000416 (miRBase)	MEME	Yes	255	hsa-miR-1[MIMAT0000416] 0.0884
					AlignACE	No	1360
					YMF	No	1197
					Amadeus	Yes	673	hsa-miR-1[MIMAT0000416] 0.1121		hsa-miR-1[MIMAT0000416] 0.1157
					Weeder	Yes	1141	hsa-miR-1[MIMAT0000416] 0.0603	hsa-miR-1[MIMAT0000416] 0.0577	hsa-miR-1[MIMAT0000416] 0.0882	hsa-miR-1[MIMAT0000416] 0.0349
					Trawler	Yes	292		hsa-miR-1[MIMAT0000416] 0.1581	hsa-miR-1[MIMAT0000416] 0.1037	hsa-miR-1[MIMAT0000416] 0.0643
miR34_Chang	Human	89	10001	MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase)	MEME	No	379
					AlignACE	No	2118
					YMF	Yes	1390				hsa-miR-34a[MIMAT0000255] 0.1428
					Amadeus	No	740
					Weeder	No	1486
					Trawler	No	330
miR34_He	Human	367	10001	MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase)	MEME	Yes	6415		hsa-miR-34b[MIMAT0000685] 0.0030 hsa-miR-34c[MIMAT0000686] 0.0030 hsa-miR-34a[MIMAT0000255] 0.1274
					AlignACE	No	32662
					YMF	No	3080
					Amadeus	Yes	802	hsa-miR-34b[MIMAT0000685] 0.0839 hsa-miR-34c[MIMAT0000686] 0.1295 hsa-miR-34a[MIMAT0000255] 0.1295		hsa-miR-34b[MIMAT0000685] 0.1065 hsa-miR-34a[MIMAT0000255] 0.1188 hsa-miR-34c[MIMAT0000686] 0.1418
					Weeder	Yes	7817	hsa-miR-34a[MIMAT0000255] 0.085 hsa-miR-34c[MIMAT0000686] 0.1589 hsa-miR-34b[MIMAT0000685] 0.17	hsa-miR-34a[MIMAT0000255] 0.0391 hsa-miR-34c[MIMAT0000686] 0.1419 hsa-miR-34b[MIMAT0000685] 0.2338	hsa-miR-34c[MIMAT0000686] 0.0626 hsa-miR-34a[MIMAT0000255] 0.0626 hsa-miR-34b[MIMAT0000685] 0.0632	hsa-miR-34b[MIMAT0000685] 0.0401 hsa-miR-34c[MIMAT0000686] 0.0508 hsa-miR-34a[MIMAT0000255] 0.0508
					Trawler	No	800
miR373_Lim	Human	43	10001	MIMAT0000726 (miRBase)	MEME	Yes	95	hsa-miR-373[MIMAT0000726] 0.1396
					AlignACE	No	353
					YMF	Yes	944	hsa-miR-373[MIMAT0000726] 0.0714
					Amadeus	Yes	588	hsa-miR-373[MIMAT0000726] 0.0		hsa-miR-373[MIMAT0000726] 0.0166
					Weeder	Yes	608	hsa-miR-373[MIMAT0000726] 0.1321	hsa-miR-373[MIMAT0000726] 0.2076	hsa-miR-373[MIMAT0000726] 0.2132	hsa-miR-373[MIMAT0000726] 0.2218
					Trawler	No	238
p53_Kannan	Human	38	1201	M00034, M00272, M00761 (Transfac)	MEME	No	122
					AlignACE	No	300
					YMF	No	852
					Amadeus	No	501
					Weeder	Yes	684			p53[M00034] 0.2153
					Trawler	No	99

Results of motif discovery tools on the compendium of metazoan TF and miRNA target sets

Results of motif discovery tools on the
compendium of metazoan TF and miRNA target sets