Text S1. Comparison of recovery rate and false positive rate between PWMs.

Ligand ID: Bicoid   Threshold score: 0

 No.  Footprint Name     Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_5490044        10.973088               7.3650179               7.9358411            
   2  eve_5489926        8.7043668               7.3650179               2.4877128            
   3  eve_5489661        8.6937717               7.2051086               1.2964335            
   4  Kr_20730480        7.6498078               5.2439214               4.1396604            
   5  tll_26676963       7.6011861               7.0850412               4.9637871            
   6  hb_4522593         7.1003942               6.9361623               -1.084182            
   7  hb_4520376         6.9712757               7.3650179               6.6027390            
   8  salm_11455772      6.9045219               6.4667662               0.1968103            
   9  tll_26676911       6.7304399               6.8160949               8.6308400            
  10  hb_4520482         6.5431339               5.6572124               2.9883308            
  11  Kr_20730539        6.5003689               7.3245162               7.4721596            
  12  Kr_20730450        6.4344212               7.2051086               0.6331775            
  13  hb_4520589         6.4165592               6.0591867               7.1123522            
  14  salm_11455642      5.9870832               6.2591169               -1.113343            
  15  eve_5489682        5.2815979               5.7101940               -1.284972            
  16  tll_26676841       5.2468857               5.7792100               0.9601759            
  17  salm_11455792      5.0076722               6.4667662               -5.860095            
  18  Kr_20730887        4.9185108               7.3245162               3.9800450            
  19  hb_4520538         4.8592632               6.5066469               8.6725818            
  20  hb_4522642         4.8412753               7.0850412               -5.458848            
  21  kni_20631194       4.6281361               6.7755932               10.424359            
  22  hb_4520451         4.1931550               5.1579875               0.2967409            
  23  hb_4520554         3.8446838               6.7755932               4.3838927            
  24  kni_20631236       3.6902845               5.3477645               6.4916818            
  25  tll_26676863       3.6378820               6.0777914               9.0844872            
  26  ems_9720614        3.0949000               4.9189089               2.0606660            
  27  salm_11455853      2.8859411               6.2186153               -4.405883            
  28  salm_11455822      2.7835126               5.3639500               -3.004377            
  29  h_8639674          2.7250920               6.8956606               -4.661284            
  30  h_8639265          2.5795114               5.5533693               2.5660183            
  31  ems_9720582        2.3965545               6.0379107               -3.759090            
  32  eve_5489833        1.7119113               4.4679525               -6.155684            
  33  h_8640856          1.6042010               5.7928444               2.7081662            
  34  hb_4520525         1.5348402               3.8005462               -4.770833            
  35  h_8639161          1.0017935               4.6090645               -6.213754            
  36  h_8641120          0.8446733               5.7928444               2.7081662            
  37  h_8639429          0.1804693               4.4066555               1.7877933            
  38  h_8639734          0.1735962               3.4576759               -2.738823            
  39  salm_11455736      -1.943340               2.4454091               0.5060910            
  40  h_8639369          -2.023610               2.6549908               -3.708958            
  41  tll_26677096       -2.162062               3.7791299               3.8021310            
  42  tll_26676938       -2.319302               3.0759018               -2.912656            
  43  h_8639419          -4.228279               0.6809580               0.9130470            
  44  hb_4520505         -4.238713               2.3517750               -7.067492            
  45  salm_11456121      -4.476342               3.9715640               -6.831886            
  46  tll_26677066       -5.784753               2.3517750               -8.420488            
  47  h_8641217          -7.348529               1.0610535               -8.560903            
  48  tll_26677188       -7.514560               0.8833913               -3.325554            
----------------------------------------------------------------------------------------------
 Recovery rate:          79%(38/48)              100%(48/48)             58%(28/48)           
----------------------------------------------------------------------------------------------


 No.  (-) control        Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_240            2.6538416               5.3178968               0.4778492            
   2  hb_100             0.8943013               1.3794925               -1.272251            
   3  eve_200            0.8868996               5.3178968               0.0991544            
   4  hb_20              -0.960085               2.8593261               -4.858646            
   5  eve_160            -2.078742               1.5192292               -4.715067            
   6  eve_220            -2.205660               2.5903798               -3.690664            
   7  hb_60              -2.761276               -0.547522               -5.619376            
   8  eve_60             -3.369785               1.5869614               -10.25134            
   9  eve_CDS_40         -3.467102               -0.853837               -4.826815            
  10  hb_40              -4.009892               2.4977997               1.9703366            
  11  eve_CDS_260        -4.085615               -0.945496               -5.180276            
  12  hb_80              -5.337456               -1.145056               -3.436799            
  13  eve_CDS_60         -5.504199               0.5623365               -9.032847            
  14  eve_120            -6.026538               -0.203174               -0.208572            
  15  eve_140            -6.026538               -0.203174               -0.208572            
  16  hb_0               -6.349643               -1.509006               -0.920037            
  17  eve_CDS_120        -6.559421               -0.143206               -2.133886            
  18  eve_100            -6.709010               -0.363024               -2.079789            
  19  eve_CDS_80         -7.211557               -2.762873               -7.356404            
  20  eve_40             -7.275197               2.1010975               -6.695371            
  21  eve_80             -7.308189               -1.529084               0.5258466            
  22  eve_0              -7.313680               1.0835710               -2.402485            
  23  eve_CDS_140        -7.435250               0.1662414               -6.176602            
  24  eve_CDS_180        -7.566895               -3.496448               -6.233216            
  25  eve_CDS_200        -7.933723               -3.950525               -3.771652            
  26  eve_CDS_240        -8.048538               5.7284627               -3.140533            
  27  eve_CDS_160        -8.152291               -3.615574               -5.539877            
  28  eve_260            -8.642178               0.3501864               -8.654665            
  29  eve_CDS_0          -9.170103               -2.345820               0.4063766            
  30  eve_CDS_280        -9.652260               -1.629750               -7.201970            
  31  eve_CDS_20         -9.758108               -1.699776               -2.010972            
  32  eve_20             -9.769919               -1.440977               -2.139178            
  33  eve_CDS_220        -11.37827               1.8423968               -7.715250            
  34  eve_CDS_100        -12.27328               -2.475388               -2.545827            
  35  eve_180            -14.01859               -0.369184               -4.908580            
----------------------------------------------------------------------------------------------
 False positive rate:    8%(3/35)                42%(15/35)              14%(5/35)            
----------------------------------------------------------------------------------------------



Ligand ID: Caudal   Threshold score: 0

 No.  Footprint Name     OneHybrid_matrix        Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  salm_11455731      6.0983639               10.393943               2.6862910            
   2  kni_20631324       6.0102301               17.334129               0.7676393            
   3  ftz_2689640        4.6032014               17.306175               1.2421593            
   4  kni_20631348       4.4825812               16.973460               3.3752177            
   5  salm_11455702      4.4154119               15.567461               -0.566257            
   6  ftz_2689567        3.7554219               16.042121               6.4788099            
   7  salm_11455957      2.3276184               14.020124               -1.760133            
   8  kni_20631265       1.9338581               16.613965               9.5663600            
   9  salm_11455649      0.5808181               10.073704               3.2679859            
  10  kni_20631387       0.5180109               12.501540               7.5764767            
  11  kni_20631234       -1.716365               11.870563               -0.350081            
  12  kni_20631444       -2.078358               15.022695               -0.820330            
  13  kni_20631296       -6.235944               12.944966               2.8630435            
----------------------------------------------------------------------------------------------
 Recovery rate:          76%(10/13)              100%(13/13)             69%(9/13)            
----------------------------------------------------------------------------------------------
						 											      
						 											      
 No.  (-) control        OneHybrid_matrix        Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  ftz_80             5.4959583               8.6447300               -5.186096            
   2  eve_CDS_120        2.5927815               6.5346495               -5.731018            
   3  eve_CDS_260        1.0323564               9.8985179               -1.923251            
   4  eve_CDS_40         0.1209072               8.7328522               -5.892737            
   5  eve_CDS_20         -0.109917               8.7672210               -3.311526            
   6  kni_20             -0.640116               6.1693792               -2.197658            
   7  eve_CDS_180        -0.680107               9.3814069               -0.148337            
   8  eve_CDS_100        -0.775649               11.392652               2.4845328            
   9  ftz_20             -0.876677               13.946507               0.3328526            
  10  eve_CDS_220        -1.314334               14.493327               -5.000259            
  11  kni_60             -1.467907               8.8263592               -2.048223            
  12  eve_CDS_280        -1.962187               13.645883               -2.214904            
  13  eve_CDS_60         -2.186115               13.364400               -2.953043            
  14  eve_CDS_80         -2.286945               7.2758475               -2.831344            
  15  kni_80             -2.572637               9.7479913               1.4036347            
  16  eve_CDS_160        -3.184340               10.361219               -3.000920            
  17  ftz_60             -3.369043               13.881431               7.6461590            
  18  ftz_0              -3.441286               9.7469138               -1.005538            
  19  eve_CDS_240        -4.037851               11.732070               2.7183376            
  20  kni_0              -4.154586               9.2592930               -6.115306            
  21  eve_CDS_200        -4.172534               8.0925780               -3.396572            
  22  kni_40             -4.354265               4.2813559               -7.543712            
  23  ftz_40             -4.841118               8.9320013               -5.411670            
  24  ftz_100            -5.184742               5.6087570               -4.567286            
  25  eve_CDS_0          -5.223245               10.397789               -2.657227            
  26  eve_CDS_140        -6.038926               9.4145835               -0.297012            
----------------------------------------------------------------------------------------------
 False positive rate:    15%(4/26)               100%(26/26)             19%(5/26)            
----------------------------------------------------------------------------------------------



Ligand ID: D-STAT   Threshold score: 0

 No.  Footprint Name     Dim_Selex_matrix        Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  phl_2234394        8.5352046		 N/A	                 -5.285522            
   2  eve_5863323        8.4353290				         -1.433060            
   3  eve_5863202        4.3196953                                       -4.342221            
----------------------------------------------------------------------------------------------
 Recovery rate:          100%(3/3)                                       0%(0/3)              
----------------------------------------------------------------------------------------------


 No.  (-) control        Dim_Selex_matrix        Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_CDS_80         2.2999741               N/A                     -2.831344            
   2  eve_CDS_40         1.1250982                                       -5.892737            
   3  eve_CDS_260        0.5866049                                       -1.923251            
   4  eve_CDS_280        -0.030519                                       -2.214904            
   5  eve_CDS_240        -0.716261                                       2.7183376            
   6  eve_CDS_140        -1.608160                                       -0.297012            
   7  eve_20             -1.673121                                       -4.910894            
   8  eve_0              -2.841899                                       3.7212347            
   9  eve_CDS_0          -3.620777                                       -2.657227            
  10  eve_CDS_60         -4.257114                                       -2.953043            
  11  eve_CDS_120        -4.903508                                       -5.731018            
  12  eve_CDS_180        -5.332334                                       -0.148337            
  13  eve_CDS_220        -5.395904                                       -5.000259            
  14  eve_CDS_100        -5.614349                                       2.4845328            
  15  eve_CDS_20         -8.231011                                       -3.311526            
  16  eve_CDS_160        -8.269221                                       -3.000920            
  17  eve_CDS_200        -8.641831                                       -3.396572            
----------------------------------------------------------------------------------------------
 False positive rate:    17%(3/17)               N/A                     17%(3/17)            
----------------------------------------------------------------------------------------------



Ligand ID: Dichaete   Threshold score: 0

 No.  Footprint Name     OneHybrid_matrix        Berman_matrix           Segal_PSSM    
----------------------------------------------------------------------------------------------
   1  hTCR_75            10.844186               N/A                     N/A
   2  hTCR_50            10.063405                            
   3  hTCR_25            7.0966673                            
   4  hTCR_0             7.0725348                            
----------------------------------------------------------------------------------------------
 Recovery rate:          100%(4/4)               N/A                     N/A            
----------------------------------------------------------------------------------------------


 No.  (-) control        OneHybrid_matrix        Berman_matrix           Segal_PSSM
----------------------------------------------------------------------------------------------
   1  eve_CDS_160        4.3972007               N/A                     N/A
   2  eve_CDS_280        2.4218104                            
   3  hTCR_50            2.2510224                            
   4  eve_CDS_100        1.3438449                            
   5  eve_CDS_120        -0.111166                            
   6  hTCR_0             -0.339239                            
   7  hTCR_25            -0.363371                            
   8  eve_CDS_60         -1.451494                            
   9  eve_CDS_140        -2.805556                            
  10  eve_CDS_80         -3.488401                            
  11  eve_CDS_40         -3.553506                            
  12  eve_CDS_240        -3.685929                            
  13  eve_CDS_20         -4.178866                            
  14  eve_CDS_260        -4.900849                            
  15  eve_CDS_220        -5.242246                            
  16  eve_CDS_180        -5.250941                            
  17  eve_CDS_200        -7.824176                            
  18  eve_CDS_0          -8.320141                            
----------------------------------------------------------------------------------------------
 False positive rate:    22%(4/18)               N/A                     N/A
----------------------------------------------------------------------------------------------



Ligand ID: Hunchback   Threshold score: 0

 No.  Footprint Name     Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  Ubx_12526647       10.791383               9.2836979               8.1808668            
   2  Ubx_12527039       10.791383               8.5672282               6.7963025            
   3  kni_20631265       10.601813               8.2763910               7.7369744            
   4  h_8640808          10.008415               8.0837292               3.3748513            
   5  Ubx_12599052       9.9224052               5.9927953               0.7755866            
   6  Ubx_12599302       9.8333793               8.1745381               5.7920626            
   7  h_8640846          9.3055018               8.2447161               4.5676700            
   8  h_8641126          9.3055018               8.2447161               4.4315029            
   9  Ubx_12590697       9.3055018               6.5272954               0.7936606            
  10  h_8638879          8.9741851               9.0234720               7.2693109            
  11  h_8641224          8.9741851               9.2836979               4.7332845            
  12  Ubx_12599100       8.9741851               9.2101435               6.8741909            
  13  abd-A_12636859     8.9741851               8.9747921               6.4816639            
  14  abd-A_12637017     8.9741851               9.0234720               3.3602017            
  15  Ubx_12590250       8.1912176               8.5793065               5.6223715            
  16  h_8639010          8.0161813               7.7182944               7.5668182            
  17  kni_20631435       7.4883038               8.3182706               0.6141237            
  18  Kr_20730350        7.3646665               7.5142154               7.9319525            
  19  kni_20630930       7.2038642               8.9747921               5.4143810            
  20  Ubx_12590381       6.9857683               9.0234720               5.0215469            
  21  Ubx_12590593       6.8997579               7.3487454               6.3983800            
  22  h_8639878          6.6965861               8.9991667               9.6478971            
  23  eve_5487658        6.5303000               6.6388262               5.0731479            
  24  Ubx_12527000       6.5303000               7.1199445               3.1998766            
  25  hb_4524060         6.5070167               6.6082196               8.9194694            
  26  hb_4523966         6.4210063               6.5792871               5.6912563            
  27  h_8639228          6.2458604               6.6842754               1.6866385            
  28  h_8639902          6.2458604               8.4347641               7.1651454            
  29  abd-A_12636914     6.2458604               7.4093886               5.9030880            
  30  Ubx_12526869       6.2028009               8.3926350               7.0271531            
  31  eve_5487626        6.1230675               6.4859628               7.2106767            
  32  salm_11456121      6.1081687               5.6006258               1.7249332            
  33  Kr_20730612        6.0340416               6.4457235               10.296807            
  34  h_8640992          6.0340416               7.1579254               9.5715166            
  35  hb_4524456         6.0340416               7.4274572               8.5105705            
  36  kni_20631139       6.0277645               7.8656323               6.7358149            
  37  eve_5487486        5.9907113               7.7104945               6.3949573            
  38  kni_20631098       5.8276082               7.4182663               6.2256704            
  39  eve_5487362        5.7385823               7.1579254               7.6222670            
  40  eve_5487588        5.7385823               8.1502329               9.7349313            
  41  abd-A_12636602     5.3397343               4.0761899               4.2689994            
  42  h_8638531          5.0888369               6.6728814               8.5080483            
  43  eve_5490184        4.9852780               6.6082196               10.761988            
  44  eve_5490101        4.8992676               8.3683298               9.6311554            
  45  h_8638772          4.8431381               5.8137674               2.4416767            
  46  Ubx_12590280       4.8431381               5.8873218               6.0730810            
  47  en_7044664         4.8118568               4.2445626               -2.527961            
  48  Ubx_12599166       4.7599791               7.4288503               4.1856834            
  49  kni_20630961       4.6333245               5.3383687               3.6482003            
  50  kni_20630793       4.3576352               5.0325494               -0.017654            
  51  hb_4524372         4.3058695               5.0996780               3.8086467            
  52  h_8638364          4.2168436               7.1038885               9.0902129            
  53  abd-A_12636642     4.0964206               8.4418843               3.8267992            
  54  h_8639754          3.9379489               7.7174710               7.0536015            
  55  Kr_20730828        3.9213843               7.8743951               7.3766966            
  56  hb_4520496         3.9213843               7.3932768               9.2499679            
  57  h_8639081          3.8979335               3.6199462               -1.919073            
  58  Ubx_12590783       3.8538530               2.9000515               -2.639599            
  59  h_8638469          3.7771477               7.0579717               5.1333971            
  60  Kr_20730587        3.6623691               5.6458252               3.0083662            
  61  kni_20630440       3.5590518               6.3328585               1.6538761            
  62  h_8639247          3.1864306               7.0463947               8.8825499            
  63  h_8639056          3.1090672               8.7233289               7.3014509            
  64  kni_20630772       3.0689710               6.1365706               2.0118584            
  65  h_8640959          3.0443909               4.2876169               -0.271253            
  66  h_8638727          3.0230568               7.7888773               6.4383373            
  67  h_8641246          3.0230568               7.0972822               6.1502663            
  68  h_8638509          2.8981066               7.6441212               3.3149771            
  69  eve_5490019        2.8981066               7.5705668               4.8689366            
  70  eve_5487609        2.7823614               5.5159194               2.6617184            
  71  Ubx_12589545       2.7760844               7.1840909               1.5573824            
  72  Ubx_12599129       2.6876320               6.7450672               0.1005821            
  73  eve_5487810        2.3332351               7.0132843               3.2425925            
  74  hb_4524271         2.2912664               6.8090140               0.9293928            
  75  h_8638596          2.1276126               5.8266786               1.3736793            
  76  Ubx_12590483       2.0990861               5.7755420               2.5394291            
  77  Ubx_12599382       1.9066014               6.7045807               1.7541502            
  78  eve_5487382        1.8959142               7.4259634               7.4933461            
  79  eve_5487762        1.6605378               6.3293016               3.8701317            
  80  hb_4522754         1.4694836               1.9346693               -4.785009            
  81  h_8639708          1.2631021               5.1071564               1.2192404            
  82  en_7044713         1.1953773               3.5205535               0.1780436            
  83  Ubx_12590861       1.1953773               3.4469990               5.9351520            
  84  Ubx_12590459       1.1383276               5.3136874               3.7657742            
  85  h_8638434          1.1129468               4.6214620               -1.421351            
  86  hb_4520980         0.6723174               4.9362199               2.3983037            
  87  Kr_20730467        0.6348696               6.6461962               0.3495103            
  88  h_8641168          0.2398395               3.5259183               -1.890665            
  89  h_8639037          0.1140310               5.9150001               5.6669322            
  90  h_8639104          0.0787162               7.1501256               7.1397478            
  91  Ubx_12590074       -0.174292               2.0809816               4.2924422            
  92  kni_20630483       -0.811324               4.9226926               4.9470252            
  93  Ubx_12589994       -0.821723               5.8005947               3.2270407            
  94  Ubx_12589579       -1.033542               6.5365431               5.9296064            
  95  Ubx_12590518       -1.364046               3.0842691               -1.263058            
  96  Kr_20730423        -1.393224               4.9112303               3.6019368            
  97  Ubx_12590892       -1.703166               3.2235676               -1.079427            
  98  kni_20630376       -2.052076               -2.021687               -2.957224            
  99  Ubx_12589643       -2.061102               2.2710567               -4.058768            
 100  eve_5487437        -2.075889               5.5087628               4.4756752            
 101  h_8638934          -3.768947               6.3172102               4.1813880            
 102  eve_5487400        -4.101929               4.5021343               -1.806276            
 103  Ubx_12590428       -4.208016               -0.258666               -4.198773            
----------------------------------------------------------------------------------------------
 Recovery rate:          87%(90/103)             98%(101/103)            86%(89/103)          
----------------------------------------------------------------------------------------------


 No.  (-) control        Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  h_80               2.6016216               4.0445150               -5.580898            
   2  h_100              -0.582647               1.5854043               -3.547998            
   3  eve_CDS_260        -1.380878               -4.687844               -8.642225            
   4  eve_CDS_40         -4.374998               -0.230411               -8.575636            
   5  eve_CDS_100        -4.967938               -4.215538               -4.563923            
   6  eve_CDS_280        -5.807399               1.8197078               -0.874750            
   7  eve_CDS_20         -5.971819               -7.803088               -10.67095            
   8  h_20               -6.067792               -0.247416               -7.843050            
   9  h_40               -6.473897               -1.526416               -12.40672            
  10  eve_CDS_60         -7.115483               -4.236869               -0.762784            
  11  h_60               -7.243523               0.2258916               -8.116877            
  12  eve_CDS_240        -7.245537               -3.017512               -9.904448            
  13  h_140              -7.252861               -8.322266               -13.65678            
  14  eve_CDS_220        -8.148940               -7.092001               -14.07147            
  15  eve_CDS_200        -8.574561               -8.001531               -17.92519            
  16  eve_CDS_80         -9.717192               1.7792783               -8.583200            
  17  h_200              -9.720738               -0.476233               -7.809695            
  18  h_180              -10.03222               -5.604268               -9.805843            
  19  eve_CDS_160        -10.70816               -2.695638               -8.382420            
  20  h_120              -10.79060               -7.856962               -9.530500            
  21  h_0                -11.39114               -2.110246               -8.075432            
  22  h_160              -12.94726               -5.919493               -16.04083            
  23  eve_CDS_0          -14.23212               -7.048858               -14.88210            
  24  eve_CDS_140        -15.94467               -8.126877               -15.27547            
  25  eve_CDS_120        -16.16161               -6.225968               -14.57863            
  26  eve_CDS_180        -16.21213               -9.856875               -10.07642            
----------------------------------------------------------------------------------------------
 False positive rate:    3%(1/26)                19%(5/26)               0%(0/26)             
----------------------------------------------------------------------------------------------



Ligand ID: Kruppel   Threshold score: 0

 No.  Footprint Name     Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  kni_20630559       9.9981367               8.9774021               7.4384508            
   2  kni_20630372       9.9424310               10.537240               7.4384508            
   3  kni_20630504       9.9424310               10.537240               7.4384508            
   4  kni_20630536       9.9424310               10.537240               7.4384508            
   5  abd-A_12636468     8.4357465               8.8590415               5.3886556            
   6  h_8641252          8.1749072               8.6258011               7.4384508            
   7  h_8639586          7.8994411               7.6511447               7.3466075            
   8  h_8639822          7.2544672               7.0234764               7.3466075            
   9  eve_5490138        7.0647428               10.164607               6.1278022            
  10  h_8640856          6.5545950               7.7908756               5.2962723            
  11  ko_21022077        6.4325818               6.1788898               5.0915014            
  12  salm_11455799      6.3768760               7.7387279               5.3421114            
  13  ko_21022227        6.3768760               7.7387279               5.0915014            
  14  salm_11455641      5.2183605               7.1046273               5.2550825            
  15  eve_5490044        5.2183605               7.1046273               5.2550825            
  16  kni_20630441       5.1246047               8.0838531               6.8528213            
  17  h_8640828          5.0217529               7.2785118               6.0359589            
  18  h_8641119          4.8583454               8.2268329               5.5066326            
  19  h_8644208          4.0381370               4.6349058               4.3027343            
  20  salm_11456017      3.8896507               8.0252591               5.0448746            
  21  Ubx_12598979       3.4957122               9.0232880               1.9771132            
  22  eve_5489953        3.3023505               5.0060901               5.3735996            
  23  h_8644086          3.0816148               5.1977576               6.7609780            
  24  eve_5489925        3.0360912               4.5092957               5.4462775            
  25  h_8639314          3.0071860               5.2226117               4.8345142            
  26  ko_21021992        2.9491848               2.4222092               2.7569117            
  27  hb_4520997         2.4805186               6.2458769               1.1274009            
  28  eve_5489850        2.3281535               6.4827401               5.5381674            
  29  h_8640881          2.3142736               8.2146978               -0.616774            
  30  eve_5489662        2.2469165               8.3509943               4.1233061            
  31  salm_11455985      1.9773764               5.9215477               3.5945198            
  32  eve_5489527        0.8999648               4.3374916               1.0847229            
  33  en_7044647         0.5993917               4.7453295               0.0278775            
  34  eve_5490095        0.4865330               7.5814288               5.5523137            
  35  eve_5489576        -2.575924               3.7206461               2.8235490            
  36  eve_5489783        -2.704274               -0.115181               3.4954824            
  37  h_8641003          -3.679820               0.4711237               -3.092882            
  38  h_8639464          -5.489224               2.3866095               4.5158304            
  39  h_8640919          -5.662034               -1.825309               -0.784895            
  40  h_8639520          -5.851846               -1.681512               4.5929048            
  41  eve_5489611        -6.393854               1.5106977               -2.049560            
  42  h_8641145          -7.269614               -0.384079               -0.610841            
  43  eve_5489809        -7.602008               -0.108621               -0.832976            
  44  hb_4520680         -7.870324               -3.019164               5.1081116            
  45  eve_5489820        -8.459755               0.7209356               0.2182020            
----------------------------------------------------------------------------------------------
 Recovery rate:          75%(34/45)              86%(39/45)              86%(39/45)           
----------------------------------------------------------------------------------------------


 No.  (-) control        Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_CDS_200        1.0553147               -3.020864               0.5785871            
   2  eve_CDS_220        -0.777373               3.3041710               -0.975570            
   3  eve_CDS_180        -2.247263               2.8199721               3.1348493            
   4  eve_CDS_260        -2.787675               2.7072307               -0.061348            
   5  eve_CDS_280        -4.248438               0.3859006               -0.857935            
   6  eve_CDS_20         -4.427810               -2.128509               2.0427529            
   7  eve_CDS_40         -4.588115               -1.405689               3.0898712            
   8  eve_CDS_120        -5.380996               -0.588201               -1.416701            
   9  eve_CDS_240        -6.116718               -0.205260               -0.011940            
  10  eve_CDS_160        -9.069754               -0.257291               -0.047272            
  11  eve_CDS_0          -9.184250               -3.419615               -3.591278            
  12  eve_CDS_140        -9.464690               -1.236760               3.4790370            
  13  eve_CDS_100        -10.00392               -0.407752               -2.922758            
  14  eve_CDS_80         -10.44789               -4.549708               1.8372679            
  15  eve_CDS_60         -16.32829               -4.979539               -4.402467            
----------------------------------------------------------------------------------------------
 False positive rate:    6%(1/15)                26%(4/15)               40%(6/15)            
----------------------------------------------------------------------------------------------



Ligand ID: Knirps   Threshold score: 0

 No.  Footprint Name     OneHybrid_matrix        Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_5487572        10.036687               8.5244732               6.0062039            
   2  eve_5487347        9.9039997               9.5037426               4.0465810            
   3  h_8639910          9.1955417               5.9820517               -1.796724            
   4  h_8639668          9.1437831               8.8632155               -8.972701            
   5  h_8639854          8.2760736               8.8760742               -6.155433            
   6  eve_5487617        7.6636390               9.2148165               1.3826007            
   7  eve_5487391        7.3272102               8.5352580               4.8806688            
   8  h_8638864          5.7562385               5.0894792               -2.506796            
   9  h_8638572          5.6211747               9.4810759               2.0620008            
  10  h_8639617          5.1510842               3.9267600               -9.618508            
  11  Kr_20730883        4.3048064               3.3787942               -1.439686            
  12  h_8639164          3.6423403               0.4405946               -4.898944            
  13  Ubx_12599840       3.2771163               2.0145315               -4.726790            
  14  h_8638499          3.0719443               2.3437008               -5.994245            
  15  h_8640868          2.6459555               2.0879319               6.4321835            
  16  eve_5487414        2.2859709               7.6945757               2.0740044            
  17  h_8639836          2.0753756               -0.976152               0.4850386            
  18  Ubx_12598892       1.9702037               1.9050115               0.1247100            
  19  h_8639069          1.6452000               2.7051098               -1.514537            
  20  Ubx_12598703       1.5947890               2.0384101               5.7830363            
  21  h_8639204          1.4748596               3.5523489               -4.772437            
  22  h_8639402          1.1016446               -0.187073               0.2647195            
  23  Ubx_12599332       0.7369820               -0.941682               -5.926651            
  24  h_8639053          0.4195767               2.9071040               -10.30127            
  25  h_8639095          0.2985901               -1.216246               -6.281819            
  26  h_8641320          -0.559095               5.2248646               -6.294450            
  27  h_8638756          -1.075716               5.6540943               4.2833805            
  28  h_8640834          -1.426912               2.1118105               4.6474151            
  29  h_8639263          -1.878056               0.9717580               -2.419408            
  30  h_8640805          -4.281435               0.0675387               3.2879290            
  31  Ubx_12600036       -4.730919               -0.030178               -2.663025            
  32  h_8639538          -5.443459               0.4405946               -6.452499            
  33  h_8639484          -6.002356               0.2087043               -1.177472            
----------------------------------------------------------------------------------------------
 Recovery rate:          75%(25/33)              84%(28/33)              42%(14/33)           
----------------------------------------------------------------------------------------------


 No.  (-) control        OneHybrid_matrix    Berman_matrix               Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_0              5.4226208               4.0574906               -3.299459            
   2  eve_CDS_240        5.1309847               5.5636069               -2.984735            
   3  eve_80             3.7051932               1.5436025               1.4652973            
   4  h_100              2.3946674               2.8736524               -3.044117            
   5  eve_CDS_40         1.3809673               -0.866926               -8.430416            
   6  h_120              0.9099147               -3.165954               -4.408316            
   7  eve_CDS_60         0.6575041               -2.175664               -2.295637            
   8  h_40               0.4963675               -0.659058               -4.462658            
   9  eve_CDS_180        0.3599392               2.1105987               3.3525957            
  10  h_280              -0.490636               0.0032735               0.1721590            
  11  eve_CDS_140        -0.497554               -0.176053               1.8647498            
  12  eve_CDS_0          -0.710846               1.2192380               4.9899442            
  13  eve_120            -0.906083               0.6828320               -6.191458            
  14  eve_100            -1.228872               -2.318185               3.0333712            
  15  eve_CDS_100        -1.682710               1.3331671               -6.418474            
  16  h_240              -1.685347               2.5683617               -8.205560            
  17  h_0                -1.720131               0.2980737               -7.632958            
  18  eve_200            -1.862505               -3.200124               -4.682347            
  19  h_60               -1.944147               0.4179278               0.2227685            
  20  eve_CDS_160        -2.043569               0.6828320               -3.784204            
  21  eve_40             -2.431163               -0.031389               -6.580445            
  22  eve_20             -2.702505               0.4191397               9.0233621            
  23  eve_160            -2.709406               4.7267150               4.8989874            
  24  eve_60             -2.746621               -2.171872               -7.959512            
  25  eve_CDS_260        -2.941330               1.7718564               0.7875777            
  26  eve_180            -3.015532               0.3440897               2.5338883            
  27  eve_CDS_280        -3.097812               -0.601728               -8.093633            
  28  eve_CDS_120        -3.192300               0.6496748               -0.390294            
  29  h_80               -3.585901               3.1388509               -0.011416            
  30  h_200              -3.908189               0.2980737               -1.675828            
  31  h_220              -3.908189               0.2980737               -1.675828            
  32  h_260              -4.284473               0.0259402               -6.484118            
  33  eve_CDS_220        -4.342924               -0.369837               -5.189943            
  34  h_300              -4.547241               2.1972956               -6.399825            
  35  eve_220            -5.577750               3.0567109               -3.368788            
  36  eve_140            -6.094589               -0.087213               -5.290916            
  37  h_140              -6.138583               -2.623476               -5.057522            
  38  h_20               -6.516852               -0.940327               -12.06100            
  39  eve_CDS_80         -6.568939               -1.129692               -4.042471            
  40  h_160              -7.112080               -0.770565               -5.095723            
  41  eve_CDS_20         -7.377405               0.4939962               -6.953047            
  42  eve_CDS_200        -7.874891               -1.398233               0.7985803            
----------------------------------------------------------------------------------------------
 False positive rate:    21%(9/42)               59%(25/42)              28%(12/42)           
----------------------------------------------------------------------------------------------



Ligand ID: Giant   Threshold score: 0

 No.  Footprint Name     Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  abd-A_12636938     8.7677278               N/A                     5.3326673            
   2  Kr_20732894        8.6359086                                       5.6847903            
   3  Kr_20730905        7.3495014                                       9.6372090            
   4  eve_5489744        4.5221414                                       -0.016712            
   5  eve_5490013        2.1334815                                       3.6097636            
   6  eve_5489681        2.0529311                                       1.5434845            
   7  kni_20630775       -1.857373                                       -3.940312            
   8  kni_20630798       -2.206533                                       -2.913412            
----------------------------------------------------------------------------------------------
 Recovery rate:          75%(6/8)                N/A                     62%(5/8)             
----------------------------------------------------------------------------------------------


 No.  (-) control        Selex_matrix            Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  eve_CDS_260        1.4324262               N/A                     0.3004162            
   2  eve_CDS_160        -0.400165                                       -8.723534            
   3  eve_CDS_60         -1.010872                                       -6.154958            
   4  eve_CDS_180        -1.911310                                       -4.541155            
   5  eve_CDS_100        -2.062146                                       -9.694348            
   6  eve_CDS_0          -2.632031                                       3.2098053            
   7  eve_CDS_280        -2.911930                                       -5.407172            
   8  eve_CDS_140        -3.358547                                       -11.48482            
   9  eve_CDS_40         -3.611286                                       -11.60369            
  10  eve_CDS_120        -3.789997                                       -9.044772            
  11  eve_CDS_240        -3.843019                                       -3.374842            
  12  eve_CDS_20         -3.986002                                       -5.130515            
  13  eve_CDS_80         -4.062556                                       -8.958537            
  14  eve_CDS_220        -4.100031                                       1.0408054            
  15  eve_CDS_200        -5.316124                                       -5.263589            
----------------------------------------------------------------------------------------------
 False positive rate:    6%(1/15)                N/A                     20%(3/15)            
----------------------------------------------------------------------------------------------



Ligand ID: Tailless   Threshold score: 0

 No.  Footprint Name     Raj_matrix              Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  Kr_20730809        8.5439050               N/A                     8.2566579            
   2  h_8641201          8.5439050                                       8.2566579            
   3  kni_20630715       8.5439050                                       8.2566579            
   4  kni_20630380       6.9865945                                       5.9021808            
   5  Ubx_12527088       6.9622653                                       4.2034754            
   6  kni_20630597       6.9622653                                       4.2034754            
   7  hb_4526812         6.3679532                                       3.0151208            
   8  Kr_20730327        6.2491608                                       4.8082637            
   9  hb_4527486         5.6182022                                       -2.689264            
  10  kni_20630700       5.3659597                                       1.7629620            
  11  hb_4526653         5.1274019                                       5.7499954            
  12  h_8639318          5.0661181                                       4.7284976            
  13  hb_4527124         4.8204487                                       1.4284497            
  14  hb_4527522         4.7608636                                       3.3733841            
  15  kni_20630475       4.4257509                                       5.1710933            
  16  Kr_20730563        4.4094602                                       -0.147306            
  17  hb_4527235         4.2823011                                       5.5897490            
  18  Kr_20730904        4.1663350                                       -1.853486            
  19  hb_4527001         4.0989413                                       4.1541186            
  20  hb_4527313         3.9254656                                       -3.300041            
  21  Ubx_12526965       3.7815579                                       2.4081560            
  22  Ubx_12599285       3.6857728                                       -1.136009            
  23  kni_20630428       3.5331368                                       0.7609061            
  24  h_8639773          3.2726247                                       1.9192959            
  25  ems_9720720        3.1998917                                       0.9344582            
  26  Ubx_12599143       3.1403397                                       5.4569038            
  27  Kr_20730462        2.8865749                                       -0.100566            
  28  Kr_20730531        2.7355858                                       -0.071053            
  29  ems_9720620        2.1285712                                       6.0015862            
  30  h_8639156          1.8827516                                       -0.410941            
  31  h_8640904          1.7389956                                       0.2149866            
  32  h_8639596          1.4127842                                       1.3464290            
  33  Ubx_12526877       0.6094125                                       0.7609061            
  34  Kr_20730480        0.4831875                                       -3.846702            
  35  h_8639259          0.3256782                                       -0.737877            
  36  kni_20630516       -0.166281                                       0.2989959            
  37  hb_4527305         -1.339012                                       -4.144493            
----------------------------------------------------------------------------------------------
 Recovery rate:          94%(35/37)              N/A                     70%(26/37)           
----------------------------------------------------------------------------------------------


 No.  (-) control        Raj_matrix              Berman_matrix           Segal_PSSM           
----------------------------------------------------------------------------------------------
   1  hb_140             5.6078647               N/A                     7.4167404            
   2  hb_120             4.9116320                                       7.0853200            
   3  eve_CDS_60         4.3709770                                       0.1556016            
   4  hb_80              3.3358546                                       -1.719416            
   5  hb_100             3.2427082                                       3.5031608            
   6  eve_CDS_260        3.1060322                                       0.5805140            
   7  eve_CDS_0          3.0564420                                       4.6929521            
   8  hb_60              3.0326968                                       1.6461201            
   9  h_80               2.9963387                                       7.1185306            
  10  h_100              2.9613339                                       6.7679101            
  11  eve_CDS_20         2.5964747                                       -3.367290            
  12  h_40               2.4299767                                       1.5811219            
  13  hb_160             2.2207501                                       3.3729176            
  14  eve_CDS_200        1.9477941                                       2.5743398            
  15  hb_200             1.8655753                                       4.2612476            
  16  h_140              1.6905140                                       0.9301752            
  17  eve_CDS_220        1.6034179                                       -0.969825            
  18  hb_0               1.3161518                                       6.6380173            
  19  h_0                1.1532405                                       0.8497578            
  20  eve_CDS_240        1.0684048                                       2.4596899            
  21  eve_CDS_160        0.9955383                                       -2.646224            
  22  h_180              0.2479177                                       -0.160792            
  23  eve_CDS_280        0.0455500                                       1.4090044            
  24  eve_CDS_40         -0.008294                                       -1.469685            
  25  hb_40              -0.123793                                       0.0685831            
  26  hb_180             -0.174239                                       -3.337048            
  27  h_120              -0.593252                                       -5.514225            
  28  eve_CDS_140        -0.670425                                       -2.517206            
  29  h_20               -0.856727                                       -1.589870            
  30  h_60               -1.018302                                       -1.519078            
  31  h_160              -1.462603                                       -1.211890            
  32  eve_CDS_100        -1.479380                                       -4.765905            
  33  eve_CDS_80         -1.645430                                       -5.235514            
  34  hb_20              -1.990097                                       -0.961808            
  35  eve_CDS_120        -3.049721                                       -6.930982            
  36  eve_CDS_180        -3.085856                                       -3.860334            
----------------------------------------------------------------------------------------------
 False positive rate:    63%(23/36)              N/A                     52%(19/36)           
----------------------------------------------------------------------------------------------



