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) ----------------------------------------------------------------------------------------------