<p>Supplementary Table 1. Validation BEAF-32 at genes identified with Fly Enhancer that had a binding cluster <1 kb from the TSS. ChIP-chip data (GEO Accession: GSE15661) was used to confirm that BEAF-32 was physically bound to each gene (*). A. gamibae orthologs (if present) are also listed in addition to whether the same Drosophila motif was identified and its relationship to the TSS. </p><p>D. melanogaster A. gambie ortholog genes identified A. gambiae BEAF-32 ChIP- identified with with Fly Enhancer Ortholog chip peak Mosquito Enhancer CG31174(-) - - - Spx(+) AGAP001538 * - Atx2(+) - * - CG11151(+) AGAP003092 - - nito(+) AGAP005127 * - CG5284(+) AGAP005777 * - AGAP010224, KdelR(+) AGAP012756 * - U2A(-) AGAP007670 * - osa(-) AGAP001786 * - CG10616(+) AGAP006119 * - CG6151(-) AGAP011546 * - CG1667(+) - * - CG15770(+) - * - CG5360(+) AGAP005115 * - CkIIalpha-i1(+) AGAP005569 * - su(s)(+) AGAP011127 * * downstream Tango2(+) AGAP002962 * - CG15743(+) AGAP001396 * - CG31195(-) AGAP001418 * - CG9253(+) AGAP009809 * - Acyp2(+) - * - CG6982(+) - * - CG8228(+) AGAP003980 * - AGAP010018, Psf2(-) AGAP012743 * - smt3(-) AGAP001701 * - sec63(+) AGAP007361 * * totally inside Vap-33-1(+) AGAP000626 * - Uhg1(+) - * - CG14820(+) - - - CG4452(+) AGAP005928 * - CG5500(+) - * - CG7600(+) AGAP002874 * - CkIalpha(+) AGAP000627 * - CG7845(-) AGAP010453 * - CG10971(-) AGAP004801 * - Pi3K92E(-) AGAP000018 * - l(1)G0168(+) - * - CG5235(-) AGAP011450 * - CG4813(-) AGAP003744 * - Gr98a(+) - - - SmB(-) AGAP005523 * - wuho(+) - * - hang(+) - * - bys(+) AGAP002923 * - CG18292(+) - * - CG3774(+) AGAP011493 * - CG17475(-) - - - CG9715(+) AGAP006128 * - CG13957(+) - * - CG11417(+) AGAP003294 * * 279 bp upstream Hira(+) AGAP009488 * - CG5399(+) - - - CG10566(+) AGAP006627 - - CG2182(-) - * - CG16890(-) AGAP010729 * - rev7(+) AGAP001326 * - CG17723(+) AGAP005918 * - CG7872(+) AGAP000831 * - CG32582(+) - * - CG7222(+) AGAP012058 * - CG32573(+) - * - CG3939(+) - - - Dredd(-) - * - up(-) AGAP002350 - - rg(+) AGAP000017 * - As(-) AGAP012366 * - su(w[a])(+) AGAP003635 * * totally inside drongo(-) AGAP010189 * - swm(+) AGAP009601 * - CR32657(+) - - - CG4699(+) - * - CG2694(+) - * - CG6650(+) AGAP006394 * - CG1599(-) AGAP000700 * - CG9866(+) - * - ras(+) AGAP011133 * - CG6299(+) - * - CG1663(+) - * - shtd(-) AGAP000374 * - PGRP-LE(-) - * - ATP7(+) - * - CG11847(+) AGAP002680 * - inv(+) - - - CG17180(+) - * - mei-9(-) AGAP002805 * * totally inside CG7326(-) - * - CG6907(+) AGAP010407 * - CG7466(+) AGAP008185 * - CG11857(+) AGAP011996 * - CG13933(-) AGAP006608 * - CG18811(-) - * - ave(+) AGAP012177 * - chico(-) - * - CG12018(+) AGAP008910 * - CG3563(+) AGAP000146 * - CG10238(-) AGAP004290 * - CG5098(+) - * - CG11975(+) AGAP012792 * - chrw(-) AGAP006159 * - CalpA(+) AGAP012069 * - CG1172(+) AGAP002354 * - CG14224(+) AGAP004294 * - Tps1(+) AGAP008227 * - smid(+) AGAP006205 * - CG6597(+) AGAP002513 * - eIF-4E(-) AGAP007172 * - CG9393(-) AGAP003981 * - CG33347(+) - - - CG9904(+) AGAP003143 * * downstream par-6(+) AGAP010494 * * @ end and overlaps GATAd(+) - * - CG14478(+) - * - Scsalpha(+) AGAP001312 * - CG31922(+) AGAP010248 * - Hsp60(+) AGAP004002 * * downstream mRpS5(+) - - - tomboy20(-) - - - Srp54(+) AGAP002265 * - CG8979(-) AGAP007418 * - CG17574(-) AGAP007609 * - CG31431(+) AGAP004218 * - CG12016(+) AGAP006740 * - CG15220(-) AGAP010177 * - HDAC4(-) AGAP000410 * - Hsromega(+) - * - CG15627(-) - - - Art9(-) - - - GABA-B-R3(+) AGAP009514 - - Cortactin(-) AGAP004625 * - CG11664(+) - - - CG10051(+) AGAP007676 - - Tak1(-) - * - Brd8(+) AGAP003845 * - CG8199(+) AGAP003136 * - aur(+) AGAP001793 * - CG3409(-) AGAP005394 * * 8912 bp upstream flw(+) AGAP003114 * - CG1623(-) - * - NFAT(+) - * - snoRNA:Psi28S- 2648(-), - - - ms(3)K81(+) - * - MAPk-Ak2(-) AGAP011890 * - CG2941(+) - * - Pros35(+) AGAP010253 * - CG10086(+) - - - CG12115(-) - - - CG4930(+) - * - Deaf1(+) AGAP004905 * - CG10232(-) - - - CG11105(-) AGAP004258 - * totally inside CG1826(+) AGAP006714 * - a6(-) - * - CG14205(+) - - - CG2641(+) - - - CG13260(+) - - - nmo(+) AGAP005898 * - gbb(+) AGAP000824 * - CG2446(-) AGAP004286 * * 25320 upstream lqf(+) AGAP007396 * * totally inside CG2982(+) - * - disco-r(-) AGAP001106 - - CG32243(-) - * - SMC1(+) AGAP002947 * - mei-217(-) - * - mei-S332(+) - * - CG8121(+) AGAP008322 * - cul-5(-) AGAP002404 * - AnnIX(+) AGAP003790 * - Psf3(-) AGAP011132 * - CG6125(-) AGAP001531 * - alpha-Man-IIb(+) AGAP004020 * - Pep(-) AGAP004864 * - CG8630(+) - - - CG8979(-) AGAP007418 * - Hsc70Cb(+) AGAP010331 * * 91625 upstream Cpr12A(+) - - - CG10664(+) AGAP008727 * - CG11357(+) - * - CG8436(+) - * - nuf(+) AGAP010445 * - CG1461(+) AGAP000327 - - CG33679(+) - * - CG2926(-) AGAP010697 * - CG6841(+) AGAP005640 * * 7643 upstream rtet(+) AGAP001391 * - ncm(-) AGAP007874 * - pxt(+) - * - exd(+) AGAP004696 * * downstream Rab40(-) AGAP000841 * - CG17788(+) - * - CG3252(-) - - - Ppn(-) - - - bic(+) AGAP006614 * - CG3253(+) - * - spas(+) AGAP002334 * - CG2662(+) AGAP010081 * - CG9849(+) - * - CG8290(+) AGAP011746 * - Aats-asp(+) AGAP005576 * - Rad51D(+) AGAP006734 * - dj-1beta(+) AGAP000705 * - CG1837(+) AGAP000044 * - CG15362(+) AGAP007577 * - CG7849(+) AGAP002077 * - CG15611(+) - - - CG15245(-) - - - Sep5(-) - * - Anxb11(-) - * - CG4949(+) - * - CG2807(+) AGAP000178 * - CG9743(-) AGAP003051 - - CG3262(+) AGAP000577 * - Ntf-2(+) AGAP000498 * - Anp(+) - * - syt(-) AGAP007942 - - CG5169(+) AGAP009961 * - CG15626(-) AGAP008107 * - snoRNA:Psi28S- 2626(-), - * - tth(-) - * - Rab10(+) AGAP000671 * - Rad51C(+) - * - CG12926(-) - - - CG31731(+) AGAP001523 * - Rab11(+) AGAP004559 * - CG15251(-) AGAP000696 - - Pfrx(+) AGAP012010 * - CG10418(+) AGAP005136 * * downstream CG4239(+) AGAP000393 * CG6923(-) - * - CG2556(+) AGAP010972 * - CG1109(+) AGAP001362 * - CG3773(+) - * - CG11404(+) - - - Nrg(+) AGAP000720 * - CG6788(+) - * - CG9072(-) - - - lic(+) AGAP000310 * - Rrp46(+) AGAP002177 * - eIF-5A(+) AGAP011284 * - CG5941(+) AGAP003344 * - CG3056(+) - * - CG15735(+) AGAP002167 * - Amph(+) AGAP005076 * * totally inside rdgBbeta(-) AGAP004469 * - CG12194(+) AGAP009523 * - CG9203(-) AGAP004082 * - CG4078(+) AGAP000634 * - CG13865(+) - * - Act57B(+) - - - CG12057(+) - - - Rst(1)JH(+) - * - CG14030(+) - * - Galpha49B(+) AGAP005079 * - CG13151(+) AGAP002349 * - CG32543(+) - - - Tsp42Ec(+) - - - mys(+) AGAP000815 * - CG31495(-) - * - CG11873(+) - * - CG8097(+) AGAP003132 * - lrrk(+) - * - CG31477(+) AGAP000260 - - fal(+) AGAP006056 * * 86 bp upstream AGAP001169, * (AGAP001170, no Gr93a(+) AGAP001170 - other information) CG14457(+) AGAP000750 - - CG5116(+) AGAP003969 * - CG10062(+) AGAP007676 - - CG16817(+) AGAP011157 * - CG7800(+) - * - Rpt3(+) AGAP003008 * - ey(+) AGAP000063 * - CG3008(+) AGAP009993 * - Dot(+) - * - crl(+) AGAP002169 * - Gtp-bp(-) AGAP010894 * *17833 upstream CG8083(+) AGAP005988 - * 1136 bp upstream CG7045(+) - * - CG12728(+) - * - CG18749(+) - * - CG11268(+) AGAP001310 * - CG8974(-) AGAP006041 * - CG3363(+) - * - RpS10b(+) AGAP000739 * - M6(+) AGAP012018 * - Dap160(-) AGAP009037 * - CG4764(+) AGAP002338 * - ctp(+) AGAP001335 * - CG1847(+) AGAP012255 * - l(2)37Ce(+) - * - eIF6(-) AGAP001380 * - unc-13(-) AGAP000065 * - pan(+) AGAP012389 * - mRpL17(+) AGAP001865 * - CHOp24(+) AGAP004743 * - Sas(+) AGAP002579 * - sec23(+) AGAP001759 * - shi(+) AGAP003018 * - BCL7-like(+) AGAP000566 * - tRNA:CR32525(+) - - - snf(+) AGAP011637 * - CG32767(-) - * - CG40006(-) AGAP002738 - - Sgt(+) AGAP003052 * * 20952 upstream</p>