% The 230 FFLs (plus two pseudo-FFLs) in the network. The classification following 
% cite [2] of the supplement, does not apply to FFLs with one or more dual links.
% X-operon	Y-operon	Z-operon	FFL-type
crp	araC	araBAD	-
crp	araC	araE	Coh-1
crp	araC	araFGH	Coh-1
crp	araC	araJ	-
fnr	arcA	acnA	-
fnr	arcA	aldA	-
fnr	arcA	caiTABCDE	-
fnr	arcA	cydAB	-
fnr	arcA	cyoABCDE	-
fnr	arcA	dcuC	-
fnr	arcA	focA-pflB	-
fnr	arcA	gadAX	-
fnr	arcA	moeAB	-
fnr	arcA	ndh	-
fnr	arcA	nuoABCEFGHIJKLMN	-
fnr	arcA	pdhR-aceEF-lpd	-
fnr	arcA	sdhCDAB--sucABCD	-
fnr	arcA	sodA	-
fnr	arcA	tpx	-
fnr	arcA	yfiD	-
arcA	betIBA	betT	Inc-2
crp	caiF	caiTABCDE	Coh-1
crp	caiF	fixABCX	Coh-1
fnr	caiF	caiTABCDE	Coh-1
fnr	caiF	fixABCX	Coh-1
cysB	cbl	tauABCD	Coh-1
nlpD-rpoS	cmk-rpsA-ihfB	dps	Coh-1
nlpD-rpoS	cmk-rpsA-ihfB	osmE	Inc-1
nlpD-rpoS	cmk-rpsA-ihfB	osmY	Inc-1
nlpD-rpoS	cmk-rpsA-ihfB	pstSCAB-phoU	Coh-1
nlpD-rpoS	cmk-rpsA-ihfB	yeiL	Coh-1
cpxRA	csgDEFG	csgBAC	Coh-2
nlpD-rpoS	csgDEFG	csgBAC	Coh-1
crp	cytR	cdd	-
crp	cytR	deoCABD	-
crp	cytR	mutY-yggX-mltC-nupG	-
crp	cytR	nupC	Inc-1
crp	cytR	ppiA	-
crp	cytR	rpoH	-
crp	cytR	tsx	-
crp	cytR	udp	Inc-1
fnr	dcuSR	dcuB-fumB	Coh-1
fnr	dcuSR	frdABCD	Coh-1
narXL	dcuSR	dcuB-fumB	Coh-2
narXL	dcuSR	frdABCD	Coh-2
crp	dgsA	malT	-
crp	dgsA	manXYZ	-
crp	dgsA	ptsG	-
crp	dgsA	ptsHI-crr	-
argP	dnaAN-recF	nrdAB	Coh-1
cmk-rpsA-ihfB	dusB-fis	acs-yjcH-actP	-
cmk-rpsA-ihfB	dusB-fis	ndh	-
cmk-rpsA-ihfB	dusB-fis	nirBDC-cysG	Coh-3
cmk-rpsA-ihfB	dusB-fis	nrfABCDEFG	Coh-3
cmk-rpsA-ihfB	dusB-fis	nuoABCEFGHIJKLMN	Inc-3
cmk-rpsA-ihfB	dusB-fis	ygjG	-
crp	dusB-fis	acnB	-
crp	dusB-fis	acs-yjcH-actP	-
crp	dusB-fis	aldB	-
crp	dusB-fis	bglGFB	-
crp	dusB-fis	glnALG	-
crp	dusB-fis	guaBA	-
crp	dusB-fis	hupA	-
crp	dusB-fis	marRAB	-
crp	dusB-fis	metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp	-
crp	dusB-fis	nirBDC-cysG	-
crp	dusB-fis	nrdAB	-
crp	dusB-fis	pdhR-aceEF-lpd	-
crp	dusB-fis	proP	-
crp	dusB-fis	ptsG	-
fldA-fur	fecIR	fecABCDE	Coh-2
crp	fldA-fur	cyoABCDE	Inc-1
crp	fldA-fur	entCEBA-ybdB	Inc-1
crp	fldA-fur	fepA-entD	Inc-1
crp	fldA-fur	fiu	Inc-1
crp	fldA-fur	flhDC	Inc-1
crp	fldA-fur	sdhCDAB--sucABCD	Coh-1
crp	fldA-fur	sodA	Inc-1
oxyR	fldA-fur	sufABCDSE	Inc-1
soxS	fldA-fur	sodA	Inc-1
flhDC	fliAZY	flgAMN	Coh-1
flhDC	fliAZY	fliDST	Coh-1
flhDC	fliAZY	fliE	Coh-1
flhDC	fliAZY	fliFGHIJK	Coh-1
flhDC	fliAZY	fliLMNOPQR	Coh-1
crp	gadAX	gadBC	Coh-2
gadE	gadAX	gadBC	Coh-1
gadW	gadAX	gadBC	Coh-2
nlpD-rpoS	gadAX	gadBC	Coh-1
nlpD-rpoS	gadE	gadAX	Coh-1
nlpD-rpoS	gadE	gadBC	Coh-1
nlpD-rpoS	gadE	hdeAB	Coh-1
fnr	gadW	gadAX	Inc-2
crp	galS	galETKM	-
crp	galS	galP	Inc-1
crp	galS	mglBAC	Inc-1
galR	galS	galETKM	-
galR	galS	galP	Inc-2
galR	galS	mglBAC	Inc-2
dusB-fis	glnALG	ygjG	-
lptB-rpoN-yhbH-ptsN-yhbJ-npr	glnALG	astCADBE	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	glnALG	glnHPQ	-
lptB-rpoN-yhbH-ptsN-yhbJ-npr	glnALG	glnK-amtB	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	glnALG	nac	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	glnALG	ygjG	Coh-1
crp	glpEGR	glpABC	Inc-1
crp	glpEGR	glpD	Inc-1
crp	glpEGR	glpFKX	Inc-1
crp	glpEGR	glpTQ	Inc-1
dusB-fis	hns	bglGFB	Coh-3
dusB-fis	hns	nirBDC-cysG	Coh-3
dusB-fis	hns	rrsB-gltT-rrlB-rrfB	Inc-1
crp	hupA	galETKM	-
cmk-rpsA-ihfB	hypABCDE-fhlA	hycABCDEFGHI	Coh-1
fnr	hypABCDE-fhlA	hyfABCDEFGHIJR-focB	Inc-3
lptB-rpoN-yhbH-ptsN-yhbJ-npr	hypABCDE-fhlA	fdhF	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	hypABCDE-fhlA	hycABCDEFGHI	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	hypABCDE-fhlA	hydN-hypF	Coh-1
lptB-rpoN-yhbH-ptsN-yhbJ-npr	hypABCDE-fhlA	hyfABCDEFGHIJR-focB	Coh-1
crp	idnDOTR	idnK	Coh-1
crp	idnDOTR	gntKU	Inc-1
gntR	idnDOTR	idnK	Coh-2
gntR	idnDOTR	gntKU	Inc-2
rpoE-rseABC	lptB-rpoN-yhbH-ptsN-yhbJ-npr	rpoH	Coh-1
crp	malI	malXY	-
crp	malT	malEFG	Coh-1
crp	malT	malK-lamB-malM	Coh-1
crp	malT	malPQ	Coh-1
crp	malT	malS	Coh-1
crp	marRAB	sodA	Coh-1
soxS	marRAB	acrAB	Coh-1
soxS	marRAB	fpr	Coh-1
soxS	marRAB	fumC	Coh-1
soxS	marRAB	inaA	Coh-1
soxS	marRAB	micF	Coh-1
soxS	marRAB	nfo	Coh-1
soxS	marRAB	poxB-ltaE-ybjT	Coh-1
soxS	marRAB	pqiAB	Coh-1
soxS	marRAB	sodA	Coh-1
soxS	marRAB	zwf	Coh-1
cpxRA	mdtABCD-baeSR	acrD	Coh-1
crp	melR	melAB	-
metJ	metR	metE	Coh-2
crp	nagBACD	chbBCARFG	-
crp	nagBACD	manXYZ	-
crp	nagBACD	nagE	-
crp	nagBACD	nanC-yjhT	-
fnr	narXL	adhE	Coh-4
fnr	narXL	aspA-dcuA	Coh-4
fnr	narXL	cydDC	Inc-4
fnr	narXL	dcuB-fumB	Coh-4
fnr	narXL	dcuSR	Coh-4
fnr	narXL	dmsABC	Coh-4
fnr	narXL	fdnGHI	-
fnr	narXL	focA-pflB	Coh-4
fnr	narXL	frdABCD	Coh-4
fnr	narXL	hcp-hcr	Inc-4
fnr	narXL	moeAB	Coh-2
fnr	narXL	napFDAGHBC-ccmABCDEFGH	Coh-4
fnr	narXL	narGHJI	Inc-4
fnr	narXL	narK	Inc-4
fnr	narXL	nirBDC-cysG	Inc-4
fnr	narXL	norVW	Inc-2
fnr	narXL	nrfABCDEFG	-
fnr	narXL	nuoABCEFGHIJKLMN	Coh-2
modEF	narXL	dmsABC	Coh-3
modEF	narXL	napFDAGHBC-ccmABCDEFGH	Inc-1
arcA	nlpD-rpoS	acnA	Coh-2
arcA	nlpD-rpoS	caiTABCDE	Inc-4
arcA	nlpD-rpoS	gadAX	Inc-4
arcA	nlpD-rpoS	hyaABCDEF	Inc-4
crp	nlpD-rpoS	acnA	-
crp	nlpD-rpoS	aldB	-
crp	nlpD-rpoS	caiTABCDE	-
crp	nlpD-rpoS	csgDEFG	-
crp	nlpD-rpoS	csiD-ygaF-gabDTP	-
crp	nlpD-rpoS	csiE	-
crp	nlpD-rpoS	gadAX	-
crp	nlpD-rpoS	gadBC	-
crp	nlpD-rpoS	galETKM	-
crp	nlpD-rpoS	glgS	-
crp	nlpD-rpoS	lsrACDBFG	-
crp	nlpD-rpoS	mglBAC	-
crp	nlpD-rpoS	mpl	-
crp	nlpD-rpoS	osmY	-
crp	nlpD-rpoS	proP	-
crp	nlpD-rpoS	sohB	-
cmk-rpsA-ihfB	ompR-envZ	flhDC	-
cmk-rpsA-ihfB	ompR-envZ	micF	Coh-2
cmk-rpsA-ihfB	ompR-envZ	nmpC	Inc-2
cmk-rpsA-ihfB	ompR-envZ	ompC	Coh-2
cmk-rpsA-ihfB	ompR-envZ	ompF	-
crp	ompR-envZ	csgDEFG	-
crp	ompR-envZ	fadL	-
crp	ompR-envZ	flhDC	-
crp	ompR-envZ	nmpC	-
crp	ompR-envZ	ompF	-
crp	oxyR	fldA-fur	Coh-1
arcA	pdhR-aceEF-lpd	lldPRD	Coh-2 (pseudo-FFL)
arcA	pdhR-aceEF-lpd	yfiD	Coh-4 (pseudo-FFL)
crp	pdhR-aceEF-lpd	yfiD	-
fnr	pdhR-aceEF-lpd	yfiD	-
crp	prpR	prpBCDE	Coh-1
rcsB	rcsA	bdm-sra	Coh-1
rcsB	rcsA	flhDC	Coh-3
rcsB	rcsA	mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ	Coh-1
rcsB	rcsA	osmB	Coh-1
rcsB	rcsA	osmC	Coh-1
rcsB	rcsA	wza-wzb-wzc-wcaAB	Coh-1
crp	rhaSR	rhaBAD	Coh-1
crp	rhaSR	rhaT	Coh-1
cpxRA	rpoE-rseABC	bacA	Inc-4
cpxRA	rpoE-rseABC	degP	Inc-4
cpxRA	rpoE-rseABC	dsbC-recJ-prfB-lysS	Inc-4
cpxRA	rpoE-rseABC	psd-yjeP	Coh-2
cpxRA	rpoE-rseABC	smpA	Coh-2
cpxRA	rpoE-rseABC	yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE	Inc-4
cpxRA	rpoE-rseABC	yidQ	Inc-4
crp	rpoH	dgsA	-
crp	rpoH	gapA	-
crp	rpoH	grpE	-
lptB-rpoN-yhbH-ptsN-yhbJ-npr	rpoH	ibpAB	Coh-1
rpoE-rseABC	rpoH	rfaDFCL	Coh-1
soxR	soxS	fumC	Coh-1
crp	uxuR	gntP	Inc-1
crp	uxuR	uidABC	Inc-1
crp	uxuR	uxuAB	Inc-1
exuR	uxuR	uxuAB	Inc-2
crp	xylFGHR	xylAB	Coh-1
cmk-rpsA-ihfB	yiaJ	yiaKLMNO-lyxK-sgbHUE	Coh-4
crp	yiaJ	yiaKLMNO-lyxK-sgbHUE	-
lptB-rpoN-yhbH-ptsN-yhbJ-npr	zraSR	zraP	Coh-1