Table of Primers used to Amplify yellow Enhancer Fragments									
	Yellow Enhancer Sub-fragment	Species	Location Relative to Exons	Amplicon Length (bp)	Length Overlap with preceding Fragment (bp)	Length Overlap with following Fragment (bp)	Forward Primer*	Reverse Primer*	X-Y coordinates	
1	mel_A1	D. melanogaster	5' intergenic	948	NA	105	CTGAggcgcgccAGCTGTGACGTTTTCAATGC	GACTggcgcgccGACCAATCTCTTCAAGGCAAAC	(-3814) to (-2867)	
2	mel_A2	D. melanogaster	5' intergenic	1023	105	90	CTGAggcgcgccAATGGCGAAACTGGAAACAC	GACTggcgcgccGGAAAGCAAAGCCGAATACC	(-2972) to (-1951)	
3	mel_A3	D. melanogaster	5' intergenic	1005	90	85	CTGAggcgcgccAATGTCCAGGCTGCCATAAG	GACTggcgcgccATATCTCTTGGCCCAAATGC	(-2039) to (-1034)	
4	mel_A4	D. melanogaster	5' intergenic	1006	85	97	CTGAggcgcgccATTATGCGTGTGGCTGGTTG	GACTggcgcgccATTCGGGTGGTTCAGTGTTC	(-1119) to (-112)	
5	mel_A5	D. melanogaster	5' intergenic	423	97	171 with 5'UTR + 43 with coding region 	CTGAggcgcgccTGCGTGAAAATCAATCATGG	GACTggcgcgccAGGTGATCAGGGTCACAAGG	(-209) to (+214)	
6	mel_A6	D. melanogaster	intron	1008	40 with exon-1	74	CTGAggcgcgccGGCAATCGGTTATTCGTCAC	GACTggcgcgccAGGTGATCAGGGTCACAAGG	(+369) to (+1377)	
7	mel_A7	D. melanogaster	intron	996	74	97	CTGAggcgcgccGGCTGTATCGATTCAAAATGC	GACTggcgcgccTCAGTCCTAAAACCTCGCAAC	(+1303) to (+2300)	
8	mel_A8	D. melanogaster	intron	991	97	68 with exon-2	CTGAggcgcgccAAGGAGAACCTCAAGACAGTCG	GACTggcgcgccCGGAATTAGCTCCGGTGAAC	(+2203) to (+3194)	
9	pse_B1	D. pseudoobscura	5' intergenic	1003	NA	97	CTGAggcgcgccTAATTGCCACGAGTGGAGTG	GACTggcgcgccCTGTGACTGTGACCCAAACG	(-5016) to (-4013)	
10	pse_B2	D. pseudoobscura	5' intergenic	985	97	80	CTGAggcgcgccACCCCTGGCAAGAGTCAAC	GACTggcgcgccTTGTTGTTAGCCATTGTTTTGC	(-4110) to (-3125)	
11	pse_B3	D. pseudoobscura	5' intergenic	1052	80	108	CTGAggcgcgccAAGTACTCATTTGAAGGGCAAAG	GACTggcgcgccTCCGACATCATTTTCCATTG	(-3206) to (-2154)	
12	pse_B4	D. pseudoobscura	5' intergenic	1016	108	118	CTGAggcgcgccGTTTCGAATGCAGTTGTTGC	GACTggcgcgccCCGCCTGTCGAGTCTGTAAC	(-2262) to (-1246)	
13	pse_B5	D. pseudoobscura	5' intergenic	1012	118	79	CTGAggcgcgccTTAACAGACACCGCAGCAAC	GACTggcgcgccGCCGTGAGCTCTCTAAGCAG	(-1364) to (-352)	
14	pse_B6	D. pseudoobscura	5' intergenic	641	79	169 with 5'UTR + 41 with coding region	CTGAggcgcgccGAAACCTGGCCAAGCAATTC	GACTggcgcgccGCCGTCAAAGCTCCTATTCC	(-431) to (+210)	
15	pse_B7	D. pseudoobscura	intron	1033	53 with exon-1	90	CTGAggcgcgccAGTCGAGCACTTTGGCAATC	GACTggcgcgccTTGTAACAGCCTGCGTTGTG	(+381) to (+1414)	
16	pse_B8	D. pseudoobscura	intron	982	90	104	CTGAggcgcgccTGTATGTGGGGGTATTATATCTGG	GACTggcgcgccTTGGTAATCTTGTCGCATTG	(+1324) to (+2306)	
17	pse_B9	D. pseudoobscura	intron	1008	104	98	CTGAggcgcgccCGTTTCGGTCTCAGTTCCAG	GACTggcgcgccTGGGATCCGATCTTTAATGC	(+2202) to (+3210)	
18	pse_B10	D. pseudoobscura	intron	942	98	45 with exon-2	CTGAggcgcgccTCAGGCAGGTTTTCCTAAATG	GACTggcgcgccTCACACTGTGGTCCATGTTG	(+3112) to (+4054)	
19	will_C1	D. willistoni	5' intergenic	1013	NA	53	CTGAggcgcgccGGCCATTCATAAAGGTGGAA	GACTggcgcgccGCCTTCAACTCATTTAATTAGGC	(-5614) to (-4601)	
20	will_C2	D. willistoni	5' intergenic	1024	53	89	CTGAggcgcgccCAAGGTGACTATCCGATTAAACC	GACTggcgcgccTGTTGTTTAACGCAATTTGAGC	(-4654) to (-3630)	
21	will_C3	D. willistoni	5' intergenic	975	89	103	CTGAggcgcgccTGGAGACGAAGATGTGATGTG	GACTggcgcgccTGCATGATCATTTATGGAAAGG	(-3719) to (-2744)	
22	will_C4	D. willistoni	5' intergenic	1044	103	86	CTGAggcgcgccGCTACAAAATACGGGGAAGC	GACTggcgcgccATGATCACCATGTGGAATGC	(-2847) to (-1803)	
23	will_C5	D. willistoni	5' intergenic	1064	86	108	CTGAggcgcgccTCAGTTCAAGTTTCTTATGTTTTGC	GACTggcgcgccTGAACGAACAATTTAATTTGAAAAC	(-1888) to (-824)	
24	will_C6	D. willistoni	5' intergenic	1045	108	133	CTGAggcgcgccTTTGACACAATGTAAGTGTTAATCAG	GACTggcgcgccTTGAAATGAAGTTGGGAAGG	(-932) to (+113)	
25	will_C7	D. willistoni	5' intergenic	345	133	248 wth 5'UTR + 77 with coding region	CTGAggcgcgccCCCAACAAATTATGGCCAAC	GACTggcgcgccGCTGCTTCCAATTGATGGAC	(-20) to (+325)	
26	will_C8	D. willistoni	intron	1024	50 with exon-1	167	CTGAggcgcgccGGAACACTTTGGCAATCGTC	GACTggcgcgccTGAAAGCAAAAACTGAATGAGG	(+448) to (+1472)	
27	will_C9	D. willistoni	intron	1017	167	94	CTGAggcgcgccCCCATAGAAAGATAATGGAGTCAG	GACTggcgcgccTCGGGACAACAAAAACAACTC	(+1305) to (+2322)	
28	will_C10	D. willistoni	intron	1022	94	109	CTGAggcgcgccTTCAGAACCTTTTTAACCTTGG	GACTggcgcgccTCATTTGAAATTGGTGGAATTG	(+2228) to (+3249)	
29	will_C11	D. willistoni	intron	1063	109	50 with exon-2	CTGAggcgcgccTTCAAGTCAATTTATAGCAGACTGAG	GACTggcgcgccACCTGTCACGCTGTGATCC	(+3140) to (+4203)	
										
* Asc 1 restriction site shown in lower case. The four nucleotides preceding it are included to facilitate efficient restriction of the DNA.										
X=starting	Y=ending