Names, Cytological Positions in Drosophila melanogaster,and Accession Nos. of NonCoding Sequences Used in This Study
| Intergenic locus | Cytological position | Drosophila melanogaster | Drosophila virilis |
| achaete-scute † | 1B1 | AL024453/AL023873 | AF060607/AF132809 |
| Antennapedia | 84B1 | AC001655 | M95827 |
| bride of sevenless | 96F9 | AC019700 | L08132 |
| brown | 59E2-3 | AC005639 | L37035 |
| decapentaplegic † | 22F1-2 | AC004369/AC019923 | U95037/X81976 |
| dopadecarboxylase † | 37C1 | AC007176 | X05065/Johnson et al. 1989 |
| D-mef2 | 46C1-2 | AC014124/AC014416 | Cripps et al. 1998; Gajeweski et al. 1997 |
| e74 | 74F1 | AC019594 | X59493 |
| engrailed | 48A2 | AC020381 | Kassis et al. 1989 |
| frmf-amide | 46C1-2 | AC015179 | AH000028 |
| fused | 17C5-7 | AE003509 | U20586 |
| fushi tarazu | 84B1 | AE001573 | Schier and Ghering 1993 |
| glass | 91A1 | AC014473 | U39746 |
| hairy † | 66D10 | AC014797 | AF329639/AF329640/Langeland and Carroll 1993 |
| hunchback | 85A6-11 | U17742 | S70575 |
| knirps | 77E2 | AC020104 | L36177 |
| paramyosin | 66D14 | AE003554 | AJ243069 |
| prospero | 86E3 | AC013194/AC012748 | AF190404 |
| runt | 19E2 | AE003570 | Wolff et al. 1999 |
| tailless | 100B1 | AC014779 | AF019361 |
| teashirt † | 40A1-4 | AC006467 | McCormick et al. 1995 |
| tinman † | 93E1 | AC020256 | Lee et al. 1997; Xu et al. 1998 |
| troponin T | 12A1-4 | AC014434 | AJ002263 |
| twist | 59C3 | AC005975 | Pan et al. 1994 |
| wingless | 27F1-2 | AC017528 | AF046865 |
| zerknullt | 84A5 | AC002512 | L17339 |
| Intronic locus | Cytologic position | Drosophila melanogaster | Drosophila virilis |
| Antennapedia | 84B1 | AC001655/AC020267 | M95827/M95828 |
| bride of sevenless | 96F9 | AC019700 | L08132 |
| corkscrew | 2D3 | AC017610 | U22356 |
| decapentaplegic | 22F1-2 | AC019923 | U63855 |
| engrailed | 48A2 | AC020381 | Kassis et al. 1986 |
| glass | 91A1 | AC014473 | U39746 |
| Gpdh | 26A7-9 | AC017294 | D10697 |
| hunchback | 85A6-11 | U17742 | X15395 |
| knirps | 77E2 | AC020104 | L36177 |
| miniparamyosin | 66D14 | AE003554 | AJ243070 |
| myosin light chain | 98A6 | AC013071 | L08053 |
| paralytic | 14D1-E1 | AC014944 | U26718 |
| pdm-2 | 33F1-2 | AC006470 | U14723 |
| prospero | 86E3 | AF190403 | AF190405 |
| rough | 97D5 | AC014838 | M35372 |
| sevenless | 10A2 | AC017584 | M34544 |
| single minded | 87E1 | AC020412 | AF071932 |
| Staufen | 55B4-5 | AC004336 | AF225924 |
| tinman | 93E1 | AC020256 | Yin et al. 1997 |
| trithorax | 88B1-2 | AC013943 | Z50038 |
| vestigial | 49D3-4 | AC014851 | Williams et al. 1994 |
[i] If a GenBank accession no. is not indicated, the data has been obtained from the primary reference or by personal communication. A dagger indicates that more than one pair of contigs were surveyed for that locus.