BEDTools software is useful for working with downloaded REDfly data in BED format

Galaxy might be a better solution for those with limited computational know-how.
Look for tools to work with REDfly data in Galaxy to be added to this site in the future.

Utility script: SelectSmallestFeature.py Use this Python script with REDfly CRM sequences in sorted BED fortmat to cluster any overlapping sequences and select the set of shortest non-overlapping intervals from each cluster.
Helpful for constructing SCRMshaw training sets and other uses.

FlyBase maintains a list of links and resources here including listings of Transcription Regulation Databases and Gene Expression Databases

FlyMine

modENCODE project
Cavalli Lab TrxG & PcG ChIP-chip browser

Bergman lab curated motif models
CORE core promoter database (Juven-Gershon lab)
Dan Pollard's matrices
Drosophila Core Promoter Database
Drosophila melanogaster Major Position Matrix Motifs (DMMPMM)
EvoPrinterHD
FlyEnhancer (Stark lab)
FlyFactorSurvey
FlyLight (Janelia Farms)
OnTheFly
The JASPAR datbase
The Transfac database
UniProbe database (Bulyk lab)

BDGP embryonic in situ database
FlyExpress embryonic in situ expression pattern search engine
Krause Lab Fly-FISH embryonic in situ database