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Sample queries:




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Specify genomic region to search
Search whole genome
Search near gene:

 Gene (CG or flybase symbol):

Upstream flanking sequence (bp):

Downstream flanking sequence (bp):

Specify clustering filter
No clustering filter (50kb max, can't be used with whole genome search)
Use clustering filter:

 min_sites:

wind_size:

Return non-conserved clusters?

Specify motifs to plot (from cis-analyst TFs)
bcd (CG1034) site_p:
cad (CG1759) site_p:
ftz (CG2047) site_p:
ftz-f1 (CG4059) site_p:
hb (CG9786) site_p:
kni (CG4717) site_p:
Kr (CG3340) site_p:
Su(H)-hi (CG3497) site_p:

User-defined motifs

User-defined motifs can be specified either by entering a collection of example sequences (formats 1-2) or by entering a frequency matrix (format 3) into the fields below. You can also upload text files using these same formats.

Note: Searches will be very slow the first time you search using a new motif, but the motif will then be cached and subsequent runs will be normal speed.

All three examples below correspond to the same binding motif (Knirps motif as described in Small, et. al., Dev Biol 1996). Key aligned residues are in red.

Format 1
Aligned sequences

> seq1
AACTAGATCA
> seq2
AAAGAGAGCA
> seq3
AACGCGGCCA
> seq4
AAGTAGATCA
> seq5
AACTAGCGCA

Format 2
Unaligned sequences

> seq1
AGTAAACTAGATCAGCC
> seq2
AAAGAGAGCAAG
> seq3
GAACGCGGCCAA
> seq4
AAGTAGATCA
> seq5
AACTAGCGCAATTT

Format 3
Frequency matrix

A| 5 5 1 0 4 0 3 0 0 5
C| 0 0 3 0 1 0 1 1 5 0
T| 0 0 0 3 0 0 0 2 0 0
G| 0 0 1 2 0 5 1 2 0 0
Motif #1 : Sequences already aligned?
 site_p:
Upload file:


Motif #2 : Sequences already aligned?
 site_p:
Upload file:


Motif #3 : Sequences already aligned?
 site_p:
Upload file:


Motif #4 : Sequences already aligned?
 site_p:
Upload file:



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last modified Jan 16 2005 10:48:56 by benb Questions, Comments, Suggestions to: benb@fruitfly.berkeley.edu