TFBS Motif Finder

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Find Motifs! Clear all previous analysis
1. Search for User-Defined Motifs
2. Select from Comprehensive List of Motifs
3. Select Motifs from Stress Categories
4. Select Motifs from Families
Add Sequence Merge Previous GEvo Analysis (paste in URL): Merge
Change order by dragging boxes
Sequence 1: Display Order
Sequence 1 Options
Sequence 2: Display Order
Sequence 2 Options
Open all sequence option menus Walk all sequences left Walk all sequences right
Apply distance to all CoGe submissions?      Pad CoGe Sequences with additional sequence:
E-mail GEvo results?
Alignment Algorithm:
Match Score (-r):
Mismatch Penalty (-q):
Gap Open Penalty (-G):
Gap Extension Penalty (-E):
Word Size (-W):
Filter query sequence (DUST/SEG) (-F):
Expectation value (-e):
Other Blast Parameters:
Other options:
Minimum HSP length for finding overlapped features:
Image Width (Pixels):
Feature Height (Pixels):
Padding between tracks (Pixels):
Color GC content green? (SLOW)
Color masked and unsequenced NTs?
Color wobble codon GC content:
Color contigs red:
Auto adjust overlapping features?
Auto adjust overlapping HSPs (SLOW)?
Draw high-quality images? (SLOW)
Color features overlapped by HSPs?
Color matches in HSPs?
Label HSPs?
Label Genomic Features?
Labels font size:
Don't show HSPs with overlaps
Don't show HSPs that are shorter than nt. (0 means no limit)
Draw: Models
Show preloaded annotations?
Restrict motif finding to annotations above?
Change HSP colors (Click Color to Adjust)
HSP 1 color: