ARS Candidate Finder
1. Upload genome
FASTA file
2. AT-rich or GC-rich regions
Choose region type
AT rich
GC rich
Minimum percentage
Maximum N percentage
Regions above this N percentage are removed. N does not receive a score.
Window size (bp)
Step size (bp)
Maximum score for this feature
3. Motif or regex search
Search by
Motif list
Regex list
Enter one motif or regex per line
[AT][AG]TTTATTTA[AT]
Select motif or regex to load an example.
Score for each match
Maximum score for this feature
4. AT or GC run length
Score rules
Example: 0-9:5, 10-15:10, 16+:20
Maximum score for this feature
5. Gap between AT or GC runs
Score rules
Example: 0-5:20, 6-10:10, 11+:5
Maximum score for this feature
6. Z-curve
Maximum score for this feature
The program calculates normalized Z-curve X, Y, Z and magnitude values.
7. Output sequence
Extra bases on each side
8. Number of candidates
Number of top candidates
9. Optional primer design
Find and rank primers for every selected candidate
Each ranked candidate has its own primer rules. Candidate output remains unchanged.
Primer highlight colour
Used for primers in Word and PDF reports. Default: dark orange.
Candidate region colour
Used for the original ARS candidate region in Word and PDF reports. Default: dark green.
Candidate 1 primer rules
Copy Candidate 1 settings to all
Min primer length
Optimal primer length
Max primer length
Min GC (%)
Max GC (%)
Min Tm (°C)
Optimal Tm (°C)
Max Tm (°C)
Max Tm difference (°C)
Protected flank (bp)
Min product size (bp)
Optimal product size (bp)
Max product size (bp)
Primer pairs to show
Failed primers to show
Show failed primers and reasons
Candidate 2 primer rules
Copy Candidate 1 settings here
Min primer length
Optimal primer length
Max primer length
Min GC (%)
Max GC (%)
Min Tm (°C)
Optimal Tm (°C)
Max Tm (°C)
Max Tm difference (°C)
Protected flank (bp)
Min product size (bp)
Optimal product size (bp)
Max product size (bp)
Primer pairs to show
Failed primers to show
Show failed primers and reasons
Candidate 3 primer rules
Copy Candidate 1 settings here
Min primer length
Optimal primer length
Max primer length
Min GC (%)
Max GC (%)
Min Tm (°C)
Optimal Tm (°C)
Max Tm (°C)
Max Tm difference (°C)
Protected flank (bp)
Min product size (bp)
Optimal product size (bp)
Max product size (bp)
Primer pairs to show
Failed primers to show
Show failed primers and reasons
Candidate 4 primer rules
Copy Candidate 1 settings here
Min primer length
Optimal primer length
Max primer length
Min GC (%)
Max GC (%)
Min Tm (°C)
Optimal Tm (°C)
Max Tm (°C)
Max Tm difference (°C)
Protected flank (bp)
Min product size (bp)
Optimal product size (bp)
Max product size (bp)
Primer pairs to show
Failed primers to show
Show failed primers and reasons
Candidate 5 primer rules
Copy Candidate 1 settings here
Min primer length
Optimal primer length
Max primer length
Min GC (%)
Max GC (%)
Min Tm (°C)
Optimal Tm (°C)
Max Tm (°C)
Max Tm difference (°C)
Protected flank (bp)
Min product size (bp)
Optimal product size (bp)
Max product size (bp)
Primer pairs to show
Failed primers to show
Show failed primers and reasons
The number of rule boxes follows “Number of top candidates”. Hairpin, self-dimer and cross-dimer results are shown as warnings and reduce ranking scores, but they do not automatically remove a primer pair.
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