ExonSurfer

Custom Transcript Selection

Select species

Upload file

Indicating exon-exon junctions

Exon-Exon junctions must be indicated in the fasta header using the format:
>SEQUENCE_NAME POS_1 POS_2 POS_3

Download sample files

Click to download sample files in fasta or genbank format to check the required header format.

Primer Parameters

Parameter	Min	Opt	Max
GC content (%)
Melting temperature (°C)
Maximum difference in Tm
Length (bases)
Number of primer pairs to design:	High (3000 pairs) Middle (1000 pairs) Low (100 pairs)
Primer junction design:	Primers spanning exon junctions Primers spanning or flanking exon junctions
Minimum 3' overlap with junction
Minimum 5' overlap with junction
Maximum self-binding at 3’ end:
Maximum pair 3’ end complementarity
Maximum 5' self complementarity
Maximum 5' complementarity
Maximum hairpin Tm

Amplicon Parameters

PCR Parameters

BLAST Parameters

Parameter	Value
Maximum E-value
Minimum percentage of identity (%)
Maximum off-target size (bases)

Assign design parameters