In silico PCR tool

Virtual (in silico) or electronic PCR (ePCR) primer or probe search against whole genome(s) or a list of chromosomes - prediction of likely PCR products and search for potential mismatches of the specified primers or probes. Search for multiple targets simultaneously within a specified range. In silico oligonucleotide searching is useful for the discovery of target binding sites with melting temperature.

Degenerate primer sequences are also accepted. Each letter represents a combination of one or several nucleotides: B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T).

Upload or paste sequence(s) in FASTA format:

Amplicon detection:		C>>T bisulfite conversion
Minimal amplicon size (bp):		Show all matching sites of primer binding
Maximal amplicon size (bp):		Show amplicon sequences
Mismatches allowed in 3'-end:		Show only amplicons lengths

Run

Clear

To export the results: select all (Ctrl-A), copy (Ctrl-C) and paste (Ctrl-V).

С >> T bisulfite conversion (bisulfite modified genome)

Sequence, design of specific PCR primers for in silico bisulphite conversion for both strands - only cytosines not followed by guanidine (CpG methylation) will be replaced by thymines:

5’aaCGaagtCCCCa-3'        5’aaCGaagtTTTTa-3'
  |||||||||||||     ->      ||||||:|::::| 
3’ttGCttCaggggt-5'        3’ttGCttTaggggt