Hello, it is so easy :

First : go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch

Second : enter your primer and forward sequences primer in the top box with following format : "forwardprimernnnnreverseprimer" example : "ACATGCCGTCACCnnnnCACTTGAATTGCAC"

please bear in mind that reverse primer must be entered as the reverse complement. You can use http://reverse-complement.com/

Third : click blast button at the bottom and wait until the result appear.

fourth : click the top one in the result as it has the most similarity. Than just substracting the range1-range2.

It is very helpful : https://www.youtube.com/watch?v=04t6PbopFas

BLAST the 2 primer sequences at NCBI and you will get a number of good hits for perfect homology. 2 of these will be on the same chromosome in different orientations within about 1000 bases of each other. Subtract the base position of the 5' base on each primer and you will have the size of the amplimer.

Hello, it is so easy :

First : go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch

Second : enter your primer and forward sequences primer in the top box with following format : "forwardprimernnnnreverseprimer" example : "ACATGCCGTCACCnnnnCACTTGAATTGCAC"

please bear in mind that reverse primer must be entered as the reverse complement. You can use http://reverse-complement.com/

Third : click blast button at the bottom and wait until the result appear.

fourth : click the top one in the result as it has the most similarity. Than just substracting the range1-range2.

It is very helpful : https://www.youtube.com/watch?v=04t6PbopFas

Hi,

If your target is the human genome, it will be better to check the primers via in silico PCR (https://genome.ucsc.edu/cgi-bin/hgPcr). There, after entering the primers, you can choose the appropriate parameters for your PCR and run a figurative PCR and see the possible product(s). I've found this more practical than blast server of NCBI.

Good luck :)

If you know the nucleotide position of the forward primer and that of the reverse primer you simply subtracte them to get the PCR bp product. So, if forward primer position is 1001-1023bp and that of the reverse is 1400-1380bp then the PCR product will be 400bp.

Thanks Lantip for your answer. Thanks Maryam for the information 

Thanks Dr. Serag. I got the position of the primers from blast so it will be easy to determine the target bp.

If you know the nucleotide position of both the primers, than the distance between them is expected amplicon size. If not, BLAST analyse both the primers in NCBI and check the gene sequence to which both primers has hits. In that particular gene sequence, locate where exactly the forward and reverse sequence is present. Now count the number of nucleotides present in between.  

Hello!

We have designed primers,  which were used for a PCR reaction. We obtained a PCR product size of about 1180 pb (even for the positive control). when sequencing those PCR products, they correspond to the cibled gene.

The problem is when I check the insilico expected size either by alignement or one of the technics suggested above or by using the next program which is so useful as well (http://www.bioinformatics.org/sms2/pcr_products.html). the expected size was completely different (it was about 1395 pb?!

Can someone help me to solve that?

Hello, it is very easy

in simple words you can subtract position of reverse primer from forward primer pluse 1 in the matching of intended gene location will obtain amplicon size in bp.

Hint// all opinions of researcher are expirt

good luck

Hanane Djenane

if you just use primers for PCR reaction i.e gene detection you can send me you gene (s) and I will design a suitable primer, but if you use primers for SNP the design is govern in a restricted condition.

or even you can sen the primers which you are designed to check by me or any other researchers

good luck and be hopeful 

 Charith Raj Adkar-Purushothama

sir i did it but i tells almost  525 in my sequence but when i do it using any software the answer is 473 for my sequence,,, why is it so?

possibly one of your primers can anneal further inside the expected site if the annealing temperature is too low in pcr. Alternatively the amplimer has 2 regions of homology and forms a loop so  runs at an unexpected size in agarose gel. If you blast the sequenced amplimer does it match exactly the expected gene or is there a gap in the sequence and have you checked that the primers were designed off the same species as was used in the blast search. When you sequenced was it from both ends as you do not get sequence of the primer or within about 30 bases of the primer with Sanger sequencing so if you only sequence from one end it will always look too short

Thanks Prof Rutland for the nice contribution

You may primer blast:

https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome

add accession number. and then you can find PCR product size and other info.

http://www.bioinformatics.org/sms2/pcr_products.html

the above site you can enter and can calculate the exact product size of the selected primers, you should get the whole gene sequence from the NCBI 

Thanks Dr. Danial

While designing PCR primers make sure whether DNA or RNA sequence is used. If you use RNA sequence for designing the primers and try to amplify DNA by PCR, you might expect longer length than expected because DNA contains introns.

 Thanks Zanan

I recommend this website.

http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgPcr

you just text forward and resever primer, then submit it.

Good luck

http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgPcr

This website isn't designed for all organisms. For example, plants are absent.

Hi, I have primer annealing temperature which is 52°c and pcr product 1000bp but I don't know which program I can use to do it?

BLAST the sequences of both primer within available gene sequence and you will get a number of amplifier after the calculation of base sequences between the primers .

Hi, first of all you can calculate the amplicon by many methods, but if need to calculation depending primer sequence you can apply the equation as bellow

amplicon size (bp)= Reverse primer position in genome - Forward primer sequence in genom + 1

sure you can making matching for your primer in the general sequence of your intended gene

Thank you

Hi Ramadan!

This video will help you a lot https://www.youtube.com/watch?v=rlK-5joOlyU

A very fruitful dicsuccsion

The in silico PCR function of genome browser is even easier for this purpose, just enter the sequence of your primers and it will give you the sequence of the final PCR product directly:

https://genome.ucsc.edu/cgi-bin/hgPcr