Contradicting Tm - (Jan/28/2007 )
I pasted the nucleotide sequence of my primers into the oligonucleotide calculator in the Biotool when I was designing my PCR primers.  The Tm resulted from the program was pretty satisfactory, in the range of 56-60 oC.  
However, when I received my primers from the company, the Tm for my primers were basically far lower than what I got from the oligonucleotide calculator in Biotool.  They turned up to be in the range of 50-53 oC.  
Why?????????  I am very curious to know the reasons behind.   
Thank you.
well there are several method of calculating tm
base stacking
basic 
salt adjusted 
I am sure there are several ways to calculate each method.
The only "true" way to know a Tm is by experimental testing. The programs are just predictions based on various algoritims, but generally give a good idea of the approximate Tm. I have seen these prediction programs vary up to 10 degrees in the calculation of a primer Tm.
Thank you for your replies, perneseblue and tap14.  
Now I understood.  
And I also managed to get my PCR product from doing gradient PCR this morning.  Apparently, the Tm gave by the company is correct.  
