it is not enough just  to have the same numbers of bases. The Tm is also determined by the order of the bases and the contribution of each base to the Tm is determined by its neighbouring bases and most calculations take the nearest neighbour base into consideration when calculating annealing temperature as well as the length, salt concentration ,secondary structure and base composition. The different methods of calculation explain why many commercial companies make and sell oligos but quote different annealing temperatures. The temperatures may differ quite a lot. A very  old paper compared 3 commonly used calculations of Tm for short GC rich oligos and they differed by over 20c in annealing temperatures

Hey!

In theory the energy needed for your primers remain the same, as the bases are the same - therefore, Tm should be the same. Anyway, you can check the Tm of your primers in online tools like this one: http://www6.appliedbiosystems.com/support/techtools/calc/index.cfm

Hope this helps! Best,

Renata

it is not enough just  to have the same numbers of bases. The Tm is also determined by the order of the bases and the contribution of each base to the Tm is determined by its neighbouring bases and most calculations take the nearest neighbour base into consideration when calculating annealing temperature as well as the length, salt concentration ,secondary structure and base composition. The different methods of calculation explain why many commercial companies make and sell oligos but quote different annealing temperatures. The temperatures may differ quite a lot. A very  old paper compared 3 commonly used calculations of Tm for short GC rich oligos and they differed by over 20c in annealing temperatures

You have already received great information from the above responders. 

Paul is correct, the local neighborhood does have an effect, and the paper he provided is a good one. So, if you do use an online Tm calculator, check the algorithm it uses. 

The easiest way to think of it is this: if the overall base composition was all that mattered, would an oligo with all A/T at one end and all G/C at the other end look the same at a given temperature (especially above the A/T melt temp.) as an oligo with the same base composition, but evenly dispersed A/T and G/C? 

Richard

Thank you all for kind explanations. I know they have difference based on sequence changes as Paul listed one good paper to explain this. However, I could not find published equation to estimate the range of difference of these sequence. Or in other words, I want to know the error of these two sequences in theory. It seems tough currently. 

if it is a practical calculation of the difference that you want you can just submit the 2 sequences to most oligo manufacturing companies online and they will have the latest formulae to calculate the Tm for oligos. For instance https://www.idtdna.com/calc/analyzer or the online address that Renata suggested