I am not very familiar with gel analysis software but to distinguish differences that small you would need a very good size standard (and top quality reproducible acrylamide gels ) with many close size points such as a sequencing reaction run in the same capillary as your sample to have any confidence that these small differences are real. Sequencing or DHPLC would be appropriate but single base differences are difficult unless they disrupt a restriction site

Hi,

I agree with comments of Paul above....these differences are 1 base so you need to have a sequencing type resolution with appropriate size standards..

 I would agree with all of the previous contributors. In order to find and analyze bands of such a small difference, I would suggest modifying the separation methods to allow for the greatest amount of separation possible. Toufic has a good point, in that there are a lot of good tools out there that you can use for image analysis of a gel and if you can see a difference with the eye, then there will be a difference detected by the software. I personally have experience with Image Lab by Bio-Rad. Overall, a fairly simple program to use, especially with Bio-Rad Chemi-Doc apparatus.

Again, I would stress for greatest resolution and quantification, ensure the greatest amount of separation between bands and have a good standard that can be used. 

Thank you all for your help,

I tried to use Image Lab software, but I have a problem with the image format. My images are JPEG which are not supported by the software. How can I convert them?