Cuffcompare *.refmap results

[mhadidi2002]

Hello,

I used cuffcompare to compare a reference GFF file with another cufflinks GFF file. When I looked at the *refmap file, there are 2 possibilities in the third column, = or c. according to the manual, = is fully matched, I supposed that this means that the coordinates are exactely the same; the exact same start and exact same end positions, but unfortunately this wasn't the case.

I would like to know what is the threshold (number of nucleotides) that can be varied between each of the 2 start and 2 end positions of both genes?

Thanks in advance,

Best,