Naive question about Cuffdiff log

[corenimo]

I have been looking at posts about following question and could not find a convincing answer.

In the logs generated by cuffdiff , we saw following lines:
-----------------------
Map Properties:
> Normalized Map Mass: 24669329.12
> Raw Map Mass: 22464890.18
> Number of Multi-Reads: 487240 (with 1308767 total hits)
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 141.07
> Estimated Std Dev: 44.85
--------------------

Here does fragment length refers to the size between two pairs, or length of total fragment, including both reads and insert between them.

For this specific example, if I have 80 bp reads at each side, does that mean they overlap, or is there 140 bp in the middle?

Thanks

[sdriscoll]

it means they overlap. most tools talk about insert size or fragment length which means the full length of the aligned fragment. mine usually overlap as well.