The counting method for TPs and FPs. All hits to the 'orange' segments count as FPs. Only one hit within A, B, or C counts as a TP for a unique position of TSS (for example, three hits within C will count only as one TP). Note that all TSS locations that were mutually different were considered as valid reference TSSs. So, alternative TSSs were considered different TSSs. Each of these had to be predicted. If one prediction falls on the intersection of A and B, then that prediction identifies two TSS locations (one that correspond to TSS related to A, and the other corresponding to TSS related to B). In other words, one prediction correctly identifies all reference TSS locations within the distance criterion.
Bajic et al. Genome Biology 2006 7(Suppl 1):S3 doi:10.1186/gb-2006-7-s1-s3