how tophat2 selects paired reads alignment

[lpantano]

Hi,

I was wondering how tophat2 selects the best hits for paired read data.

If u have read1 mapping to location1 perfectly, and read2 to a location1+inner side but with one mismatch. And also read2 maps to location2 perfectly.

Do you know if tophat2 will give you read1 in location1 and read2 in location2 because are the best hits, or it will give the read1 and read2 in location1?

thanks a lot!