Bowtie got different alignments for fliped paired-end

[狗熊趴趴]

Chaps I encountered this problem while I was trying to process our paired-end sequencing data with Bowtie. If I flip the paire-end files for option -1 and -2, I got very different alignment! Intuitively, I had thought flipping the paired-end should give the same alignment? And what if the paired-ends are not indexed? Has anyone ever handled in the same question before?

Here is an example:
bowtie -v 3 -k 1 hg18/hg18 --fr -c -1 GGTCATCCT -2 ACGGGTCGT
bowtie -v 3 -k 1 hg18/hg18 --fr -c -2 GGTCATCCT -1 ACGGGTCGT

Thank you