Penalise trailing gaps with Bowtie2. Assume forced end-toend

Question

[anonymous]

I would like to know what options I can use to Bowtie to to penalise this scenario

query......: | . | . | . | | | | | | | CAGCACTAGCGC | | | | | | | | | |

reference: ATCGATCGCTCAGCACTAGCGCTCAGCATCAG

(the dots are only to align the two sequenced, | represent effectively gaps in the start and end of the reference)

Over this scenario

query......: CAGCACTAGCGC

reference: CAGCACTAGCGC

Thanks