Are there any tools that support wobble-base pair alignment?

Question

[Renqing]

I have a requirement:
I have an siRNA sequence about 17 nt in length, and I want to perform alignment at the transcriptome level to identify off-target sequences (sequences with up to 3 mismatches). I would like G-T wobble-base pairs not to be considered as mismatches. Is there a tool that can achieve this? Currently, my idea is to replace G with A and T with C in the siRNA sequence and use Bowtie for sequence alignment.

Thanks!!!