You are not alone! I'm sure we are all on the same boat. ?
I'm sure you still have a chance if your grades/test scores are good. But, if you can afford it, I would consider applying to some master's programs! The deadlines for master's programs are usually in January/February, so you would still have time to draft application essays and let your letter writers know that you are applying to more schools. I just graduated with a master's degree, and I think it helped me a TON in terms of gaining more research experience and becoming a more competitive applicant. Though I am still nervous and scared about what will happen, I definitely feel a lot more confident than I would have if I applied straight out of undergrad. I have a publication, several poster presentations, and experience working in a variety of research labs on my resume. I think that research experience is important to admission committees just as much as research fit, so I would consider master's programs as a back-up option to gain that extra experience if you were to not gain admission into a doctorate program right away.
Are you thinking of publishing your honors thesis in the future? If not, I would consider talking to your advisor about that! Having plans to publish your research I'm sure will also help you out.