Hi! I usually use Noplag Plagiarism Detection Software (Check the website: https://noplag.com/.) You can check your students thesis against Internet, publications and huge database of essays, articles, dissertations, coursework’s and many more. For example, you can also upload thesis in the following formats: doc, docx, rft, txt, odt, pdf and html, as well as you can copy and paste the thesis texts.. And after scanning you can share report with your students or download it.
There is one great anti-plagiarism software that I can suggest you - oxphrase.com.
You can check up to 30,000 words each time. It uses efficient word-count method that calculates your words carefully. Big spaces in your document will not be counted as words (e.g. it is enough for a book or Master/PhD thesis). You can upload text formats such as (Microsoft Word) [.docx] or (Adobe Acrobat) [.pdf]. You also can export readable PDF report. oxphrase is an accurate, fast and secure plagiarism checker for businesses, education and private use. They provide one month for free, you can try.
Since there is no guarantee that the original content of your manuscript might not be copied and sold to others before it is published by you, I discourage using any free-software-checkers for plagiarism; some of them are betrayers. On the other hand, I don't believe that there is a completely free one!
Furthermore, if you are insisting to use anti-plagiarism software, offline checker programs are better than online ones. If I were you, I prefer to use my own words instead.
In any way, it is not well for your reputation if there were accusations of plagiarism. This is because plagiarism is a sin! If it is, severe action may be taken and/or legal notice may be given.