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Will it be an issue if the signature on my AN form does not match the one on previous applications/etc? I noticed on the UKVI SAR form it said the signature must match the one that they hold for you in their records.

Problem is I applied for DCPR and also did B1 English test at Trinity College using my old passport from 2006 as ID and I haven't used the signature in it since 2008. I managed to near enough match the signature for both with some practice attempts

I now have a new passport with my new signature which is significantly different from the old one. Should I include a short covering letter with the AN explaining that I changed my signature a long time ago? I was going to send new and old passports anyway

I think sending a quick explanation with the application is a good idea. Just in case you get an overzealous caseworker
It shouldn't be a problem though, especially if you are sending both passports with your application.