I could swear that when I used mummer(nucmer) in the past, with the default -mum option, it would not find any hits off of the main diagonal, for the simple reason that there can be no unique seeds off of the main diagonal. However now I am seeing that off-diagonal hits are found. I'm not sure what version of mummer I'm using, unfortunately…but is this possible?
By default, mummer now runs in "-mumreference" mode, which only forces matches to be unique in the reference (and not necessarily the query). That may be contributing to what you see. You can switch back to full uniqueness with the -mum option. Also, if the "off diagonal" hits show up in mummerplot as blue, they are reverse complement hits, which often appear off diagonal.
Ah, yes I think they are reverse complement hits! Thank you. But I think for a self-alignment the first issue, regarding mumreference, is not relevant is it? Because if reference and query are the same, then uniqueness in query is the same as uniqueness overall.
That's right. When aligning something against itself, mum or mumref shouldn't make a difference.
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