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I have done a branch checkout on master but magit rectangle is on origin/master and not only on master.

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Quoting the manual:

Magit displays references in logs a bit differently from how Git does it.

Local branches are blue and remote branches are green. Of course that depends on the used theme, as do the colors used for other types of references. The current branch has a box around it, as do remote branches that are their respective remote's HEAD branch.

If a local branch and its push-target point at the same commit, then their names are combined to preserve space and to make that relationship visible. For example:

origin/feature
[green][blue-]

instead of

feature origin/feature
[blue-] [green-------]

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