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I am using emacs win32 on cygwin. and I encountered this commonly seen 'replace tab with space ' issue on emacs. but slightly different.

I have configured like this:

(setq tab-width 4)
(setq indent-tabs-mode nil)

this works well for Pressing Tab. but some times I need to align a block of python code with Shift + > and using this key combination, I still get the Tab characters in the underlying document.

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What is Shift + > bound to? (And how do you even type that?) Check what the command bound to that key sequence (whatever it is really) is doing. There likely is either a way to tell it to use SPC chars instead or a hook to let you untabify afterward. –  Drew Apr 22 at 14:56
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