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Do bear in mind that writers of letters of reference know how the game is played and they may be willing to change what they write based on where you apply.
For example, they might write a far stronger letter to a poorly ranked program, because they don't want to lie to their friends in a top ranked program and pretend you are good, but they have no problem with passing you off as good to others. (This happens on the job market as well)
Hence the importance of asking letter writers what category of institution you should apply to and if they can strongly support you to that category.
Of course, if your letter writers completely don't care about you at all, then the above is moot. It is only relevant if they care, but they still think you're not a strong candidate. Then they might be quite willing to help you get to some category of program that you are a good match for.
Writing a falsely strong letter only has a cost when the letter writer cares about their reputation with the recipients. Hence I think many letter writers have a generic perfectly nice letter for use for the private sector, etc (where they typically don't care what use you put it to) but worry more about telling the truth if you apply to their own PhD granting institution.
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