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For example, why was the 19th Shuttle mission named STS-51F instead of something more obvious like STS-19?

Side note: One reason I'm asking is because in the DVD commentary of Apollo 13, Tom Hanks or someone like that mentioned that after that mission, "you won't find the number 13 anywhere in official NASA titles or launch date/times" (my rough paraphrasing). Not quite sure if this is true, although it seems to be for Space Shuttle missions at least.

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Wikipedia has a good summary of this.

STS-1 to STS-9 were numbered sequentially by order of launch, then it switched to a number based on fiscal year (5 for FY 1985), launch site code (1 for KSC, 2 for Vandenberg), and letter. The letters were assigned sequentially at the time of planning, but schedule slips etc meant that they were not launched in this order.

After Challenger they dropped this system, and returned to a numeric STS-xx name. As with the letter codes, these were assigned sequentially but got out of sequence as time went on and schedules were moved around - the first flights were 26, 27, 29, 30, 28...

(The STS-xx numeric codes were still used internally during the "letter sequence", referring to the specific payload/mission rather than the launch, but these wouldn't usually be public. This meant that there were some duplicates on internal paperwork, eg two STS-26s, and so the new ones were sometimes listed as STS-26R.)

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    $\begingroup$ Excellent answer. Mostly it was KSC processing who kept the number codes; JSC switched to the weird fiscal codes. $\endgroup$ – Organic Marble Jan 3 '16 at 18:06
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    $\begingroup$ @OrganicMarble Ah, the many idiosyncrasies of splitting up the bureaucracy for the sake of more state votes. Oh what a tangled web is woven for us! $\endgroup$ – DrZ214 Jan 3 '16 at 18:22

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