I've taken the conference champions and the top at-large teams into the field of forty eight; there are another sixteen bubble teams that have been placed in the play-in bracket. Some of the teams in the six through nine seeds of what I think of as the tournament per se may prefer being put in the play-in tournament, but it seems to me that the somewhat weaker (and not too much that) competition isn't enough to compensate for the single-elimination format. These teams are probably better off trying to win three of four in their brackets than trying to win four of four against the other play-in teams. You also may note that I have Pittsburgh against Miami in the second round, i.e. there's not a lot of concern here for conferences.
seedRedWhiteBlue Play-in
1KansasMarylandDukeStanford
2AlabamaCincinnatiOklahomaMichigan St
3ArizonaConnecticutPittsburghWake Forest
4MarquetteGonzagaIllinoisUCLA
5Mississippi StKentuckyGeorgiaNotre Dame
6IndianaFloridaMiami-FloridaNC State
7Southern CalCaliforniaOregonSt John's
8XavierOhio StTexasUtah
9Oklahoma StTexas TechHawaiiTulsa
10San Diego StKent StWestern KyWisconsin
11PennCreightonCentral ConnMississippi
12DavidsonUNC WilmingtonValparaisoPepperdine
13UC Santa BarbaraMcNeese StHamptonMissouri
14Murray StFlorida AtlIll-ChicagoBoston College
15MontanaBoston UHoly CrossSouthern Illinois
16SienaAlcorn StWinthropCharlotte
Presented in more of a "bracket" order:
1KansasMarylandDukeStanfordquarterfinalsemifinalfinal
16SienaAlcorn StWinthropCharlotte
8XavierOhio StTexasUtah
9Oklahoma StTexas TechHawaiiTulsa

4MarquetteGonzagaIllinoisUCLAquarterfinal
13UC Santa BarbaraMcNeese StHamptonMissouri
5Mississippi StKentuckyGeorgiaNotre Dame
12DavidsonUNC WilmingtonValparaisoPepperdine

2AlabamaCincinnatiOklahomaMichigan Stquarterfinalsemifinal
15MontanaBoston UHoly CrossSouthern Illinois
7Southern CalCaliforniaOregonSt John's
10San Diego StKent StWestern KyWisconsin

3ArizonaConnecticutPittsburghWake Forestquarterfinal
14Murray StFlorida AtlIll-ChicagoBoston College
6IndianaFloridaMiami-FloridaNC State
11PennCreightonCentral ConnMississippi
but remember that the three main brackets continue to play games after the first loss, even though that's not represented above.

Missouri beats Stanford, and Southern Illinois beats NC State; Missouri wins the final round of the play-in tournament. This, and other fourth-round results, are reflected in the first column of the table below; note that (aside from Missouri and Southern Illinois) every team in that first column has already lost a game.

round of 16quarterfinalssemifinalsfinals
KansasKansasKansas
MissouriMissouri
Southern Ill
Kent St.Kent St.Kent St.
Texas Tech
PittPittsburgh
Texas
Illinois--
ArizonaArizona
Marquette
Connecticut--
Miss St.Miss St.
Penn (or 'bama)
MarylandMaryland
HawaiiHawaii
W Kentucky
XavierXavierDuke
USC
DukeDuke
Oregon
OklahomaOklahomaOklahoma
CaliforniaCalifornia
Ohio St.
Indiana--
CincinnatiCincinnati
Gonzaga