Aug 14 (Reuters) - Alphabet's early bet on SpaceX has multiplied more than 100-fold, with the Google parent disclosing a stake worth about $94 billion at the end of June compared with the $900 million investment it said it made in Elon Musk's rocket company in 2015.

Alphabet has emerged as by far the largest single institutional holder of SpaceX following its $86 billion IPO in June, according to a Reuters analysis of quarterly filings made public so far.

The filings shed new light on the scale of positions acquired by SpaceX's backers as the company transitioned from a closely held startup to a publicly traded giant. Together with separate public disclosures on early investments, including Alphabet's, they also highlight how dramatically the value of some early investments in SpaceX has grown.

Because the 13F filing data is compiled once per quarter and disclosed within six weeks of quarter-end, the information is dated and will not capture any buying or selling done by these large investors since June 30. There are other limitations as well, given the vast universe of SpaceX investments and the evolving schedule of when they stand to become eligible to be sold in public markets.

"It's very, very difficult to tease out which of these institutions were holding pre-IPO shares," said Steve Sosnick, market strategist at Interactive Brokers.

Alphabet is an exception because the company publicly disclosed that it invested $900 million in SpaceX in 2015, providing a rare benchmark against which to compare the value of its current holding.

Alphabet did not immediately respond to a request for comment.

Sosnick added that the 13F filings did not reveal investors' lockup status or intentions with respect to realizing profits on pre-IPO positions.

Alphabet held 551.2 million SpaceX shares at the end of the second quarter, according to the firm's filing, worth about $94.2 billion at SpaceX's June 30 share price of $170.86.

At Wednesday's price, Alphabet's disclosed position would be worth about $81.8 billion, still about 90 times the size of Google's original investment.

Gigafund Management was a distant second in the ranks of SpaceX institutional investors with a position of 171.8 million shares, followed by Baillie Gifford with 51.4 million, BlackRock ( BLK ) with 51 million and Ontario Teachers' Pension Plan with 50.7 million.

Together with Alphabet, these five holders accounted for the lion's share of all SpaceX shares reported in the 13F reports filed as of Thursday afternoon and analyzed by Reuters, highlighting the concentration of reported institutional ownership among a handful of investors.

SpaceX went public on June 12 at $135 a share. Its shares have since retreated from their end-June level. SpaceX closed at $146.15 on Wednesday, 8.3% above its IPO price but 14% below the June 30 close.

Sosnick told Reuters that SpaceX remains one of the most actively traded stocks among customers at Interactive Brokers, receiving a "fresh jolt of buying last week when market fears about what would happen when the first lockup expiry arrived proved to be unfounded."

Retail owners of SpaceX shares, who do not have to submit their holdings to the SEC, turned into net sellers of the stock on Friday for the first time since the IPO, according to data from Vanda Research.

The research firm, which tracks the activity of self-directed individual investors, calculated that this group sold a net $4.5 million on that day. SpaceX shares were down 3% on Thursday but have risen 30% since August 5.