By Christopher M. Matthews 

Prosecutors reversed their position on a key legal issue Friday, after a New York judge indicated their case against Sergey Aleynikov, the former Goldman Sachs Group Inc. programmer accused of stealing the bank's code, could be on thin ice.

Jurors in New York State court began deliberating over Mr. Aleynikov's fate Wednesday but have struggled with the decades-old laws under which he is charged with stealing Goldman's high-frequency trading code. The jury has sent repeated notes to Justice Daniel Conviser requesting clarifications on legal terms and asking to have his instructions on the law read back to them.

From Justice Conviser's view, the confusion stems from the fact that the prosecutors from the Manhattan district attorney's office refused to allow the jury to have a copy of his instructions on the law, often called the "charge." Mr. Aleynikov's lawyer had requested they have the charge, but under New York rules both sides have to agree to provide it.

"There's absolutely no question that it's impairing their ability to reach a fair and impartial verdict," Justice Conviser said late Friday afternoon after the jury requested another reading of the charge. "You should agree to give it to them."

Justice Conviser went a step further and said that while he thought prosecutors were acting in good faith he could potentially reverse any conviction on this issue. All discussions on the matter occurred outside the presence of the jury.

After a break, prosecutors said they would agree give the jury the charge, though they still held the reservations that caused them to oppose it--namely, that Justice Conviser's instructions are incomplete.

The trial, now in its third week, ended Friday without a verdict, deliberations will resume Monday.

Mr. Aleynikov's case has taken a long and winding road to reach the jury. He was initially arrested and charged by federal prosecutors in 2009 for allegedly stealing Goldman's high-frequency-trading computer code from bank computers during his last days at the firm. He was convicted in 2010 in federal court, imprisoned for a year, acquitted on appeal and then rearrested on state charges in 2012 by the Manhattan district attorney's office.

The district attorney dusted off laws written long before the advent of the computer age in their case against Mr. Aleynikov, and the lawyers, the judge and the jury have been wrestling with their application to this case's facts.

The trial has been unusual in that both sides almost entirely agree on what took place, but dispute whether New York state law applies. The three charged counts accuse Mr. Aleynikov of unlawfully using secret scientific material in order to appropriate the "major portion" of its economic value as well as duplicating it for his own use.

He faces up to four years in prison if convicted on all charges.

Both sides have furiously debated the meaning of the statute's language throughout the trial, an argument that continued even into the jury's deliberations.

After a note from the jury Friday asking for clarity on a legal definition, Justice Conviser asked prosecutors why they thought "the major portion" of the code's economic value didn't mean the majority of its value. No witnesses during the trial testified about precisely how much the code was worth, and Mr. Aleynikov's lawyer has argued his client didn't appropriate the major portion of its value because Goldman continued to use the code, and make money with it, long after Mr. Aleynikov left.

Prosecutors cited case law Friday that said two people could simultaneously possess the "the major portion" of something's economic value, such as a credit-card code, for example.

Justice Conviser said he was unconvinced and that they would continue the debate Monday.

Write to Christopher M. Matthews at christopher.matthews@wsj.com

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