Working with DNA evidence, San Francisco homicide inspectors believe they have cleared the only person police ever named as a suspect in the Zodiac killings that terrorized the Bay Area three decades ago.

Genetic traces from envelopes that contained the serial killer's apocalyptic and police-taunting letters in the 1960s appear to have cleared a school teacher and child molester whom Vallejo police and others once identified as the Zodiac, according to inspectors Kelly Carroll and Michael Maloney.

"Arthur Leigh Allen does not match the partial DNA fingerprint developed from bona fide Zodiac letters," said Carroll.

Allen was named by Vallejo Police Capt. Roy Conway as his department's Zodiac suspect after Allen's death at age 58 in 1992.

Maloney and Carroll, who took over the cold case investigation in 2000, also said they recently discovered additional evidence in the Zodiac case that may soon allow them to create a full DNA profile of the Zodiac, who killed five Bay Area residents in 1968 and 1969.

The killer, who struck in Solano and Napa counties and in San Francisco, sent coded letters announcing his crimes.

The killer's taunting messages to police -- "This is Zodiac speaking" and "I am in control of all things" -- have recently been compared to the tarot card message left for police by the sniper who has killed eight and wounded two more in the Washington, D.C., suburbs.

"I am God," was scrawled across the tarot card of death found near the scene where a 13-year-old schoolboy was shot and critically wounded.

The Zodiac sent 21 letters about his crimes to Bay Area newspapers in the late 1960s. Each was signed with a cross within a circle. His crimes and cryptograms baffled police and fascinated amateur detectives for three decades.

Books have been written and Web sites are maintained -- all with theories about who the killer might have been.

The serial killer's known crimes began with the fatal shooting of two Vallejo teenagers on their first date. He then killed two other people, one in Vallejo and another in Napa County, before his final homicide, an execution- style slaying of a San Francisco cab driver in October 1969.

"When I die, I will be reborn in paradice (sic) and the (word missing) I have killed will become my slaves," one of his coded letters stated.

LETTERS TO NEWSPAPERS

Several envelopes in which those letters were mailed to newspapers, including The Chronicle, allowed the San Francisco police DNA lab headed by Dr.

Cydne Holt, to reach its new conclusions.

Although they had been analyzed for handwriting and traditional fingerprints, DNA analysis, Carroll pointed out, "was science fiction back in 1969."

An effort was made to DNA-test the letters six years ago, with inconclusive results. But powerful new technology has been developed since.

Holt retrieved saliva traces beneath a stamp and was able to replicate a DNA sample large enough to test.

That sample was compared to brain tissue recovered from the 1992 autopsy of Allen, who was identified as the elusive killer in two books by Robert Graysmith, the most recent of which, "Zodiac Unmasked," was published this year.

Vallejo police had originally zeroed in on Allen, a former teacher and trailer park resident, after the first two Zodiac killings when an acquaintance told officers that Allen fantasized about committing mass murder. Until the end of his life, Allen denied he was the Zodiac, or that he had killed anybody.

"This damned thing has been haunting me for 22 years," Allen told an interviewer in 1991. "The only thing in my favor is, I've never killed anyone."

10-HOUR LIE-DETECTOR TEST

Since he was targeted as a Zodiac suspect in 1971, Allen told a reporter in 1991, he had been fingerprinted, interrogated, made to give handwriting samples and subjected to a 10-hour Justice Department lie-detector test.

Despite the fact that he passed every evidentiary test, he said, Vallejo police subjected his home to a search again some 20 years later -- taking handguns, some explosives and his Zodiac brand watch.

Inspectors Carroll and Maloney say the new DNA lab results eliminate Allen as the person who licked the envelopes and stamps from the confirmed Zodiac letters.

And now, say the inspectors, they may have evidence that will lead to the killer's identity.

"We have something we haven't had to this point, a partial DNA fingerprint, " said Carroll. "It is not enough at this time to submit" to DNA databases of known criminals, he said, but other new evidence that is still being analyzed, "may yield more useable DNA" within weeks or months.

In April, Maloney and Carroll found three other Zodiac letters, all dated July 31, 1969, that had not previously been in possession of the San Francisco Police Department. Evidence from the case, Carroll pointed out, has been "fragmented" among different law enforcement agencies.

"They had been overlooked for a period of time and were essentially rediscovered a few months ago," Carroll said. One of those envelopes has now been subjected to genetic testing without yielding useable results, and two remain to be tested.

Informed of the scientific tests that appear to clear the man he named as a suspect, author Graysmith, a former Chronicle editorial cartoonist, commented: "I've always wondered if there wasn't more than one person involved, someone running interference for Allen. It's what makes it one of the great mysteries of all times."

Indeed, since the Zodiac's first killings, police in the four jurisdictions where he killed, as well as investigators for the state and the FBI, have checked out an estimated 2,500 suspects without making an arrest.

Carroll said testing could proceed faster except that the SFPD laboratory is understaffed and underfunded and has a backlog of cases. "There are tremendous demands on Dr. Holt's extremely limited resources."

E-mail the author at mikeweiss@sfchronicle.com.