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U.S. Border patrol agents called deputies to help after the boat was found near 27th Street just before 4 a.m.
Agents said they had been observing the boat first spotted north of La Jolla around 3:40 a.m. Once it was intercepted near Dog Beach, agents said they found 18 to 20 bales of a narcotics aboard.
No weapons were found on the boat.
Two people, the only passengers on the boat, were taken into custody.