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Plaistow’s Jack Pepin, of Atkinson Resort and Country Club, picks up his ball on the 14th green during the final day of the NHGA Junior Championship held at Beaver Meadow Golf Club in Concord on Wednesday. Pepin won the championship by three strokes.

CONCORD — It was the start Jack Pepin was hoping for.

Pepin, a 16-year-old Plaistow resident who will be a junior at Timberlane Regional High School in the fall, entered the final round of the New Hampshire Golf Association’s Boys’ Junior Championship in a three-way tie for first place, but birdied the first two holes in Wednesday’s final round at Beaver Meadow Golf Course, finished the round with a 1-under-par 71 and won the championship flight with a three-day total of 219.

Pepin, who was representing Atkinson Resort and Country Club, improved his score on each day of the tournament. He opened with a 75 on Monday and put himself in good position with a 73 Tuesday. He finished three strokes ahead of Brookline resident Colin McCaigue and four ahead of Atkinson’s Matt Gover.

“Feels great,” Pepin said. “(The strong start) definitely helped, because I knew I could make the putts and the shots that I needed. The back nine was pretty stressful. There were a lot of shots that I hit that didn’t go right, but they weren’t so far off that I couldn’t make par.”

Pepin’s stress level may have peaked when he was walking to the 15th green and realized McCaigue was within two shots of the lead. Pepin responded by making a 14-foot birdie putt on the par-4 15th that allowed him to play a little more conservative over the final three holes.

“It was definitely a tough round, especially when you have the lead because you need to make sure you don’t make a mistake that kind of compromises your lead,” Pepin said.” I did that pretty well today.”

Like Pepin, McCaigue shot a 1-under-par 71 Wednesday, but said a poor back nine during his round of 75 Tuesday ended up costing him a shot at the tournament championship. He began Wednesday’s final round trailing the leaders by three strokes.

“The first couple days I was hitting the ball pretty well but the putting wasn’t there, and today a lot of those putts started to fall and that represents itself in my score,” McCaigue said. “I hit the ball pretty solid the whole week. You always want something more, but if the putts fell the first two days I would have been around par all three days, which would have been nice.

“(Tuesday) I was even through 13 and I was playing pretty well and I unfortunately went out of bounds on hole 14 and ended up making double (bogey). One bad swing cost me a few strokes there. Then I made one bogey coming in. If I had to put a location on it I would say the back nine of the second round kind of got away from me a little bit.”

McCaigue, who was playing out of Amherst Country Club, will be a senior at the Derryfield School in Manchester this fall.

“I’m pretty satisfied with my performance,” he said. “I would have liked to get the win, but it was my first time in this tournament. My goal was to finish in the top three and I accomplished that.”

Laconia Country Club’s Evan Rollins and North Conway Country Club’s Ben Dougherty each had a share of the lead entering Wednesday’s final round. Rollins finished in a tie for fourth with Amherst Country Club’s Gunnar Senatore. Both had a three-day total of 225. Dougherty was sixth at 226.

Thomas Murdough of Bald Peak Colony Club won the first flight with a 233, and Concord Country Club’s Jason Howe won the second flight with a 250.