* Ugandan troops fight with Seleka in C. African Republic
* Seleka denies links with LRA, accuses Uganda of looting
* Any ties likely local, rather than strategic -analyst
By Elias Biryabarema and Crispin Dembassa-Kette
KAMPALA/BANGUI, July 1 (Reuters) - Uganda's army said on Tuesday the mainly Muslim Seleka group in Central African Republic was now its enemy as the fighters were "in bed" with the Lord's Resistance Army (LRA) rebels they are hunting there.
A spokesman for the Ugandan army said its forces in CAR had clashed for the first time with Seleka, killing 12 and suffering one casualty. A Seleka official told Reuters on Monday that 15 of their fighters and three Ugandan soldiers were killed.
"Seleka had never tasted our fire. I think it was important that they taste our fire so that they are careful," Paddy Ankunda, spokesman for Uganda People's Defence Forces (UPDF) said, when asked about clashes on Sunday and Monday in CAR.
The LRA, led by Joseph Kony, is using CAR as one of its rear bases for attacks across regions straddling CAR, South Sudan and the Democratic Republic of Congo.
Uganda heads a 5,000-strong African Union force tracking down the rebels but has no specific mandate to confront Seleka, which seized power in CAR in March last year and was pushed out under international pressure in January.
"We know we don't have that mandate but since they are in bed with our enemy, we'll treat them as such," said Ankunda, accusing Seleka of forcing civilians to give food and medicine to the LRA and trading ivory and minerals with them.
Seleka's time in power in Bangui was marked by rights abuses, prompting mainly Christian self-defence militia to spring up across the country. Nearly a million people - around a quarter of the population - have been forced from their homes in cycles of sectarian violence.
Tit-for-tat killings continue and Seleka fighters still occupy pockets of the country.
Colonel Christian Djuma Narkoyo, deputy spokesman for Seleka's armed wing, dismissed Uganda's claims as "lies."
"If they have proof, let them show it. ... There is no reason for us to collaborate with the LRA," he said.
Narkoyo accused Uganda's troops, whose mission to hunt down LRA fighters across the region has received support from U.S. Special Forces, of plundering CAR for gold, diamonds and ivory.
U.S. State Department spokesman Will Stevens said Washington was aware of reports of incidents between Ugandan forces and Seleka rebels, but added that "U.S. forces were not present during the incident, nor were they involved in the planning or support of the Ugandan mission that may have led to the incident."
Independent researcher Ledio Cakaj, who specialises in monitoring LRA activity, said some members of the LRA and Seleka had been in contact over the last year in CAR but there was no formal relationship, largely as both groups are very fragmented.
Cakaj said the relationship was more about protecting local and personal interests than a strategic alliance. LRA fighters have sought sanctuary and food in the area, while Seleka leaders hoped to get diamonds, gold and ivory in return, he said.
(Additional reporting and writing by David Lewis; Additional reporting by Lesley Wroughton in Washington; Editing by Robin Pomeroy and Jan Paschal)