WASHINGTON: Pakistan says it wants an apology from the United States in order to jump-start a number of initiatives between the two countries that would help the hunt for al Qaeda in Pakistan and smooth the end of the war in Afghanistan.    Pakistan wants the US to apologise for a border incident in November 2011 in which the US killed 24 Pakistani troops in an air strike.

The US has expressed regret for the incident, a diplomatic step removed from an apology, and said it was a tragic case of mistaken identity, in which each side mistook the other for militants and both sides erroneously fired on the other.

Secretary of State Hillary Rodham Clinton even explored the possibilities of an apology with a Pakistani diplomat in a London meeting but then backed off when the Pakistanis insisted the apology be timed for maximum political impact.

The Pakistanis have put the apology at the top of a long list of demands to address what they see as insults to national pride and sovereignty—from the Navy Seal raid onto Pakistani territory last year that killed Osama bin Laden to the steady US drone strikes on Pakistani territory. A lot of these demands are now up in the air with the news Tuesday that Pakistan's high court had dismissed the prime minister, a move that could usher in months of turmoil in the country's government.

From the US point of view, Pakistan has not done enough to stop attacks on US troops carried out by the Taliban and members of the Haqqani clan.

So the two nominal allies are at a standoff. A look at what that means for the war and counter-terrorism efforts

Supply routes

Pakistan shut its borders to Nato re-supply convoys heading to Afghanistan because of the deadly November incident. The US and Nato had been trucking supplies in and out of the Afghan war zone from the Pakistani port of Karachi. The Pakistanis charged the US $500 per truck. Because the US has not apologised for the air strike, Pakistan has closed that route, and supplies to US and Nato troops have been taking a northern route that Defense Secretary Leon Panetta says is costing an extra $100 million a month now and could grow as the US starts to withdraw equipment in advance of the 2014 troop drawdown in Afghanistan. Negotiations have stalled over reopening the routes, mostly over the apology, and it's clear the Pakistanis plan to charge double or more to use their route if they reopen it.

Military aid  

For the Pakistanis, the impasse over the apology means other longstanding issues cannot be resolved, like the resumption of all US security aid to Pakistan. Pakistan still receives roughly $1.2 billion in annual security assistance, but last summer the US halted or suspended hundreds of millions of dollars in aid—and reimbursements to Pakistan for helping secure Afghanistan's border—over another dispute. That one was over Pakistan's irritation that the US didn't brief its leaders before launching the successful raid against bin Laden, who had been living for some time in the Pakistani garrison town of Abbotabad.

In retaliation, Pakistan expelled US military trainers, and the US cut off some aid.

Intelligence sharing

Fewer US and Pakistani military officers are sharing training or intelligence. They previously jointly operated mobile US intelligence centres throughout the Pakistani tribal areas, monitoring together information coming from US drones, which helped Pakistani troops track militants bent on killing inside Pakistan.

Now unilateral US drone strikes continue to bite at al Qaeda targets, with a recent strike killing al Qaeda deputy Abu Yahya al-Libi, while Pakistan is on its own when it comes to hunting the branch of the Taliban that sends suicide bombers to hit Pakistani military and civilian targets. Joint US-Pakistani efforts at one time helped take down dozens of targets that were dangerous to both sides, including mastermind of the Sept 11, 2001 attacks Khalid Sheikh Mohammed.

CIA operations

CIA officers once were able to roam fairly freely, often working together with Pakistan's intelligence operatives to go after targets in joint raids. Now, CIA officers are closely tracked and often harassed, and the Pakistani intelligence chief, who had been invited by the CIA, postponed his scheduled visit last month to the US.

The bitterness has taken on a personal tone. President Barack Obama kept Pakistani President Asif Ali Zardari waiting in a hallway at the Nato summit in Chicago and had him meet with Clinton instead of a leader-to-leader meeting. And Panetta, during a visit to Pakistan's arch rival, India, made a joke before an Indian audience about keeping the Pakistani government in the dark over the bin Laden raid.