WITH Waits AS
    (SELECT
        wait_type,
        wait_time_ms / 1000.0 AS WaitS,
        (wait_time_ms - signal_wait_time_ms) / 1000.0 AS ResourceS,
        signal_wait_time_ms / 1000.0 AS SignalS,
        waiting_tasks_count AS WaitCount,
        100.0 * wait_time_ms / SUM (wait_time_ms) OVER() AS Percentage,
        ROW_NUMBER() OVER(ORDER BY wait_time_ms DESC) AS RowNum
    FROM sys.dm_os_wait_stats
    WHERE wait_type NOT IN (
        'CLR_SEMAPHORE', 'LAZYWRITER_SLEEP', 'RESOURCE_QUEUE', 'SLEEP_TASK',
        'SLEEP_SYSTEMTASK', 'SQLTRACE_BUFFER_FLUSH', 'WAITFOR', 'LOGMGR_QUEUE',
        'CHECKPOINT_QUEUE', 'REQUEST_FOR_DEADLOCK_SEARCH', 'XE_TIMER_EVENT', 'BROKER_TO_FLUSH',
        'BROKER_TASK_STOP', 'CLR_MANUAL_EVENT', 'CLR_AUTO_EVENT', 'DISPATCHER_QUEUE_SEMAPHORE',
        'FT_IFTS_SCHEDULER_IDLE_WAIT', 'XE_DISPATCHER_WAIT', 'XE_DISPATCHER_JOIN', 'BROKER_EVENTHANDLER',
        'TRACEWRITE', 'FT_IFTSHC_MUTEX', 'SQLTRACE_INCREMENTAL_FLUSH_SLEEP',
        'BROKER_RECEIVE_WAITFOR', 'ONDEMAND_TASK_QUEUE', 'DBMIRROR_EVENTS_QUEUE',
        'DBMIRRORING_CMD', 'BROKER_TRANSMITTER', 'SQLTRACE_WAIT_ENTRIES',
        'SLEEP_BPOOL_FLUSH', 'SQLTRACE_LOCK')
    )
SELECT
    W1.wait_type AS WaitType, 
    CAST (W1.WaitS AS DECIMAL(14, 2)) AS Wait_S,
    CAST (W1.ResourceS AS DECIMAL(14, 2)) AS Resource_S,
    CAST (W1.SignalS AS DECIMAL(14, 2)) AS Signal_S,
    W1.WaitCount AS WaitCount,
    CAST (W1.Percentage AS DECIMAL(4, 2)) AS Percentage,
    CAST ((W1.WaitS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgWait_S,
    CAST ((W1.ResourceS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgRes_S,
    CAST ((W1.SignalS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgSig_S
FROM Waits AS W1
    INNER JOIN Waits AS W2 ON W2.RowNum <= W1.RowNum
GROUP BY W1.RowNum, W1.wait_type, W1.WaitS, W1.ResourceS, W1.SignalS, W1.WaitCount, W1.Percentage
HAVING SUM (W2.Percentage) - W1.Percentage < 95; -- percentage threshold
GO

SELECT  
	[Impact] = (avg_total_user_cost * avg_user_impact) * (user_seeks + user_scans),  
	[Table] = [statement],
	[CreateIndexStatement] = 'CREATE NONCLUSTERED INDEX ix_' 
		+ sys.objects.name COLLATE DATABASE_DEFAULT 
		+ '_' 
		+ REPLACE(REPLACE(REPLACE(ISNULL(mid.equality_columns,'')+ISNULL(mid.inequality_columns,''), '[', ''), ']',''), ', ','_')
		+ ' ON ' 
		+ [statement] 
		+ ' ( ' + IsNull(mid.equality_columns, '') 
		+ CASE WHEN mid.inequality_columns IS NULL THEN '' ELSE 
			CASE WHEN mid.equality_columns IS NULL THEN '' ELSE ',' END 
		+ mid.inequality_columns END + ' ) ' 
		+ CASE WHEN mid.included_columns IS NULL THEN '' ELSE 'INCLUDE (' + mid.included_columns + ')' END 
		+ ';', 
	mid.equality_columns,
	mid.inequality_columns,
	mid.included_columns
FROM sys.dm_db_missing_index_group_stats AS migs 
	INNER JOIN sys.dm_db_missing_index_groups AS mig ON migs.group_handle = mig.index_group_handle 
	INNER JOIN sys.dm_db_missing_index_details AS mid ON mig.index_handle = mid.index_handle 
	INNER JOIN sys.objects WITH (nolock) ON mid.OBJECT_ID = sys.objects.OBJECT_ID 
WHERE (migs.group_handle IN 
		(SELECT TOP (500) group_handle 
		FROM sys.dm_db_missing_index_group_stats WITH (nolock) 
		ORDER BY (avg_total_user_cost * avg_user_impact) * (user_seeks + user_scans) DESC))  
	AND OBJECTPROPERTY(sys.objects.OBJECT_ID, 'isusertable') = 1 
ORDER BY [Impact] DESC , [CreateIndexStatement] DESC

quote:

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1) Are the files sitting on the same drive layout as before? i.e dat,log,tempdb
2) Have you analysed the query on the timeout? Have you checked the Execution Plan?
3)Is there any anti-virus ?
4)Check for high levels of blocks\deadlocks

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