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I know the Transpennine Express timetable used to be inconsistent, the trains leaving Liverpool Lime Street used to alternate between terminating at Hull, Scarborough, Middlesbrough and Sunderland. When First took over they made all trains from Liverpool go to Scarborough.
The trains leaving Manchester Piccadilly for Chester are similar leave at 15 and 24 minutes past the hour, but there are reasons for this such as Manchester to Chester via Newton-le-Willows trains have to co-ordinated with Liverpool to Manchester via Newton-le-Willows trains, as well as London to North Wales trains. Also the Chester to Manchester via Altrincham trains take longer so if they were co-ordinated at Manchester, they may not be at Chester.
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