In the past decade or so, it has become far more common to find certain trains that have a mix of general manifest (box cars, covered hoppers, lumber, etc) along with intermodal. BNSF's QSPOALT, which runs from Spokane, WA to Alliance, TX, is an example of such a train. The front half of the train is general manifest, but the second half is mixed TOFC and COFC.
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