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New experimantal implementation for Highcharts 4.1 is available at http://jsfiddle.net/gh/get/jquery/1.7.2/highslide-software/highcharts.com/tree/master/samples/highcharts/studies/alignthresholds/.
This implementation looks a the threshold on the primary axis (the one first defined), and aligns the threshold of any following axis to that of the primary axis.
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Function does not work when there is no 0 in the yAxis (all values are negative)