Embodiments of the present invention analyze a plurality of parallel channels and identify specific channel(s) that have skew outside of an acceptable skew error margin. In certain embodiments, this skew is identified by determining the timing misalignment between a channel under test and a deskew channel. Other channels within the plurality of channels are masked by transmitting a repeating masked bit pattern. This timing misalignment may be measured by comparing a segment within the channel under test to a corresponding segment within the deskew channel and identifying a time differential between the two segments.