Why does the alignment position detected by Probe Match tool differ from the probe interrogation position information associated with the probe sequence record?
The probe interrogation position, provided with the probe sequence information, indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns (the 13th base of a 25mer probe). The position information generated by the Probe Match tool is strictly based on the alignment against the query (input) sequence. Because the consensus/exemplar may not be co-linear with your input sequence, the probe interrogation position in a probe sequence record may not match the output from the Probe Match tool.