signal ratios for probes with mismatches near the 3' or 5' end. Average log2 signal ratio for probes with each length of perfect match, due to one mismatch closer to the 3' or 5' end of the probe. If there was no effect based on which end of the probe the mismatch was closer to, we would expect to see equal scatter above and below the identity line for mismatches near either the 3' or the 5' end. Probes with 3' mismatches are mostly above the line and probes with 5' mismatches are mostly below. Note that the 3' end of the probe is attached to the array surface.