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Table 2 Discrepancies from the probe genome perfect complementarities in inverted repeat regions

From: A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Discrepancy Number of probes affected
70/70 > Identity ≥ 65/65, 0 Mismatches, 0 Gaps 2
Identity = 69/70, 1 Mismatch, 0 Gaps 7
Identity = 69/70 or 70/71, 0 Mismatches, 1 Gap 4
Identity = 68/70 or 70/72, 0 Mismatches, 2 Gaps 2
Identity = 70/76, 0 Mismatches, 6 Gaps 1
  1. Discrepancy occurs when the probe targets IRA and IRB in regions that are not perfectly identical. In this case, the probe is designed to match one IR and is not 100% complementary to the other one. Level of identity of the probe to the second IR region is presented as number of probe bases perfectly aligning to target region/total length of aligning probe sequence. Probe 5' or 3' ends that do not match the second IR, do not add up to the reported total alignment length. Number of internal mismatches and gaps in alignment is also shown