Table 2

Comparison of manually-designed (calibration) and automatically-designed Southern blot probes.

Probe set

Length (bases)

Average score ratio (self/second hit)

Average repetitive & low-complexity DNA (%)

Unique hit to genome

Passed empirical selection criteria


(n = 8)

791.6 ± 85.9

19.5 ± 10.8

18.2 ± 10.8




(n = 124)

818.1 ± 25.0

23.7 ± 1.3

4.1 ± 1.0*



Shown are the average length (± standard error) of the probes in the calibration and automatically designed sets, together with their average score ratio, which is calculated as the ratio of the score of the on-target hit of the probe to the genomic locus of interest, and the highest-scoring off-target second best hit. The average combined percentage repetitive and low-complexity DNA content (as estimated by RepeatMasker and DUST) is shown for each of the probes. Also shown are the number of probes in each set that had a unique hit to their target genomic locus, with no off-target hits i.e. no apparent cross-reactivity. * p < 0.05 Student's t-test.

Croning et al. BMC Genomics 2010 11:74   doi:10.1186/1471-2164-11-74

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