> I am screening A. thaliana genomic library with a heterologous probe.
> banding pattern on the S. blots whole insert (9-17 Kb) of the isolated clones used as probe not matching that obtained with the screening probe
Your inserts should hybridize with the bands recognized by the probe
used in the screening if they correspond to the right thing. You would
also expect, that since the inserts are up to 17 kb long, they would
hybridize to extra bands.
If the hybridization conditions were right you probably saw a single
band per restriction digest on genomic southerns with the screening
probe (you could see more than a single band if the probe is a cDNA
comprised of multiple exons spliced together or if there are
restriction sites for the enzyme used in the digestion of the genomic
DNA within your probe).
Hope this helps.