Hello,
I've been running einverted queries with the same sequence, with the
only difference in parameters being max repeat (e.g. 1000, 2000, 4000,
6000, 8000, 10000 & 20000). Other parameters are gap: 12, threshold:
50, match: 3 & mismatch: -4.
I'd expect that this would result in an ever increasing number of
results, as the max repeat parameter increases. However, this is not
what I'm seeing.
E.g. when max repeat is 2000, there are 3 results from the sequence
prior to >10kb loci.
It's the same result when max repeat is 4000.
However, when max repeat is 6000, there are 2 results prior to >10kb
loci, and 1 of them is not reported by 2000 & 4000 queries. In this
particular result the gap between the inverted repeats is only 2
nucleotides!
When max repeat is 8000, there's only 1 result prior to >10kb loci,
which is also reported by 2000, 4000 & 6000 queries.
When max repeat is 1000, there are 4 results prior to >10kb loci.
Could somebody perhaps explain these unexpected result, and perhaps
suggest proper parameters for finding all inverted repeats from a
>150kb sequence.
Thanks,
-heikki
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