All the following patterns can be entered in multiple equivalent ways; shown is the simplest possible way.
* A = a list of all hits.
* ABCDEF = any sequence of six sequential hits on a single strand.
* ABAB = direct repeat of 2 hits with no gap on the same strand (equivalent to ABAB).
* AB[0:2]<BA = inverted and everted repeats of 2 hits with gaps of 0, 1, or 2 bases.
* A|!B = all sequences of two different sequential hits, regardless of which strand each hit is on, equivalent to A!B and A<!B.
* ABC[3:3]DEF, ABC[3:3]<DEF = any sequence of 3 hits on one strand, a 3 base gap, and any sequence of 3 hits on the same or other strand with a 3 base gap. Note this is different from ABC[3:3]|DEF, because this last pattern also includes patterns such as ABC[3:3]<D>E<F.
* A[0:3]A, A[0:3]A[0:3]A, A[0:3]A[0:3]A[0:3]A = 2, 3, and 4 repeats of hit on the same strand, each separated by 0 to 3 bases.
In many cases, alternate pattern forms will lead to equivalent hits, but presented differently. For example, >AA and <AA will give rise to the same hits, the output files for each pattern will differ in that the strands designated for each hit will be reversed (and therefore the sequences will all be reverse complements).
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