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Generating multiple pattern alignments with each sequence

In the previous examples, only the best scoring alignment of the pattern with the sequence entries is output. However, a pattern may match equally well at more than one position in a sequence (for example, if a repeat is present). The following example, illustrates the principal of generating multiple pattern alignments, though the results are of limited interest.


mode = scan

The only new command necessary is the PATTERN_LEVEL=N command. This specifies that the top N ways of aligning the pattern to EACH sequence will be output.

As before, the program PATT may be used to compress the results and store them in the file bash_ge_4_scan1_top20.patt2out. Inspection of this file shows that in this example, the alternative pattern alignments have identical scores and differ only in the positioning of the first group of pattern elements.