This task is achieved through a variable gap penalty function that tends to place gaps in solvent exposed and curved regions, outside secondary structure segments, and between two positions that are close in space.
This is reinforced by our finding that, even using the same correct guide-tree, different alignments will place gaps in different patterns, compatible with the guide-tree, but mostly at positions that do not correspond with real sites of past insertions and deletion events.
It was cruel on the Sandgrounders, who belied the 88-place gap between the sides and it was especially harsh on their goalkeeper, David Raya Martin, who produced heroics for them.
Warrington Town made light of a 100-place gap between themselves and Exeter in the football pyramid to reach the FA Cup second round at Cantilever Park.
Warrington are managed by Shaun Reid, brother of former England international Peter, and his group of part-time players made light of the 100-place gap between themselves and Exeter in round one.
On a freezing, rain-soaked night that provided trademark conditions for an FA Cup shock, a dismal United allowed League Two side Cambridge United to deservedly bridge a 76-place gap between the clubs to earn a fourth-round replay at Old Trafford.
Look up Global Citizen Year, which places gap-year students in Africa and Latin America.
Prince is flattered by imitators, as other companies have placed gaps in racket frames between the pinholes for stringing.
Sequences were aligned manually, and at eight places gaps of one to two bases were inserted to keep all sequences in alignment.
For both COI and ITS2 the alignments were unambiguous, the former with no gaps, and the latter with only a few, unambiguously placed gaps.
