Caveats

• Any two sequences can be forced into alignment

• If the underlying model (i.e., scoring matrix and gap penalties) is inappropriate, the alignment will be useless

THESEALGRITHMSARETR--YINGTFINDTHEBESTWAYTMATCHTWSEQENCES

TH S+ + T Y FIND YT SE

THISDESNTMEANT-HATTHEYWILLFINDAN-------YTHING---SEFL----

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