Alignments & Scores

Global (e.g. haplotype)

ACCACACA

::xx::x:

ACACCATA

Score= 5(+1) + 3(-1) = 2

Suffix (shotgun assembly)

ACCACACA

:::

ACACCATA

Score= 3(+1) =3

Local (motif)

ACCACACA

::::

ACACCATA

Score= 4(+1) = 4

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