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  sequence B: - t g a t

or

  sequence A: - - a t c t
                  | |
  sequence B: t g a t - -

(and exponentially many other ways, of course). Note that
Needleman-Wunsch considers I<global> alignments, over the entire
length of both sequences; each item is either aligned with an item of
the other sequence, or corresponds to a I<gap> (which is always
aligned with an item - aligning two gaps wouldn't help anything). This
approach is especially suitable for comparing sequences of comparable
length and somewhat similar along their whole lengths - that is,
without long stretches that have nothing to do with each other. If
your sequences don't satisfy these requirements, consider using local
alignment, which, strictly speaking, isn't Needleman-Wunsch, but is
similar enough to be implemented in this module as well - see below
for details.

In the example above, the second alignment has more gaps than the
first, but perhaps your a's are structurally important and you like
them lined up so much that you'd still prefer the second
alignment. Conversely, if c is "almost the same" as g, it might be the