Where did Thomas Jefferson see the Indians as belonging in the nation?

In Thomas Jefferson's vision of America, Native Americans
needed to become "civilized" or be removed from the
scene.

On the one hand, Jefferson wanted to civilize the
Native Americans.  In his second inaugural address, for example, Jefferson sets out his
ideas about the fate of the Natives.  He says that

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...humanity enjoins us to teach them agriculture
and the domestic arts; to encourage them to that industry which alone can enable them to
maintain their place in
existence...

As this shows,
Jefferson had a vision in which the Native Americans would be helped to assimilate into
white society.  This was, to him, the only way that they could continue to exist in a
country where they had been overwhelmed by the numbers of white
settlers.

Jefferson believed that this was the only choice
for the Native Americans.  They could live as white people lived (and they should be
helped to do so) or they could leave the country.  As he said in href="http://www.adl.org/education/curriculum_connections/Excerpt_Jefferson1803.asp">this
letter to William Henry Harrison, who was then governor of the Indiana
Territory,

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...they will in time either incorporate with us
as citizens of the United States or remove beyond the
Mississippi...

To Jefferson,
Americans needed to be small farmers.  Native Americans could change to that way of life
or they could leave the country.  That was his vision for how Indians fit into the new
country.