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This is a string formatting symbol. Suppose you have several items a,b,c in Sage (or Python more generally) you wish to print, but you want them to be printed in the midst of a longer statement.

a, b, c, = 1, 2, 3

Then to do so, rather than something error-prone like this

print('My first number is ' + str(a) + ' then I have ' + str(b) + ' and also ' + str(c))

or several variants thereon, it is easier and more adaptable to do

print('My first number is %s then I have %s and also %s' %(a, b, c))

This says that you replace each %s with the next item in the tuple (a,b,c). If now you realized they were in the wrong order, it's very easy to fix that:

print('My first number is %s then I have %s and also %s' %(c, b, a))

Note that %s is for string formatting; there are other ways to format numbers as well. The one in your example is padding with extra spaces.

print('My first number is %6s then I have %6s and also %6s' %(a, b, c))

See this link for an active example.

The Python documentation for this is quite technical; see this site for some good examples.