The riff of CttE's intro is based on the D minor harmonic scale
D E F G A Bb C# D
However we can consider more exactly that it uses its 2nd degree mode:
E F G A Bb C# D E
(to quote Chris "to see exactly what they are, you have to go look in the package" )

Other notes are used, but my point is that this particular scale is let's say the basis.
2. Rhythm
Rhytmically, considering the quadruple compound time signature of 12 by 8, we would have three 8ths in each beat (those are not triplets), and consequently 12 each bar.
Note that are some rhytmic variations, this is a streamlined version only.
Thus our 2-bar riff has 24 notes to be found:)
3. Analising the notes
As this is a compound time signature (3 notes per beat) let's make a kind of grid in text format with the yet nameless notes.
|1-2-3 1-2-3 1-2-3 1-2-3|1-2-3 1-2-3 1-2-3 1-2-3|
the notes in the 1 position have the typical accent of being in the first subdivision of each beat.
No wonder they are the most consensual for listners for they are the "easiest" to listen, since they are exactly the scale notes.
This scale also features when the bass comes in on the very beginning - the longer notes (two per bar) and on the closing of the intro... the very fast ones.
|E-_-_ F-_-_ G-_-_ A-_-_|Bb-_-_ C#-_-_ D-_-_ E-_-_|
Now what's the subdivision with the next biggest weight (accent) on a compound time sig? The 3rd. Adding the notes I hear on all 3rd subdivisions,
we can see that they still belong to the scale.
|E-_-D F-_-D G-_-D A-_-D|Bb-_-A C#-_-A D-_-A E-_-A|
Only "D's and 'A's? That makes sense. Think of the D's and the A's as if it were
continuous pedal notes that would be like a bass for the melody notes (the scale notes on position 1)
So this is actually very modal-like, with the 1st bar based on the fundamental/final (D) and the second bar based of the dominant (A)
and most rightly creating the tension to resolve on the next repetition.
Just imagine if the riff used these two (instead of three) notes per subdivision, it would be already very well defined.
So that leaves us with the 2nd and "weakest" position.
If we first concentrate on the 1st bar, we have (by my ears)
|E-C#-D F-C#-D G-C#-D A-C#-D|
That C# can be viwed as a scale note, after all it belongs to the scale. And makes sense as it is the 7th degree of D, played on the "off" subdivision
and leading to the D note.
on the second bar my ears tell me this on the 1st time Chris plays:
|Bb-G#-A C#-A-A D-C#-A E-G#-A|
However on the second time
|Bb-A-A C#-A-A D-C#-A E-A-A|
that means, the 'G#'s are mere chromatisms to 'A' (don't belong to the original scale) and they are sometimes substituted be the 'A' itself on the middle position.
Another side conclusion is that the C# on the 1st bar can also be thought as a chromatism to D,
and in a streamlined version of the riff, (almost) all second notes would be chromatisms to the third notes (C#-D and G#-A), being the 3rd beat of the 2nd bar the exception (D-C#-A).
This seems to me it's not intentional, instead it's the "heat" of the performance / recording session that makes this wonderful variations. However, and as i am doing a post-analisys
it streeses the point that the notes in the middle position of a three-subdivision are the ones with less weight so that they carry these chromatisms and even may not be played everytime the same way
as the riff is strongly defined with the remaining notes.
On the third repetition Chris "breaks the rule" a bit further on the 2nd bar
|Bb-A-A D-G#-A D-C#-A E-A-A|
Here the "theoretical" C# on the 2nd beat (1st subdivision) was played as D, and thus it appeared twice on the 1st position notes (Bb__ D___ D___ E___).
What I think it's beautiful here it's that this little "chaos" serves beautifully the music, whether some notes are played accidentally or sound "out of the logic", that is one of the many beauties
of Yes music and Chris' playing in particular.
Throughout the recording and counltess live versions you will hear many other variations. It means that each time Chris will play his basslines, he will not be
playing only the music he wrote. He will be still recreating his own music.
Miguel
P.S.: so the "streamlined" fingering would be:
A7_E9_10
A8_E9_10
A10_E9_10
D7_E9_10
A13_A11/12_A12
D11_A12_A12
D12_D11_A12
D14_A11/12_A12