+.. image:: images/window_overview.png
+ :alt: Mussa Window
+ :align: center
+
+Legend:
+
+ 1. `DNA Sequence (Black bars)`_
+
+ 2. Annotation_
+
+ 3. Motif_
+
+ 4. `Conservation tracks`_
+
+ 5. `Motif Toggle`_
+
+ 6. `Zoom Factor`_ (Base pairs per pixel)
+
+ 7. `Dynamic Threshold`_
+
+ 8. `Sequence Information Bar`_
+
+ 9. `Sequence Scroll Bar`_
+
+
+DNA Sequence (black bars)
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. image:: images/sequence_bar.png
+ :alt: Sequence Bar
+ :align: center
+
+Each of the black bars represents one of the loaded sequences, in this
+case the sequence around the gene 'MCK' in human, mouse, and rabit.
+
+FIXME: Should I mention the repeats here?
+
+
+Annotation
+~~~~~~~~~~
+
+.. figure:: images/annotation.png
+ :alt: Annotation
+ :align: center
+
+ Annotation shown in green on sequence bar.
+
+
+Annotations can be included on any of the sequences using the `Load a
+mussa parameter file`_ method of loading your sequences. You can
+define annotations by location or using an exact subsequence and you
+may also choose any color for display of the annoation; see the
+`Annotation File Format`_ section for details.
+
+Note: Currently there is no way to add annotations using the GUI (only
+via the .mupa file). We plan to add this feature in the future, but it
+likely will not make it into the first release.
+
+
+Motif
+~~~~~
+
+.. figure:: images/motif.png
+ :alt: Motif
+ :align: center
+
+ Motif shown in light blue on sequence bar.
+
+The only real difference between an annotation and motif in mussagl is
+that you can define motifs from within the GUI. See the `Motifs`_
+section for more information.
+
+
+Conservation tracks
+~~~~~~~~~~~~~~~~~~~
+
+.. figure:: images/conservation_tracks.png
+ :alt: Conservation Tracks
+ :align: center
+
+ Conservations tracks shown as red lines between sequence bars.
+
+The red lines between the sequence bars represent conservation between
+the sequences. The amount of sequence conservation shown will depend
+on the relatedness of your sequences and the `dynamic threshold` you
+are using. Sequences with lots of repeats will cause major slow downs
+in calculating the matches.
+
+
+Motif Toggle
+~~~~~~~~~~~~
+
+.. image:: images/motif_toggle.png
+ :alt: Motif Toggle
+ :align: center
+
+Toggles motifs on and off. This will not turn on and off annotations.
+
+Note: As of the current build (#200), this feature hasn't been
+implemented.
+
+
+Zoom Factor
+~~~~~~~~~~~
+
+.. image:: images/zoom_factor.png
+ :alt: Zoom Factor
+ :align: center
+
+The zoom factor represents the number of base pairs represented per
+pixel. When you zoom in far enough the sequence will switch from
+seeing a black bar, representing the sequence, to the actual sequence
+(well, ASCII representation of sequence).
+
+