What do the red cylinders and green arrows under the sequence alignment mean?

[MolSoft ICM Knowledge Base]

Question: What do the red cylinders and green arrows under the sequence alignment mean?

Answer:

If the one or more of the sequences contain secondary structure annotation then you will see colored cylinders and arrows under the alignment. Red Cylinder = alpha helix, green arrow = beta sheet, blue cylinder = pi helix, magenta cylinder = 3/10 helix.