When two MSAs are compared in the MSA comparator, the consistency (agreement) between the two alignments in the sub-section of the reference alignment under the selection bar can be seen by clicking on the Show button (see section 7.1 of User's manual). In the previous releases of SuiteMSA (1.2 and earlier, see Figure 1.A), consistency was coded in two colors:

• Blue: 100% consistent
• Red: Not 100% consistent

In this release (1.3) the degree of consistency (x) has been color-coded in five levels as follows:

• Blue: x = 100% (the residue is aligned completely consistently)
• Green: 67% < x < 100%
• Yellow: 33% < x ≤ 67%
• Magenta: 1% < x ≤ 33%
• Red: x = 0% (the residue is aligned completely different between alignments)

The degree of consistency for each residue in a column is determined by the number of residues in the column that are consistently aligned against the residue between the two MSAs. For example, consider an alignment with 11 sequences. In a column where no gap exists, there are 11 residues. When compared to a second alignment, a residue in such a no-gap column can be said to be 100% consistently aligned, if all 10 other residues are also found in the same column in the second alignment. If it is aligned with only 7 of the 10 residues, it is 70% consistent, and so forth.

Figure 1.B shows the MSA Comparator in the new color-coding with different degrees of consistency and indicating some regions of extreme inconsistency.

All color-coded highlighting may be removed by clicking on the Clear button.