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- No colors — do not color the characters background (i. e. white background is used for all characters).
- Jalview — use the following background colors: A - green, C - orange, G - red, T/U - blue. Gaps and characters of the extended nucleotide alphabets are not colored.
- Percentage Identity — a character background color depends on the character presence in the column of the alignment: below 40% - white, 41-60% - light slate blue, 61-80% - medium slate blue, 81-100% dark slate blue.
- Percentage Identity (colored) — colors depend also on percentage of characters in a column, the following rules are applied (in the order of priority):
- If all characters (100%) are the same and there are no gaps, the characters in the column have yellow background and red font.
- If there are 50% of one character in the column and 50% of another (gaps are not taken into account), one half of the characters has green background and black font (the half to be colored is determined based on the following characters priorities: T>U>G>C>A>B>D>H>K>M>R>S>V>W>Y>N).
- If there is one or several characters in a column with percentage number more or equal to the threshold parameter (see the Threshold parameter on the Highlighting tab of the Options Panel), then most frequent characters are colored as follows: light blue background color and blue font. Note that gaps are considered as characters when calculating percentage number in the column in this case. Also, if required, the same characters priorities are applied as in the previous rule.
- If the rules above are not applied for a character, then it remains uncolored, i.e. white background color and black font are used.
- Percentage Identity (gray) — — this coloring scheme is similar to Percentage Identity scheme, but shades of gray color are used instead of the slate blue color.
- UGENE — this is the default coloring scheme, the following background colors are used: A - yellow, C - light green, G - blue, T/U - light red.
- UGENE Sanger —
- A custom scheme
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