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Help on table headings and more detailed information about interactions will appear here when you select an appropriate link.

Last modified on 10 July 2001.

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Base Triple Position Numbers :

• The position numbers of the underlying base pair appear in parentheses, separated by a colon, with the third nucleotide's position number following.
• Nucleotide numbers refer to the appropriate reference sequence:
  • tRNA: Saccharomyces cerevisiae Phe
  • 16S rRNA: Escherichia coli
  • 23S rRNA: Escherichia coli
• Selecting a base triple link presents the appropriate base triple frequency table in the Table Window.

AI:

Additional Information: Presently unused; provides an opportunity to present any other information about the triple.

Help for Base Triple Frequency Tables

Aln:

Sequence Alignment ID Code. Appears on a gray background.

Explanations of Individual Codes for RNA molecules:

• tRNA
• 16S rRNA
• 23S rRNA

Base Triple Types:

The bases are presented in the following order: (5' nucleotide of base pair:3' nucleotide of base pair)third nucleotide.

The frequencies appearing in these columns are calculated as:

		[# sequences with noted base triple]
	% TR =	------------------------------------  * 100%
		     [total number of sequences]

Frequencies greater than 10% appear in bold type; values less than 0.1 are shown as "--."

gap:

The percentage of sequences with deletions at at least one position for the given base triple is shown on a cyan background.

		[# sequences with at least one -]
	% gap =	---------------------------------  * 100%
		   [total number of sequences]

Other:

The total percentage of sequences not shown is summarized on a magenta background.

N:

Number of Triple Types Occuring: Total number of non-gap triple types which occur in a given alignment. This number can be used to calculate the average frequencies of triple types in the "Other" category.

CovT#: Covary Scores:

Score the percentage of triple combinations which involve pure covariation with the dominant triple. Range between 0 and 1. CovT1 is unfiltered; CovT2 is filtered. Shown on a yellow background.

Conservation:

Conservation Values for the three positions. Shown on a yellow background.

Seq:

Number of sequences with sequence information (A, G, C, U, -) at the three base triple positions. Appears on a gray background.