Last modified on 10 July 2001.

Help for Base Triple Lists:

Item Description
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:
  • Selecting a base triple link presents the appropriate base triple frequency table in the Table Frame.
AI: Additional Information: Presently unused; provides an opportunity to present any other information about the triple.

Help for Base Triple Frequency Tables:

Item Description
Aln: Sequence Alignment ID Code. Appears on a gray background.

Explanations of Individual Codes for RNA molecules:
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.