Last modified on 25 September 2007.

Help for "Base Pair Lists"

Item Description
HEI: Helical Element Identifier. A helical element is the largest possible helix which contains no multi-stem loop structure. The numerical identifier corresponds to the lowest numbered nucleotide (in the reference sequence) within a helical element. A comment is associated with those helical elements that have a link. Background colors are assigned as follows:
Base Pair Position Numbers:
AI: Additional Information: Indicates one or more of the following:
  • B = tertiary structure: base pair.
  • K = tertiary structure: pseudoknot.
  • R = tertiary structure: base triple; appears as link when a base triple frequency table exists.
C: Comparative Support Color Code. Red denotes strong support, green significant support, black weak support, and gray no support.

Help for "Base Pair Frequencies"

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

Explanations of Individual Codes for RNA molecules:
Base Pair Types: The 5' nucleotide (with a lower position number) appears first in each pair, and the 3' nucleotide (higher position number) appears second.

Different classes of pairing appear on colored backgrounds (described below).

The frequencies appearing in these columns are calculated as:

Base Pair Percentage Equation

Frequencies greater than 2% appear in bold type; values of 0.0 are shown as "--."

Pairing Type Base Pairs Background Color (Legacy Pages) Background Color (New Format Pages)
Watson-Crick GC, CG, AU, and UA White Gray
Wobble GU and UG Yellow
Non-Canonical AA, AC, AG, CA, CC, CU, GA, GG, UC, and UU Gray White


gap: The percentage of sequences with deletions at one or both positions for the given base pair are shown on a cyan background.

Gap Percentage Equation
Seq: Number of sequences with sequence information (A, G, C, U, -) at the two base pair positions. Appears on a gray background.

Help for "Base Pair Collective Scoring Data":

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

Explanations of Individual Codes for RNA molecules:
Xch, Ych: Numbers of phylogenetic changes (at positions x and y respectively). Shown on a cyan background.
PE: Number of phylogenetic events. Shown on a cyan background.
PES: Phylogenetic event score. Shown on a cyan background.
Cov1: Covary1 score. Shown on a magenta background.
Cov3: Covary3 score. Shown on a magenta background.
C1+C3: Sum of the Covary1 and Covary3 scores. Shown on a magenta background. Primary filtering criterion for collective scoring.
WC: Fraction of Watson-Crick (GC, CG, AU, and UA) base pairs. Shown on a yellow background. Calculated as:

Watson-Crick Value Equation
WCGU: Fraction of Watson-Crick plus Wobble (GU and UG) base pairs. Shown on a yellow background. Calculated as:

Watson-Crick-GU Value Equation
Cons: Conservation Values (for positions x and y, respectively). Appear on a green background. Calculated as:

Conservation Value Equation

where Pi is the frequency of occurence of base i at a given position and PΔ is the frequency of deletions at that position.
DfDel: Difference in amount of deletion between positions x and y. Appears on a gray background. Used as a prefilter in the collective scoring process.
PNuc: Percentage of sequences with nucleotides at both positions x and y. Appears on a gray background. Used as a prefilter in the collective scoring process.
Seq: Number of sequences with sequence information (A, G, C, U, -) at the two base pair positions. Appears on a gray background.