Table 6

Significant values from the "RNA Structure Query System." The 5' and 3' ends of helices and loops are based on the global orientation determined from the 5' and 3' ends of the entire RNA molecule. Values are for the Bacterial 16S and 23S rRNA comparative structure models.

Number/Type of Nucleotides

Structural Element

Short Name

High

Low

single nuc

total

paired (helix)

G (36.57%)

A (14.46%)

5' helix end

G (46.23%)

U(13.52%)

3' helix end

C (38.07%)

A (10.57%)

5' loop end

G (37.06%)

C (10.33%)

adjacent nucs

total

GG (9.863%)

UU (4.093%)

in helix

GG (14.06%)

AA (1.981%)

3'helix 5'loop

CG (14.75%)

UC(1.495%)

loop/helix ratio

AA (5.67934)

CC (.112825)

base pairs

total

GC/CG (28.29%)

CU/UC (0.1351%)

5'helix end

GC (38.76%)

UC (0.09088%)

3'helix end

CG (38.77%)

CU (0.09089%)

Highest

three nucs

total

GGG (3.0%), GAA (2.6%), AAG (2.6%), GGA (2.5%), AGG (2.4%)

000

GAA (7.5%), AAA (6.7%), UAA (5.2%)

011

AGC (9.3%), AGG (8.8%)

100

CGA (7.6%), UGA (5.8%), GGA (5.3%)

110

GCG (6.9%), GGG (4.8%), GGA (4.7%)

001

AAG (14.4%), AAC (6.9%), GAG (5.4%)

101

CAG (7.2%)

Cannone et al. BMC Bioinformatics 2002 3:2   doi:10.1186/1471-2105-3-2