CRW: A Story - Manuscript Table 1

Last modified on 14 July 2000.

Table 1. Characterization of nucleotides at loop-helix junctions for loops with unpaired 5' nucleotides in 16 S and 23 S rRNA.

Loop Type Total A AA AG AAG AAG:U

Total Measured 527 294 (56%) 113 (21%) 136 (26%) 56 (11%) 13 (2%)

Predicted --- 135 (26%) 35 (7%) 43 (8%) 11 (2%) 2 (0.4%)

Hairpin Measured 91 53 (58%) 21 (23%) 26 (29%) 9 (10%) 0 (--)

Predicted --- 24 (25%) 6 (6%) 8 (8%) 2 (2%) 0 (--)

Multi-Stem Measured 202 110 (54%) 45 (22%) 48 (24%) 20 (10%) 1 (1%)

Predicted --- 51 (26%) 13 (7%) 16 (8%) 4 (2%) 1 (1%)

Internal Measured 163 95 (58%) 40 (25%) 50 (31%) 24 (15%) 10 (6%)

Predicted --- 42 (26%) 11 (7%) 13 (8%) 3 (2%) 1 (1%)

Bulge Measured 71 36 (51%) 7 (10%) 12 (17%) 3 (4%) 2 (3%)

Predicted --- 18 (25%) 5 (7%) 6 (8%) 1 (1%) 0 (--)

Loop Type		Total	A	AA	AG	AAG	AAG:U

Total	Measured	527	294 (56%)	113 (21%)	136 (26%)	56 (11%)	13 (2%)
Predicted	---	135 (26%)	35 (7%)	43 (8%)	11 (2%)	2 (0.4%)

Hairpin	Measured	91	53 (58%)	21 (23%)	26 (29%)	9 (10%)	0 (--)
Predicted	---	24 (25%)	6 (6%)	8 (8%)	2 (2%)	0 (--)

Multi-Stem	Measured	202	110 (54%)	45 (22%)	48 (24%)	20 (10%)	1 (1%)
Predicted	---	51 (26%)	13 (7%)	16 (8%)	4 (2%)	1 (1%)

Internal	Measured	163	95 (58%)	40 (25%)	50 (31%)	24 (15%)	10 (6%)
Predicted	---	42 (26%)	11 (7%)	13 (8%)	3 (2%)	1 (1%)

Bulge	Measured	71	36 (51%)	7 (10%)	12 (17%)	3 (4%)	2 (3%)
Predicted	---	18 (25%)	5 (7%)	6 (8%)	1 (1%)	0 (--)

Junctions were counted if an A-motif occurred in greater than 50% (33% for AAG:U) of the sequences in the bacterial 16 S and 23 S rRNA alignments (http://www.rna.icmb.utexas.edu/). Predicted values were calculated with nucleotide frequencies: A (25.7%), G (31.4%), and U (20.5%); values are rounded to the nearest whole number. Percentages are calculated with respect to the total number of positions for that loop type; values are rounded to the nearest whole number, with -- used to represent zero.