Conservation categories are defined: Categories A-E: a nucleotide exists in > 95% of the sequences studied. "Category A": the existing nucleotide is 98%-100% conserved. "Category B": the existing nucleotide is 90%-98% conserved. "Category C": the existing nucleotide is 80%-90% conserved. "Category D": the existing nucleotide is < 80% conserved. "Category E": sum of Categories A-D. "Category N": nucleotide exists in < 95% of the sequences studied. Other abbreviations used: IP: intron position. nt: nucleotide.
Information 16S rRNA 23S rRNA
3DOM ALL 3DOM ALL
General/Overall rRNA Nucleotide Conservation Category A 355 (23.0%) 178 (11.5%) 595 (20.5%) 150 (5.2%)
Category B 156 (10.1%) 175 (11.3%) 349 (12.0%) 203 (7.0%)
Category C 80 (5.2%) 116 (7.5%) 283 (9.7%) 168 (5.8%)
Category D 546 (35.4%) 395 (25.6%) 1204 (41.5%) 647 (22.3%)
Category E 1137 (73.7%) 864 (56.0%) 2431 (83.7%) 1168 (40.2%)
Category N 405 (26.3%) 678 (44.0%) 473 (16.3%) 1736 (59.8%)
TOTAL 1542 (100.0%) 1542 (100.0%) 2904 (100.0%) 2904 (100.0%)
(rRNA) Distance to Nearest "Category A" nt 1 Position 530 (34.4%) 274 (17.8%) 913 (31.4%) 240 (8.3%)
2 Positions 117 (7.6%) 77 (5.0%) 219 (7.5%) 68 (2.3%)
3 Positions 89 (5.8%) 66 (4.3%) 161 (5.5%) 51 (1.8%)
4 or More Positions 806 (52.3%) 1125 (73.0%) 1611 (55.5%) 2545 (87.6%)
(rRNA) Distance to Nearest "Category A" or "B" nt 1 Position 713 (46.2%) 505 (32.7%) 1346 (46.3%) 532 (18.3%)
2 Positions 151 (9.8%) 142 (9.2%) 325 (11.2%) 169 (5.8%)
3 Positions 69 (4.5%) 64 (4.2%) 147 (5.1%) 73 (2.5%)
4 or More Positions 609 (39.5%) 831 (53.9%) 1086 (37.4%) 2130 (73.3%)
Intron Positions (IP) All Introns 84 (100.0%) 84 (100.0%) 69 (100.0%) 69 (100.0%)
Group I Introns 39 (46.4%) 39 (46.4%) 41 (59.4%) 41 (59.4%)
Group II Introns 3 (3.6%) 3 (3.6%) 8 (11.6%) 8 (11.6%)
Archaeal Introns 14 (16.7%) 14 (16.7%) 6 (8.7%) 6 (8.7%)
Spliceosomal Introns 22 (26.2%) 22 (26.2%) 14 (20.3%) 14 (20.3%)
Other Introns 12 (14.3%) 12 (14.3%) 3 (4.3%) 3 (4.3%)
All Introns
# of Introns (All Introns) Total 84 (100.0%) 84 (100.0%) 69 (100.0%) 69 (100.0%)
Conservation of nt Prior to IP Category A 31 (36.9%) 18 (21.4%) 30 (43.5%) 17 (24.6%)
Category B 15 (17.9%) 14 (16.7%) 9 (13.0%) 12 (17.4%)
Category C 3 (3.6%) 12 (14.3%) 3 (4.3%) 5 (7.2%)
Category D 32 (38.1%) 25 (29.8%) 27 (39.1%) 28 (40.6%)
Category N 3 (3.6%) 15 (17.9%) --0 --- 7 (10.1%)
Conservation of nt Following IP Category A 38 (45.2%) 18 (21.4%) 24 (34.8%) 14 (20.3%)
Category B 12 (14.3%) 15 (17.9%) 13 (18.8%) 5 (7.2%)
Category C 5 (6.0%) 13 (15.5%) 6 (8.7%) 4 (5.8%)
Category D 26 (31.0%) 22 (26.2%) 25 (36.2%) 37 (53.6%)
Category N 3 (3.6%) 16 (19.0%) 1 (1.4%) 9 (13.0%)
Distance to Nearest "Category A" nt 1 Position 50 (59.5%) 30 (35.7%) 38 (55.1%) 22 (31.9%)
2 Positions 15 (17.9%) 11 (13.1%) 16 (23.2%) 11 (15.9%)
3 Positions 7 (8.3%) 9 (10.7%) 5 (7.2%) 7 (10.1%)
4 or More Positions 12 (14.3%) 34 (40.5%) 10 (14.5%) 29 (42.0%)
IP Adjacent to at least one "Category A" nt 50 (59.5%) 30 (35.7%) 38 (55.1%) 22 (31.9%)
IP within Two Positions of at least one "Category A" nt 65 (77.4%) 41 (48.8%) 54 (78.3%) 33 (47.8%)
IP within Three Positions of at least one "Category A" nt 72 (85.7%) 50 (59.5%) 59 (85.5%) 40 (58.0%)
IP Flanked by Two "Category A" nt 19 (22.6%) 6 (7.1%) 16 (23.2%) 9 (13.0%)
Distance to Nearest "Category B" nt 1 Position 63 (75.0%) 54 (64.3%) 59 (85.5%) 35 (50.7%)
2 Positions 11 (13.1%) 11 (13.1%) 10 (14.5%) 16 (23.2%)
3 Positions 3 (3.6%) 7 (8.3%) 3 (4.3%) 3 (4.3%)
4 or More Positions 7 (8.3%) 24 (28.6%) 9 (13.0%) 18 (26.1%)
IP Adjacent to at least one "Category A" or "B" nt 63 (75.0%) 54 (64.3%) 59 (85.5%) 35 (50.7%)
IP within Two Positions of at least one "Category A" or "B" nt 74 (88.1%) 65 (77.4%) 69 (100.0%) 51 (73.9%)
IP within Three Positions of at least one "Category A" or "B" nt 77 (91.7%) 72 (85.7%) 72 (104.3%) 54 (78.3%)
IP Flanked on Both Sides by "Category E" nt 80 (95.2%) 67 (79.8%) 68 (98.6%) 60 (87.0%)
Group I Introns
# of Introns (Group I Introns) Total 39 (100.0%) 39 (100.0%) 41 (100.0%) 41 (100.0%)
Conservation of nt Prior to IP Category A 16 (41.0%) 11 (28.2%) 17 (41.5%) 10 (24.4%)
Category B 2 (5.1%) 4 (10.3%) 5 (12.2%) 4 (9.8%)
Category C 1 (2.6%) 4 (10.3%) 1 (2.4%) 4 (9.8%)
Category D 17 (43.6%) 13 (33.3%) 18 (43.9%) 20 (48.8%)
Category N 3 (7.7%) 7 (17.9%) --0 --- 3 (7.3%)
Conservation of nt Following IP Category A 20 (51.3%) 12 (30.8%) 15 (36.6%) 6 (14.6%)
Category B 3 (7.7%) 6 (15.4%) 7 (17.1%) 5 (12.2%)
Category C 4 (10.3%) 6 (15.4%) 3 (7.3%) 1 (2.4%)
Category D 9 (23.1%) 8 (20.5%) 15 (36.6%) 25 (61.0%)
Category N 3 (7.7%) 7 (17.9%) 1 (2.4%) 4 (9.8%)
Distance to Nearest "Category A" nt 1 Position 25 (64.1%) 19 (48.7%) 23 (56.1%) 12 (29.3%)
2 Positions 6 (15.4%) 5 (12.8%) 10 (24.4%) 7 (17.1%)
3 Positions 2 (5.1%) 5 (12.8%) 2 (4.9%) 3 (7.3%)
4 or More Positions 6 (15.4%) 10 (25.6%) 6 (14.6%) 19 (46.3%)
IP Adjacent to at least one "Category A" nt 25 (64.1%) 19 (48.7%) 23 (56.1%) 12 (29.3%)
IP within Two Positions of at least one "Category A" nt 31 (79.5%) 24 (61.5%) 33 (80.5%) 19 (46.3%)
IP within Three Positions of at least one "Category A" nt 33 (84.6%) 29 (74.4%) 35 (85.4%) 22 (53.7%)
IP Flanked by Two "Category A" nt 11 (28.2%) 4 (10.3%) 9 (22.0%) 4 (9.8%)
Distance to Nearest "Category B" nt 1 Position 27 (69.2%) 23 (59.0%) 30 (73.2%) 19 (46.3%)
2 Positions 5 (12.8%) 4 (10.3%) 6 (14.6%) 10 (24.4%)
3 Positions 2 (5.1%) 3 (7.7%) 1 (2.4%) 1 (2.4%)
4 or More Positions 5 (12.8%) 9 (23.1%) 4 (9.8%) 11 (26.8%)
IP Adjacent to at least one "Category A" or "B" nt 27 (69.2%) 23 (59.0%) 30 (73.2%) 19 (46.3%)
IP within Two Positions of at least one "Category A" or "B" nt 32 (82.1%) 27 (69.2%) 36 (87.8%) 29 (70.7%)
IP within Three Positions of at least one "Category A" or "B" nt 34 (87.2%) 30 (76.9%) 37 (90.2%) 30 (73.2%)
IP Flanked on Both Sides by "Category E" nt 35 (89.7%) 32 (82.1%) 40 (97.6%) 37 (90.2%)
Group II Introns
# of Introns (Group II Introns) Total 3 (100.0%) 3 (100.0%) 8 (100.0%) 8 (100.0%)
Conservation of nt Prior to IP Category A 2 (66.7%) 1 (33.3%) 4 (50.0%) 3 (37.5%)
Category B --0 --- 1 (33.3%) 2 (25.0%) 2 (25.0%)
Category C --0 --- --0 --- --0 --- --0 ---
Category D 1 (33.3%) 1 (33.3%) 2 (25.0%) 3 (37.5%)
Category N --0 --- --0 --- --0 --- --0 ---
Conservation of nt Following IP Category A --0 --- --0 --- 3 (37.5%) 3 (37.5%)
Category B 1 (33.3%) --0 --- 3 (37.5%) --0 ---
Category C 1 (33.3%) 2 (66.7%) --0 --- --0 ---
Category D 1 (33.3%) 1 (33.3%) 2 (25.0%) 5 (62.5%)
Category N --0 --- --0 --- --0 --- --0 ---
Distance to Nearest "Category A" nt 1 Position 2 (66.7%) 1 (33.3%) 4 (50.0%) 4 (50.0%)
2 Positions 1 (33.3%) 2 (66.7%) 3 (37.5%) 2 (25.0%)
3 Positions --0 --- --0 --- 1 (12.5%) 1 (12.5%)
4 or More Positions --0 --- --0 --- --0 --- 1 (12.5%)
IP Adjacent to at least one "Category A" nt 2 (66.7%) 1 (33.3%) 4 (50.0%) 4 (50.0%)
IP within Two Positions of at least one "Category A" nt 3 (100.0%) 3 (100.0%) 7 (87.5%) 6 (75.0%)
IP within Three Positions of at least one "Category A" nt 3 (100.0%) 3 (100.0%) 8 (100.0%) 7 (87.5%)
IP Flanked by Two "Category A" nt --0 --- --0 --- 3 (37.5%) 2 (25.0%)
Distance to Nearest "Category B" nt 1 Position 3 (100.0%) 2 (66.7%) 7 (87.5%) 5 (62.5%)
2 Positions --0 --- 1 (33.3%) 1 (12.5%) 3 (37.5%)
3 Positions --0 --- --0 --- --0 --- --0 ---
4 or More Positions --0 --- --0 --- --0 --- --0 ---
IP Adjacent to at least one "Category A" or "B" nt 3 (100.0%) 2 (66.7%) 7 (87.5%) 5 (62.5%)
IP within Two Positions of at least one "Category A" or "B" nt 3 (100.0%) 3 (100.0%) 8 (100.0%) 8 (100.0%)
IP within Three Positions of at least one "Category A" or "B" nt 3 (100.0%) 3 (100.0%) 8 (100.0%) 8 (100.0%)
IP Flanked on Both Sides by "Category E" nt 3 (100.0%) 3 (100.0%) 8 (100.0%) 8 (100.0%)
Archaeal Introns
# of Introns (Archaeal Introns) Total 14 (100.0%) 14 (100.0%) 6 (100.0%) 6 (100.0%)
Conservation of nt Prior to IP Category A 8 (57.1%) 4 (28.6%) 5 (83.3%) 3 (50.0%)
Category B 5 (35.7%) 7 (50.0%) --0 --- 2 (33.3%)
Category C --0 --- 1 (7.1%) 1 (16.7%) --0 ---
Category D 1 (7.1%) 1 (7.1%) --0 --- --0 ---
Category N --0 --- 1 (7.1%) --0 --- 1 (16.7%)
Conservation of nt Following IP Category A 8 (57.1%) 4 (28.6%) 4 (66.7%) 4 (66.7%)
Category B 2 (14.3%) 4 (28.6%) --0 --- --0 ---
Category C --0 --- 1 (7.1%) 1 (16.7%) --0 ---
Category D 4 (28.6%) 4 (28.6%) 1 (16.7%) --0 ---
Category N --0 --- 1 (7.1%) --0 --- 2 (33.3%)
Distance to Nearest "Category A" nt 1 Position 11 (78.6%) 7 (50.0%) 5 (83.3%) 4 (66.7%)
2 Positions 1 (7.1%) 1 (7.1%) --0 --- --0 ---
3 Positions 1 (7.1%) --0 --- --0 --- --0 ---
4 or More Positions 1 (7.1%) 6 (42.9%) 1 (16.7%) 2 (33.3%)
IP Adjacent to at least one "Category A" nt 11 (78.6%) 7 (50.0%) 5 (83.3%) 4 (66.7%)
IP within Two Positions of at least one "Category A" nt 12 (85.7%) 8 (57.1%) 5 (83.3%) 4 (66.7%)
IP within Three Positions of at least one "Category A" nt 13 (92.9%) 8 (57.1%) 5 (83.3%) 4 (66.7%)
IP Flanked by Two "Category A" nt 5 (35.7%) 1 (7.1%) 4 (66.7%) 3 (50.0%)
Distance to Nearest "Category B" nt 1 Position 13 (92.9%) 12 (85.7%) 5 (83.3%) 5 (83.3%)
2 Positions 1 (7.1%) --0 --- --0 --- --0 ---
3 Positions --0 --- 1 (7.1%) --0 --- --0 ---
4 or More Positions --0 --- 1 (7.1%) 1 (16.7%) 1 (16.7%)
IP Adjacent to at least one "Category A" or "B" nt 13 (92.9%) 12 (85.7%) 5 (83.3%) 5 (83.3%)
IP within Two Positions of at least one "Category A" or "B" nt 14 (100.0%) 12 (85.7%) 5 (83.3%) 5 (83.3%)
IP within Three Positions of at least one "Category A" or "B" nt 14 (100.0%) 13 (92.9%) 5 (83.3%) 5 (83.3%)
IP Flanked on Both Sides by "Category E" nt 14 (100.0%) 13 (92.9%) 6 (100.0%) 4 (66.7%)
Spliceosomal Introns
# of Introns (Spliceosomal Introns) Total 22 (100.0%) 22 (100.0%) 14 (100.0%) 14 (100.0%)
Conservation of nt Prior to IP Category A 3 (13.6%) --0 --- 4 (28.6%) 1 (7.1%)
Category B 8 (36.4%) 2 (9.1%) 2 (14.3%) 4 (28.6%)
Category C 2 (9.1%) 7 (31.8%) 1 (7.1%) 1 (7.1%)
Category D 9 (40.9%) 6 (27.3%) 7 (50.0%) 5 (35.7%)
Category N --0 --- 7 (31.8%) --0 --- 3 (21.4%)
Conservation of nt Following IP Category A 8 (36.4%) 1 (4.5%) 2 (14.3%) 1 (7.1%)
Category B 4 (18.2%) 3 (13.6%) 4 (28.6%) --0 ---
Category C --0 --- 3 (13.6%) 1 (7.1%) 2 (14.3%)
Category D 10 (45.5%) 7 (31.8%) 7 (50.0%) 8 (57.1%)
Category N --0 --- 8 (36.4%) --0 --- 3 (21.4%)
Distance to Nearest "Category A" nt 1 Position 10 (45.5%) 1 (4.5%) 6 (42.9%) 2 (14.3%)
2 Positions 6 (27.3%) 3 (13.6%) 4 (28.6%) 2 (14.3%)
3 Positions 3 (13.6%) 3 (13.6%) 2 (14.3%) 3 (21.4%)
4 or More Positions 3 (13.6%) 15 (68.2%) 2 (14.3%) 7 (50.0%)
IP Adjacent to at least one "Category A" nt 10 (45.5%) 1 (4.5%) 6 (42.9%) 2 (14.3%)
IP within Two Positions of at least one "Category A" nt 16 (72.7%) 4 (18.2%) 10 (71.4%) 4 (28.6%)
IP within Three Positions of at least one "Category A" nt 19 (86.4%) 7 (31.8%) 12 (85.7%) 7 (50.0%)
IP Flanked by Two "Category A" nt 1 (4.5%) --0 --- --0 --- --0 ---
Distance to Nearest "Category B" nt 1 Position 16 (72.7%) 5 (22.7%) 10 (71.4%) 5 (35.7%)
2 Positions 4 (18.2%) 4 (18.2%) 2 (14.3%) 3 (21.4%)
3 Positions 1 (4.5%) 2 (9.1%) 1 (7.1%) 2 (14.3%)
4 or More Positions 1 (4.5%) 11 (50.0%) 1 (7.1%) 4 (28.6%)
IP Adjacent to at least one "Category A" or "B" nt 16 (72.7%) 5 (22.7%) 10 (71.4%) 5 (35.7%)
IP within Two Positions of at least one "Category A" or "B" nt 20 (90.9%) 9 (40.9%) 12 (85.7%) 8 (57.1%)
IP within Three Positions of at least one "Category A" or "B" nt 21 (95.5%) 11 (50.0%) 13 (92.9%) 10 (71.4%)
IP Flanked on Both Sides by "Category E" nt 22 (100.0%) 13 (59.1%) 14 (100.0%) 11 (78.6%)
Other Introns
# of Introns (Other Introns) Total 12 (100.0%) 12 (100.0%) 3 (100.0%) 3 (100.0%)
Conservation of nt Prior to IP Category A 6 (50.0%) 6 (50.0%) 1 (33.3%) --0 ---
Category B --0 --- --0 --- --0 --- 1 (33.3%)
Category C --0 --- --0 --- --0 --- --0 ---
Category D 6 (50.0%) 6 (50.0%) 2 (66.7%) 2 (66.7%)
Category N --0 --- --0 --- --0 --- --0 ---
Conservation of nt Following IP Category A 5 (41.7%) 4 (33.3%) --0 --- --0 ---
Category B 2 (16.7%) 2 (16.7%) 1 (33.3%) --0 ---
Category C 2 (16.7%) 3 (25.0%) 1 (33.3%) 1 (33.3%)
Category D 3 (25.0%) 3 (25.0%) 1 (33.3%) 2 (66.7%)
Category N --0 --- --0 --- --0 --- --0 ---
Distance to Nearest "Category A" nt 1 Position 7 (58.3%) 7 (58.3%) 1 (33.3%) --0 ---
2 Positions 2 (16.7%) 1 (8.3%) 1 (33.3%) --0 ---
3 Positions 1 (8.3%) 1 (8.3%) --0 --- 1 (33.3%)
4 or More Positions 2 (16.7%) 3 (25.0%) 1 (33.3%) 2 (66.7%)
IP Adjacent to at least one "Category A" nt 7 (58.3%) 7 (58.3%) 1 (33.3%) --0 ---
IP within Two Positions of at least one "Category A" nt 9 (75.0%) 8 (66.7%) 2 (66.7%) --0 ---
IP within Three Positions of at least one "Category A" nt 10 (83.3%) 9 (75.0%) 2 (66.7%) 1 (33.3%)
IP Flanked by Two "Category A" nt 4 (33.3%) 3 (25.0%) --0 --- --0 ---
Distance to Nearest "Category B" nt 1 Position 9 (75.0%) 8 (66.7%) 1 (33.3%) 1 (33.3%)
2 Positions 2 (16.7%) 1 (8.3%) 1 (33.3%) 1 (33.3%)
3 Positions --0 --- 1 (8.3%) --0 --- --0 ---
4 or More Positions 1 (8.3%) 2 (16.7%) 1 (33.3%) 1 (33.3%)
IP Adjacent to at least one "Category A" or "B" nt 9 (75.0%) 8 (66.7%) 1 (33.3%) 1 (33.3%)
IP within Two Positions of at least one "Category A" or "B" nt 11 (91.7%) 9 (75.0%) 2 (66.7%) 2 (66.7%)
IP within Three Positions of at least one "Category A" or "B" nt 11 (91.7%) 10 (83.3%) 2 (66.7%) 2 (66.7%)
IP Flanked on Both Sides by "Category E" nt 12 (100.0%) 12 (100.0%) 3 (100.0%) 3 (100.0%)