About This Page:
This page first provides some general reference information about the 16S rRNA data set used to generate the base pair frequency data. Links to this information appear at appropriate places within the base pair frequency tables and associated help files.
Then, the list of base pairs is shown. When a link is selected from this table, the base pair frequencies and other selected data will appear in a separate tab or window (depending upon your browser settings).
16S rRNA Reference Sequence: Escherichia coli.
| GenBank Accession #: J01695 | Secondary Structure: PS | PDF |
Alignments Used:
| Code | Descriptions | # Sequences |
|---|---|---|
| B | (eu)Bacteria | 5859 |
| A | Archaea | 264 |
| C | Chloroplasts | 182 |
| E | Eucarya | 1054 |
| M | Mitochondria | 1160 |
The three phylogenetic domains are defined in (Woese, C. R., Kandler, O., & Wheelis, M.L. (1990) Proc. Natl. Acad. Sci. USA 87:4576-4579): Archaea, (eu)Bacteria, and Eucarya (nuclear).
16S rRNA AA.AG@helix.ends Base Pair List
| BP/X | EP | Or | LT | M | Conf | SN | Stacking | XN |
|---|---|---|---|---|---|---|---|---|
| 16:919 |  |
5' | M | U | A1 | 16,919 | 17:918 | AA |
| 26:557 |  |
5' | M | C | absent | ag | ||
| 59:353 |  |
3' | M | 2C | absent | aa | ||
| 60:107 | |
5' | M | 2C | G3 | 107 | 61:106 | AG |
| 112:315 | 5' | M | I | 112,315 | 113:314 | GA | ||
| 143:220 | 3' | M | I | 143,220 | 142:221 | GA | ||
| 148:174 | |
3' | I | GA | NH / ND | nGC | ||
| 159:162 |  |
3' | H | T, U | S | 159,162 | 158:163 | AG |
| 197:220 | |
5' | M | C | G3 | 220 | 198:219 (192:221) | AG |
| 246:282 | |
3' | I | C, X | absent | aa | ||
| 297:300 | |
3' | H | T, U | S | 297,300 | 296:301 | AG |
| 315:338 | |
5' | M | C | absent | aa | ||
| 321:332 | 3' | H | U | I | 321,332 | 320:333, 322:329 | GA | |
| 338:351 | |
5' | M | C | I | 338,351 | 339:350 (316:337) | AG |
| 374:389 | |
5' | I | C | absent | aa | ||
| 380:383 | |
3' | H | T | S | 380,383 | 379:384 | AG |
| 410:432 | |
3' | I | GA | S | 410,432 | 409:433 | AG |
| 447:487 | |
3' | I | E | S | 447,487 | 446:488 | AG |
| 451:482 | |
3' | I | GA | absent | aa | ||
| 520:529 | |
5' | I | X | S | 520,529 | 521:528 | AG |
| 675:715 | |
3' | I | GA | A1 | 675,715 | 674:716, 676:714 | AA |
| 676:714 | |
5' | I | GA | I | 676,714 | 675:715, 677:713 | AG |
| 687:700 | |
5' | I | G3 | 700 | 688:699 | AG | |
| 691:696 | |
3' | H | U | S | 691,696 | 690:697 | AG |
| 780:802 |  |
3' | I | EL | A3 | 780,802 | 779:803, 781:801 | AA |
| 782:800 | |
5' | I | EL | S | 782,800 | 781:801, 783:799 | AG |
| 860:869 | |
5' | M | X | S | 860,869 | 861:868 | AG |
| 888:909 | |
3' | I | S | 888,909 | 887:910, 889:908 | AG | |
| 898:901 | |
3' | H | T, U | S | 898,901 | 897:902 | AG |
| 945:1236 | 5' | M | I | 945,1236 | 946:1235 | GA | ||
| 959:976 | |
5' | M | GA | absent | ag | ||
| 983:1222 | |
5' | M | G1 | 1222 | 984:1221 | AG | |
| 1013:1016 | |
3' | H | T, U | S | 1013,1016 | 1012:1017 | AG |
| 1067:1108 | |
5' | M | C | G3 | 1108 | 1068:1107 | AG |
| 1077:1080 | |
3' | H | T, U | S | 1077,1080 | 1076:1081 | AG |
| 1157:1179 | |
5' | M | absent | aa | |||
| 1160:1176 | 5' | I | I | 1160,1176 | 1161:1175 | GA | ||
| 1248:1289 | |
3' | I | GU | A7-1 | 1248,1289 | 1247:1290 | AA |
| 1266:1269 | |
3' | H | T, U | S | 1266,1269 | 1265:1270 | AG |
| 1304:1333 | |
3' | I | X | S | 1304,1333 | 1303:1334, 1305:1332 | AG |
| 1306:1331 | |
5' | I | S | 1306,1331 | 1305:1332, 1307:1330 | AG | |
| 1349:1373 | |
5' | M | E | S | 1349,1373 | 1348:1374, 1350:1372 | AG |
| 1357:1365 | 3' | H | U | I | 1357,1365 | 1356:1366 | GA | |
| 1398:1505 | |
5' | M | absent | ag | |||
| 1408:1493 | |
3' | I | C* | A1 | 1408 | 1407:1494 | AA |
| 1417:1483 | |
3' | I | GA | S | 1417,1483 | 1416:1484, 1418:1482 | AG |
| 1418:1482 | |
5' | I | GA | S | 1418,1482 | 1417:1483, 1419:1481 | AG |
| 1516:1519 | |
3' | H | T | S | 1516 | 1515:1520 | AG |
