Primers for amplification and sequencing
C. trachomatis and C. pneumoniae
| Target gene | Forward primer | Reversed primer |
|---|
| gatA | GCTTTAGAATTARSARAWGCT | GATCCTCCGGTATCYGATCC |
| oppA_3 | ATGCGCAAGATATCAGTGGG | AAAGCTCCRSTWGMTATMGGWAG |
| hflX | GCTTCTARAGTACTTTTAAATG | TATTTRGAAATYTTTKCSAGYCG |
| gidA | GGAGTCWCTACWAAAGAAGG | TCGTAYTGYACATCRAAAGG |
| enoA | CCTATGATGAATCTKATCAATGG | TCTTCTTCRGCWAGMCCATCT |
| hemN | AGATCTTCTTCWGGRGGWAGAGA | TTCYTTCAKAACSTAGGTTTT |
| fumC | ATTAAAAAATGTGCTGCT | CCTTCAGGAACATTYAACCC |
R = A or G; S = G or C; W = A or T; Y = C or T; M = A or C; K = G or T;
MLST Chlamydiales
These primers work with: C. abortus, C. psittaci, C. caviae, C. felis, C. muridarum and C. pecorum (they should also work with C. trachomatis and C. pneumoniae).
Set 1
| Gene | Primer name | Sequence |
|---|
| enoA | YPenoA5 | 5-CCWATGATGAAYCTYATTAACGG-3 |
| YPenoA6 | 5-TCTTCYTCAGCRAGGCCATCT-3 |
| fumC | YPfumC5 | 5-ATYAAAMAATGTGCWGCT-3 |
| YPfumC6 | 5-CCWTYAGGAACATTYAATCC-3 |
| gatA | YPgatA5 | 5-GCYTTAGAGTTAAGARATGCT-3 |
| YPgatA6 | 5-GAKCCWCCWGTATCAGAWCC-3 |
| gidA | YPgidA5 | 5-GGYGTYACMACRAAAGAAGG-3 |
| YPgidA6 | 5-TYATAYTGCACATCRAAAGG-3 |
| hemN | YPhemN5 | 5-AGATCTTCTTCAGGRGGRAGRG-3 |
| YPhemN6 | 5-TTTMTYCAGWMCYTWGGATTTAA-3 |
| hflX | YPhflX5 | 5-GCTTCTARRGTACTTTTAAATG-3 |
| YPhflX6 | 5-ATWTTAGAGATCTTTGCTAGYCG-3 |
| oppA | YPoppA5 | 5-ATGCGCAAGATATCAWTGGG-3 |
| YPoppA6 | 5-AARGCRCTACTSGCRATMGGSARG-3 |
Set 2
| Gene | Primer name | Sequence |
|---|
| enoA | YPenoA3 | 5-CCTATGATGAATCTCATTAATGG-3 |
| YPenoA4 | 5-CCCAACCATCAAAATCTTCTTCCG -3 |
| fumC | YPfumC3 | 5-GCTGCTAAGGCAAATCGTG-3 |
| YPfumC4 | 5-CAGGAACATTTAATCCTGTTCC-3 |
| gatA | YPgatA3 | 5-GCCTTAGAGTTAAGAAATGCCG-3 |
| YPgatA4 | 5-CCCCCTGTATCGGAACCTAACGC-3 |
| gidA | YPgidA5 | 5-GGYGTYACMACRAAAGAAGG-3 |
| YPgidA6 | 5-TYATAYTGCACATCRAAAGG-3 |
| hemN | AvdEhemN7 | 5-GTTTATTTGATCTTTCCGAAGC-3 |
| AvdEhemN9 | 5-GGCATTTTGCAAATATATGCCACGG-3 |
| hflX | YPhflX5 | 5-GCTTCTARRGTACTTTTAAATG-3 |
| YPhflX6 | 5-ATWTTAGAGATCTTTGCTAGYCG-3 |
| oppA | YPoppA3 | 5-ATGCGCAAGATATCAATGGG-3 |
| YPoppA4 | 5-GGCAAGGTTTGGTGTAACTCGC-3 |
Citing the database
The preferred format for citing this website in publications is:
This publication made use of the Chlamydiales MLST website (http://pubmlst.org/ chlamydiales/) developed by Keith Jolley and sited at the University of Oxford (Jolley & Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust.
Status
Sequence database
Sequences: 130
Profiles (MLST): 46
Last updated: 2010-04-14
Isolate database
Isolates: 133
Last updated: 2010-10-19