Table 1. Phase-variable genes and repeat tract specific PCR primers.
| Gene | Gene size (bp) | Location of Repeat Tract | In-frame Repeat Number1 | Primer name | Sequence (5' → 3') |
|---|---|---|---|---|---|
| cj0031 | 3,732 | +2,572 | 9G | cj0031-fwd-FAM cj0032-rev |
GGCTTTGATCTCATCATCGG GCAAAGCTTCCCCATATCCT |
| cj0045c | 723 | +709 | 11G2 | cj0045-fwd-FAM cj0045-rev |
TTTTACACTAGAACACAGAAG CCTTAAAGTGCGAAAAATGTG |
| cj0046 | 1,407 | +610 | (11G) | cj0046-fwd-NED cj0046-rev |
TCAAATACTGCAAGAGCAGG TAGAAGCATTAGGCGTGG |
| cj0171 | 744 | +243 | 8G | cj0171-fwd-NED cj0171-rev |
TGGTTGTGGAAATGGAGTGC GCTCCTTCATTGCATAGTTC |
| cj0275 | 1,251 | +694 | 8G | cj0275-fwd-NED cj0275-rev |
ATTACTCGTGATGTAAGTGG AAACCTACAACTTTATCTCC |
| cj0565 | 729 | -58 | (10G) | cj0565-fwd cj0565-rev-VIC |
AATTTCACTTCCCCCTTGACT TTTTGCAACATCGCGTAGAA |
| cj0617 | 609 | +559 | 10G | cj0617-fwd-VIC cj0617-rev |
TGGTATAATGCAAGCTATGG AAATCAATACTCCAAGGAGC |
| cj0628 (capA) | 3,432 | +501 | 11G/10G3 | CapA-fwd-FAM CapA-rev |
TATTTCTAATGATGGGCAAC GAACGAACATTTACACCCAT |
| cj0676 | 1,656 | +854 | 10G | cj0676-fwd-NED cj0676-rev |
ATGCTTATTCCTAGTGCCTG TGCATTTAAACCCAAAGAATCC |
| cj0685c | 1,350 | +877 | 9C | cj0685-fwd-FAM cj0685-rev |
GATAGCGAATATAACCTCTAAATTC GAAGAAATCCGCCAATCAAAG |
| cj1139c | 909 | +330 | 8G | cj1139-fwd-VIC cj1139-rev |
GCAACTTCACCTTATATC TAAATTCTTTGTTGTTGTATTTTCC |
| cj1144c | 843 | +294 | 10G | cj1144-fwd-NED cj1144-rev |
GATGTTGTGATTCTTG GTAGCAGCGTTTAGTG |
| cj1295 | 1,305 | +143 | 9G | cj1295-fwd-NED cj1295-rev |
TTCCTATCCCTAGGAGTATC ATAGGCTTCTTTAACATTCC |
| cj1296 | 792 | +309 | 10G | cj1296-fwd-NED cj1296-rev |
ATAAAGTGCATTCTAAAGGC CAGCAAAGGAAAAAATAGGG |
| cj1305c | 1,215 | +579 | 9G | cj1305-fwd-VIC cj1305-rev |
CAACTTTTATCCCACCTAATGGAG AAAGCCGAACCCGAATTATC |
| cj1306c | 1,224 | +579 | 9G | cj1306-fwd-NED cj1306-rev |
TTTATTCCTTCGCGTGGAGA AAAAATGATCGCCCTGCAT |
| cj1310c | 1,212 | +579 | 9G | cj1310-fwd-FAM cj1310-rev |
GAACAAATTATTCCTCTTATAG TCGAAATAAAATTCCCCTTGA |
| cj1318 | 1,947 | +167 | 11G | cj1318-fwd-FAM cj1318-35-rev |
TCCGTGCGTCCTTCTTTTGGAC GTTTGCAACTCTTTAATGGG |
| cj1321 | 540 | -37 | (10G) | cj1321-fwd-VIC cj1321-rev |
AAAAAGGAATGATGCGTTGC CCCGCTCCTATGATGATGAC |
| cj1326 | 672 | +252 | 9G | cj1326-fwd-FAM cj1326-rev |
CTTTTGGAATAGATATAGTTCC TTAGAGGTATGTAGTAAAGAC |
| cj1335 | 1,944 | +168 | 11G | cj1335-fwd-NED cj1318-35-rev |
CACAATTGGTTTATCCAAGG GTTTGCAACTCTTTAATGGG |
| cj1342c | 1,239 | +560 | 9G | cj1342-fwd-FAM cj1342-rev |
TTGGCAATCGTCCTCAAACC GCCAAATGCGCTAAATATCC |
| cj1420c | 771 | +393 | 9G | cj1420-fwd-FAM cj1420-rev |
GCTAGTTCTTTCCATTGGAC CTACAATGTGGCGAGGATTC |
| cj1421c | 1,836 | +87 | 9G | cj1421-22-fwd cj1421-rev-VIC |
TTGGGTATTTAAGTTGGGGAAA TCAAAACCCATCTTTATCATTTTCT |
| cj1422c | 1,875 | +87 | 9G | cj1421-22-fwd cj1422-rev-NED |
TTGGGTATTTAAGTTGGGGAAA AATGATTTTGCTTTGCAGGAA |
| cj1426c | 849 | +294 | 10G | cj1426-fwd-FAM cj1426-rev |
TATAGCCGATCCACAAGG GATATAACTTTGCCCGCCAC |
| cj1429c | 924 | +291 | 10G | cj1429-fwd-FAM cj1429-rev |
ATGGAGATGGTGGTTATGTG ACTATCCGAAACACCCAAAG |
| cj1437c | 1,101 | +876 | 9G | cj1437-fwd-VIC cj1437-rev |
GTGCTAGGATGGAATTTGTG CAAACAAGGTGAAAACCTCC |
1Values in brackets indicate the arbitrary number of repeats coded as ON because the repeat tract is intergenic or within a pseudogene.
2G11 would allow the translation to extend by another 15 amino acids, overlapping the start of cj0044c; G9 and G10 (consensus) have little effect.
3capA fragment varies between 11168 strains due to variation in the polyT tract immediately upstream of polyG tract (6T in the lab strain and the hypermotile 11168H strain, 5T in the chicken-adapted 11168ca strain).