TABLE 1.
Oligonucleotides used in this study
| Namea | Sequence (5′-3′) | Positionb |
|---|---|---|
| Oligonucleotides used in qRT-PCR | ||
| SM16Sf | ACGCTCTAAAAAGGCGTGGGAATA | |
| SM16Sr | TTGAGCTCGGGTCTTTAAGCAGTG | |
| Orf1f | CCGTTACCTAACGTCACATAACCGTACT | 34 |
| Orf1r | GCTGTAACTGAGACTTCCACCTCGTC | 185 |
| FoxDf | CAACGAATGCACCTACCGAACC | 1131 |
| FoxDr | GGGAAATGACATGGCGAGCATA | 1282 |
| FoxCf | GAGTGGAACCATCGGTGCTATCAG | 1862 |
| FoxCr | TTGCTGTATTCCAAGGAGGAGCTG | 2013 |
| FoxBf | TGGTCCCTTGTAGGAACCTAGAGCA | 4081 |
| FoxBr | TTTTTCGTGCTCGTGATTGTAGCTG | 4227 |
| FoxGf | AAGGTGGCCCATGAAGTACTCC | 5320 |
| FoxGr | CAAATAACTCCAGCACCGCAATG | 5471 |
| FoxHf | CCATGAGGAAGTGGAGGACTAAAGC | 7232 |
| FoxHr | GACGAGAACACTTTGACGTGACGA | 7379 |
| FoxIf | TTCCTCTATGCATATATAACGGGGTTG | 8300 |
| FoxIr | CATAGTTCACATGTGTCACAAAGGAAGA | 8446 |
| FoxJf | GGTTAACGAGATGAGTGGGAGCA | 9120 |
| FoxJr | AGGTTAACAATCCGAAGCCTGCTA | 9271 |
| FoxEf | GGGGTTGTGGAATTGAAGGACA | 9734 |
| FoxEr | AGACCAGCACCCCAAATGAGC | 9885 |
| FoxFf | ACATCCGTCTCCACAGCGATAATG | 11788 |
| FoxFr | CACGCTCACAAGAAAAGCGTATCC | 11937 |
| FoxAf | GGCAGAATTCCAGGCAGATTGATA | 13038 |
| FoxAr | TCCGAAGATGTTAATGCCAAGTCC | 13187 |
| Orf2f | CGTCACAAGCCCCACTTTGAG | 14818 |
| Orf2r | GCCGAACAAACGCGGTATCTC | 14965 |
| SORf | GGGAATGGAGAAGGAATTTGAGGA | |
| SORr | TGATGCCATGACTTTGCAGATAGC | |
| Additional oligonucleotides | ||
| FoxDr2 | CGGTGCACTGTCGATTTTAGCC | 952 |
| FoxDf2 | AAGGCTCTCCTTCCGCTTAGGTG | 1352 |
| FoxCr2 | CTTCATGTACCCCGAAAGGTTC | 2603 |
| FoxCf2 | CTCAGGACAAGCCATCCAGGAG | 3029 |
| FoxGr2 | TTCCAAGGATGTCTCCTATGAAGC | 5289 |
| FoxGf2 | AAAAGGTTCCCATGGCTTAACGAC | 5750 |
| FoxHr2 | TCCTCAATGTGACGGAAGGATCA | 6838 |
| FoxHf2 | CAAGGGTGACCTTAGGATAA | 7125 |
| FoxEr2 | GCTGGATTGAATATGATGTATACAAG | 10247 |
| FoxFf2 | ACAAGGTATCTATAAGGGCCAACG | 11035 |
| FoxAr2 | TGTAACGGATTCAGAAACGTGAAC | 12949 |
| FoxAf2 | AAGCTGAACCCACTCAACCAACTC | 13579 |
a
Oligonucleotides are named for the ORF in which they bind. Primers used in pairs have identical names and bind in forward (f) or reverse (r) orientation.
b
Position of the 5′ nucleotide on the DNA fragment containing the fox genes.