TABLE 2.
Sequence alignment of primers and mumps virus strain sequences available on genomic databases
| Primer (positions)a | Sequenceb |
|---|---|
| Mumps SH-2S | 5′ AATGAATMTCMIRGGGTCGTAACGTCTC 3′ |
| external sense | AATGAATCTCCTGGGGTCGTAACGTCTC (35) |
| (6621-6648) | AATGAATCTCCTAGGGTCGTAACGTCTC (35) |
| AATGAATCTCATGGGGTCGTAACGTCTC (23) | |
| AATGAATCTCCCGGGGTCGTAACGTCTC (13) | |
| AATGAATCTCCTGGGGTCGTAACGTCTC (12) | |
| AATGAATCTCCTGGGGTCGTAACGTCTC (12) | |
| AATGAATATCCTGGGGTCGTAACGTCTC (5) | |
| AATGAATCTCCTAGGGTCGTAACGTCTC (3) | |
| AATGAATCTCCTGGGGTCGGAACGTCTC (2) | |
| AATGAATCTCCTAGGGTCGTAACGTCTC (1) | |
| AATGAATCCCCTAGGGTCGTAACGTCTC (1) | |
| AATGAATCTCCTAGGGTCGTAACTTCTC (1) | |
| AATGAATCTCCTGGGGTCCTAACGTCTC (1) | |
| AATGAATCTCCAGGGGTCGTTACGTCTC (1) | |
| Mumps SH-1S | 5′ GTSACCCTGCIGTIGSACTATG 3′ |
| internal sense | GTGACCCTGCCGTTGCACTATG (120) |
| (6249-6271) | GTGACCCTGCCGTAGCACTATG (9) |
| GTGACCCTGCCGTCGCACTATG (4) | |
| GTGACCCTGCCGTAACACTATG (4) | |
| GTCACCCTGCTGTTGCACTATG (2) | |
| GTGACCCTGCCGTTGAACTATG (1) | |
| GTGACCCTGCCGTTGGACTATG (1) | |
| GTGACCCCGCCGTTGCACTATG (1) | |
| GTGACCCTGCGGTTGCACTATG (1) | |
| Mumps SH-2AS | 5′ GRAAGATCYYYARIYIGGRCRAGTCC 3′ |
| external | GAAAGATCTCCAGTTAGGACAAGTCT (21) |
| antisense | GAAAGATCTCCAGCTGGGACAAGTCC (19) |
| (6441-6466) | GGAAGATCTCCAGTTAGGACAAGTCC (17) |
| GAAAGATATCCAGTTAGGACAAGTCT (12) | |
| GAAAGATCCCCAGTTAGGACAAGTCC (10) | |
| GAAAGATCTCCAGTTGGGACAAGTCC (10) | |
| GAAAGATCTCCAGTTAGGACGAGTCT (9) | |
| GAAAGATCTCCAGATAGGACAAGTCC (6) | |
| GAAAGATCTCCAACCCGGACAAGTCC (5) | |
| GAAAGATCCTCAGTTAGGGCAAGTCC (4) | |
| GAAAGATCTCCAGTTAGGACGAGTCC (4) | |
| GATAGATCTCCATTTAGGACAAGTCC (4) | |
| GAAAGATCCCCAATTAGGACAAGTCC (3) | |
| GAAAGATCTCCAGTTTGAACACGTCC (3) | |
| GAAAGATCTCCAATTAGGACAAGTCC (2) | |
| GAAAGATCTCCAGTTAGGACAAGTCC (2) | |
| GGAAGATCTCCAGTTAGGACACGTCC (1) | |
| GGAAGATCCCCAGGTGGGACAAGTCC (1) | |
| GAAAGATCTCCAGTTAGGGCAAGTCC (1) | |
| GAAAGATCCCTAGTTAGGACAAGTCT (1) | |
| GAACGATCTCCAGTTAGGACAAGTCT (1) | |
| GATAGATCTCCATTTAGGACAGGTCC (1) | |
| GATAGATCTCTATTTAGGACAAGTCC (1) | |
| GAAAGATCTCCATCTAGGACAAATCC (1) | |
| GAAAGGTCTCCAGCTGGGAAAAGTCC (1) | |
| GAAAGATCTCCAGCTGGGAAAAGTCC (1) | |
| GAAAGATCTCCAGCGGGGAAAAGTCC (1) | |
| GAAAGATCTCCAGCCCGGACAAGTCC (1) | |
| GAGAGATCTCCAGCCAGGACAAGTCC (1) | |
| Mumps SH-1AS | 5′ GATCAMYCACTCTAGAAAGATCYCYAR 3′ |
| internal | GATCACTCACTCTAGAAAGATCTCCAG (54) |
| antisense | GATCACCCACTCTAGAAAGATCTCCAG (16) |
| (6427-6453) | GATCACTCACTCTAGAAAGATATCCAG (12) |
| GATCACTCACCCTAGGAAGATCTCCAG (10) | |
| GATCACTCACTCTAGGAAGATCTCCAG (8) | |
| GATCACTCACTCTAGAAAGATCTCCAA (7) | |
| GATCACTCATTCTAGATAGATCTCCAT (5) | |
| GATCAATCACTCTAGAAAGATCCCCAG (5) | |
| GATCAATCACTCTAGAAAGATCCTCAG (4) | |
| GATCACTCACTCTAGAAAGATCCCCAA (4) | |
| GATCACTCACTCTAAGAAGATCCCCAG (1) | |
| GATCACTCACTCTAGAAAGATCTCTAG (1) | |
| GATCACTCACTCTAGAAAGATCTCTAG (1) | |
| GATCACCCACTCTAGAAAGATCCCTAG (1) | |
| GATAACCCACTCTAGAAAGATCTCCAG (1) | |
| GATCACCCACTCTAGAAAAATCTCCAG (1) | |
| GATCATTCACTTTAGAAAGATCTCCAG (1) | |
| GATCACCCACTTTAGAAAGATCTCCAG (1) | |
| GATCATCAACTCTAGAAAGATCTCCAG (1) | |
| GATCACTCACTCTAGAACGATCTCCAG (1) | |
| GACCACCCACTCTAGAACGATCTCCAG (1) | |
| GATCACTCACTCTAGAAAGGTCTCCAG (1) | |
| GATCACTCACTCTAGAGAGATCTCCAG (1) | |
| GATCACTCATTCTAGATAGATCTCTAT (1) | |
| GATCACTCACTCTAGAAAGATCTCCAT (1) | |
| GATCACTCACCCTAGAAAGATCTCCAG (1) |
a
Positions refer to reference strain NC_002200.
b
Pattern of sequence primer binding site followed by its frequency (in parentheses). The observed mismatches are in boldface type.