WASP Web-based Allele Specific Primer design tool
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Section A: Input
Assay Name (Optional):
File Uploading:
Manual Input:
example
Data Format:
Bracketing
IUPAC
Mismatch at the penultimate position of primers:
Yes
No
Section B: Parameters for primer design
Primer Length
optimal:
Min:
Max:
GC%
optimal:
Min:
Max:
Tm
optimal:
Min:
Max:
Max Tm Diff:
Max Self Complementarity:
Max 3' Self Complementarity:
Max polyX in primer:
Number primer pairs to return:
1
2
3
4
5
Reset
Submit
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Example
×
>SNPID 1 CAAGCCGGGCTACGTCCGAGGGTAACAACATGATCAAAACCACAGCAGGAACCACAATAAGGAACAAGACTCAGGTTAAAGCAAACACAGCGACAGCTCCTGCGCCGCATCTCCTGGTTCCAGTGGCGGCACTGAACTCGCGGCAATTTGTCCCGCCTCTTTCGCTTCACGGCAGCCAATCGCTTCCGCCAGAGAAAGAAAGGCGCCGAAATGAAACCCGCCTCCGTTCGCCTTCGGAACTGTCGTCACTTCCGTCCTCAGACTTGGAGGGGCGGGGATGAGGAGGGCGGGGAGGACGACGAGGGCGAAGAGGGTGGGTGAGAGCCCCGGAGCCCGAGCCGAAGGGCGAGCCGCAAACGCTAAGTCGCTGGCCATTGGTGGACATGGCGCAGGCGCGTTTGCTCCGACGGGCCGAATGTTTTGGGGCAGTGTTTTGAGCGCGGAGACCGCGTGATACTGGATGCGCATGGGCATACCGTGCTCTGCGGCTGCTTGGCGTTGCTTCTTCCTCCAGAAGTGGGCGCTGGGCAGTCACGCAGGGTTTGAACCGGAAGCGGGAGTAGGTAGCTGCGTGGCTAACGGAGAAAAGAAGCCGTGGCC[G/A]CGGGAGGAGGCGAGAGGAGTCGGGATCTGCGCTGCAGCCACCGCCGCGGTTGATACTACTTTGACCTTCCGAGTGCAGTGGTAGGGGCGCGGAGGCAACGCAGCGGCTTCTGCGCTGGGAAATTCAGTCGTGTGCGACCCAGTCTGTCCTCTCCCCAGACCGCCAATCTCATGCACCCCTCCAGAGTGGCCCTTGACTCCTCCCTCTCCTCACTCCATCTTTCCTGGCCTCTCTCCGGGTGCTTAGCGGACTTGGCCAATAACCTCCTCCTTTTAAACGCCCTGAATTGAACCCTGCCTCCTGCGCATCCTCTTTTTGTGTCACCTTAGGGTTCAGATTTAACTACGCGACTTGACTAGTCATCTTTTGATCTCTCTCTCGTATTTAGTACTTTTAGTCAGCGAGCATTTATTGATATTTCAACTTCAGCCTCGCGGTTAAGAGCTTGGGCTCTGGAATCATACGGCTGGAATTGGAATTCTGTCAGTCGTGTGGCCGCTCTCTACTGTCTTGTGAAGATAAGTGAGATAATCTTGACCTGTGGTGAGCACTCGTGAGCGTTAGCTGCTGTATTTACCAGGTACAGATAAGACAACTACA >SNPID 2 GACCCTGAAGCTCCAGCGTGAGGCCTGGCATTGAATGAAATATATTTTGTGGGTTTTCAGCTGCTGAAGTCATAGGAATGGATGAGACCAAGAAAACAAAGCTGTTTTTGAGGTATGAGCGGAAGAAGAGATATCAGGAGACTTTCGAAACAGTCATAACGGAAGTTAATATGATCATTGCTAACATTTGCTGTGTTTCAGGCACTGTAAGCATGTATATGGGTCCTTAAAGGGACTCATAGAGGTAGGTACTAGTATTGTTTTTCCTTTTATCATTGAGAAACTGAGGTTTGAAGAGATTAGTGAACTTGCTCTAGATTATACAGTTTGTAAGTGGCTGAACCAGGATTTGAACTAATACAATCTGACTACAGAGGCCACACTCCTTAGCACTAGAAAAGAATGGCATGCCAAGGGCAGAGTTATTTCTAGGAAGATGGGATATAAGCGTCATTGTCAAGTTGTGCAAAGGGGTCAACTTGGTTGAGATCTAAAAAGGAACACTGAATTCGTCAATTCAGAGGCTCGTAGGAAGTAGGAAATCCTTATCTTTTCGTTTGAACCTTGAGTGGAACCTAGATATTCTGGATTAATGTATAA[A/G]TGAAGTTCATCTTTATATGGTGACACTCATACTCTAGTTGACTACCTAATAGTTCCTCTGCCTTCTTTCAGTTCCGCCAACATACTGTGTTCTTTAACATTGTAGAACCCTTTGGCTATGCTAGTCTCCTTCCCTGAAGTGTTGGTCCTCTAGCCCTTTTTTTGATTGGCACCAGTTAGTTCAGATCTTGGCTTTATTATAAACTCCTCTGAGATATATGTTCCCTGACAGTTTATCTAAAATGATTCTCTCTACAGTTATTTTCTATTACTGTGTTTTTGTTTCCTCAGAGGCATACATCACAATTTGGAATTATGCATTGGTTTATCAATTTACTTGTTTATTGTCACCCTGCTGCCCAGATATGACTTCATGAGGGTAGGATTTGTATCTGTTTAGTTCATTATTTGTCTAGCTATAAGTAGTAAATATTGTTTGCATCTATCAGTGAATGAGCATCTTCTGTTTATGTAGATAATACTGAACTGTTTTGTTTTCTTCAAAGTAATCATTAAGCTGAAGGTAAGAAAAACAAGTTCAAGGAAGTCACACCATGGGGAAAAAAAAGTCAAGTTTAGGGCTGCCTCTTCCGGGAAGTGT >SNPID 3 CTGTTTTCTATTCATCTTTCATGTCTCAATTTAAATGTCATGTTTCTTTGGTCTCAGAGTAATAAAAAGTAAATATACTTCCCCCATCTCCCGCCCCGCAGAGCCTTCCTCTGTTGCCCAGGCTGGAGTACAGTGGCTCGATCTTGGCTCACTGAAAGCTCTGCCTCCCAGATTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGCGCGCCACCAAGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCGAACTCCTGACCTTGTGATCCTCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGTCCAGTGTAAATTATACTTTTATTTTAATCCTGCTACTACTGCAAGCAAGGCAAACATTTTTGTGTTACAGCATTACTTGTATAGATTTTAAGAAAATCTCATTTTAAATACGGAAATGTTAAGAAAAATTATTGTGCCTTTGACCAGAATGTGCCTCTAATTGTACAGTTAAATCTAACTATAAATACTGCAGTATAAAATAATTATATACACATTTTTTCACACCTCTTTCTC[T/C]CTATATATGCATATATACATATACATATATATACCTATATGTATTTTTTTTACAGACAGTGATGTGTGTTCTGAAATTGTGAACCATGAGTCTAGTACTTAATGATCTGCTTATCTGCTGCCGTCAACTAGAACATGATAGAGCTACAGAACGAAAGGTAGTAAATTACTTAAATTCAATTTTTCCTTGAAATAAGTGTGATTAGTAACCCATTATTATTTCCTTTTTATTTTCAGAAAGAAGTTGAGAAATTTAAGCGCCTGATTCGAGATCCTGAAACAATTAAACATCTAGATCGGCATTCAGATTCCAAACAAGGAAAATATTTGAATTGGGATGCTGTTTTTAGGTATTCTATTCAAATTTATTTTACTGTCTTTATTTTTCTCTTTCATATTTATTTCTGTTGTGATATTACTTTTGTGTGTAAGTCTTAACATTTATCTTTGCTTCCTATATATCATTATGCCTTGCATATGAATTTGGCATTTAATATTTATCCAAAACATAATTTTTAAAGGTTGTTCATATAGAAACTTAAAAATTATAAATTATTTCTTCAATAAAATGTTTTAGACATATCTCACTCAAAATTGAGAG