Primers

VNTR amplification primers

Name       Sequence
INS-1296   CTGCTGAGGACTTGCTGCTTG
INS-23+    CAGAAGGACAGTGATCTGGGT
INS-23-    CAGAAGGACAGTGATCTGGGA
  
MVR-PCR primers

Name       Sequence
TAG        TCATGCGTCCATGGTCCGGA
INS-MA     TCATGCGTCCATGGTCCGGAACCCCTGTCCCCAC
INS-MB     TCATGCGTCCATGGTCCGGAACCCCTGTCCCCAGG
INS-MC     TCATGCGTCCATGGTCCGGAACCCCTGTCCCCAG
INS-ME     TCATGCGTCCATGGTCCGGAACCCCTATCCCCAC
INS-MF     TCATGCGTCCATGGTCCGGAACCCCTGTCCCCGGG
INS-MH     TCATGCGTCCATGGTCCGGAACCCCTGTGCCCAC
  
Primers for fragmenting large alleles

Name       Sequence
INS-MBR    CTGCTGAGGACTTGCTGCTTGGGGGACAGGGGTCCT
INS-MEF    CAGAAGGACAGTGATCTGGGATCCCCACACCCCTA
INS-MER    CTGCTGAGGACTTGCTGCTTGCAGGGGTGTGGGGAT
INS-MFF    CAGAAGGACAGTGATCTGGGAACCCCTGTCCCCGGG
INS-MFR    CTGCTGAGGACTTGCTGCTTGGGGGACAGGGGTCCC
INS-MHF    CAGAAGGACAGTGATCTGGGACCCACACCCCTGTG
INS-MHR    CTGCTGAGGACTTGCTGCTTGACAGGGGTGTGGGC
  
Sequencing primers

Name       Sequence
5F1        GAGCAGGGCTGGACCTGTGA
5F2        CCCGGCAGTCTCTAGTGGAA
5F3        GCACCTGCTTCTCAGCGCAA
5F4        TCCCAGCCCTTGAGAGAAACA
5F5        GGGTGTCTCTGAAGGGCTGT
5F6        CTGGTGCTAAGAGGCAGGTA
5R1        GCCGCCATGGATGGGCCAA
3F1        CCTCCAGCTCTCCTGGTCTA
3F2        GACGTGGCTGGGCTCGTGAA
3R4        GCACACTAGGTAGAGAGCTTC
3F8        GAGGCTTCTTCTACACACCCAA
3F3        TCCCTGTGGCCCAGTCAGAA
3F4        GTGGGTGACCCTCCCTCTAA
3F5        GGGTGCCCACAGGTGCCAA
3F6        GCCCAGGTCCAGCCAGACA
3F6-NEST   CCACTGGTGCCTTGGAGGAA
3R5        TGCAATCCTCAGGGCCTCAT
3R3        TGCTTCTCCTGGGCTGCAATC
3F7        TGCTGGAGCTGAGGTATGTGA
3R2        ACAGCTTGGCCGATGGCTGA
3R1-NEST   GGAGCAGTTAGATGGACCCAA
3R1        CTTGTGACTGGGGAGCAGTTA
  
  
Allele-specific oligonucleotides  
  
SNP      Allele Sequence
   
INS-1    C      5´-CCCCTGGCTGCAGCAGCC-3´
         T      5´-CCCCTGGTTGCAGCAGCC-3´
         
INS-2    A      5´-TGAGGACATCCTGTGGAA-3´
         G      5´-TGAGGACGTCCTGTGGAA-3´
         
INS-3    C      5´-CCCCCTGCCCTGGGATGG-3´
         T      5´-CCCCCTGTCCTGGGATGG-3´
         
INS-4    C      5´-GAGCCACCGTGAAGGTGG-3´
         T      5´-GAGCCACTGTGAAGGTGG-3´
         
INS-5    C      5´-CCATCGACGTGCTGGACA-3´
         T      5´-CCATCGATGTGCTGGACA-3´
         
INS-6    A      5´-AATCACCATCACAATAAA-3´
         G      5´-AATCACCGTCACAATAAA-3´
         
INS-7    C      5´-CCACAGACACAGACCCTG-3´
         G      5´-CCACAGAGACAGACCCTG-3´
         
INS-9    A      5´-GGCCTGGAAGGGAGCAGG-3´
         C      5´-GGCCTGGCAGGGAGCAGG-3´
         
INS-10   C      5´-CACTACACGCTGCTGGGA-3´
         T      5´-CACTACATGCTGCTGGGA-3´
         
INS-11   C      5´-AGCTCCCCGGCCGACAAC-3´
         T      5´-AGCTCCCTGGCCGACAAC-3´
         
INS-12   C      5´-CTCCCCCCATCCAGCCTC-3´
         T      5´-CTCCCCCTATCCAGCCTC-3´
         
INS-14   C      5´-GAAAGGGCGGAAGGGAGG-3´
         T      5´-GAAAGGGTGGAAGGGAGG-3´
         
INS-16   A      5´-AGGCTAAGGCCAGGGTGG-3´
         G      5´-AGGCTGAGGCCAGGGTGG-3´
         
INS-17   A      5´-GGTGTCAAGGGACCTGGC-3´
         T      5´-GGTGTCATGGGACCTGGC-3´
         
INS-18   A      5´-TGCCGCCACCCCCAGATC-3´
         G      5´-TGCCGCCGCCCCCAGATC-3´
         
INS-19   C      5´-GATCACACGGAAGATGAG-3´
         T      5´-GATCACATGGAAGATGAG-3´
         
INS-20   C      5´-CAGGTCCCCAGGTCATGC-3´
         T      5´-CAGGTCCTCAGGTCATGC-3´
         
INS-21   A      5´-CACTYCCACTCTCCCACC-3´
         C      5´-CACTYCCCCTCTCCCACC-3´
         
INS-24   C      5´-GGGTTGACAGGTAGRGGA-3´
         G      5´-GGGTTGAGAGGTAGRGGA-3´
         
INS-25   A      5´-AGGTAGAGGAGATGGGCT-3´
         G      5´-AGGTAGGGGAGATGGGCT-3´
         
INS-69   +      5´-AGGTCTTTGCGTTCCAAG-3´
         -      5´-GCAGGTCTGTTCCAAGGG-3´
         
INS-26   A      5´-GCTCARGATTCCAGGGTG-3´
         G      5´-GCTCARGGTTCCAGGGTG-3´
         
INS-27   A      5´-GCCTGTCACCCAGATCAC-3´
         T      5´-GCCTGTCTCCCAGATCAC-3´
         
INS-72   C       5´-TCACTGTCCTTCTGCCAT-3´
         T       5´-TCACTGTTCTTCTGCCAT-3´
         
INS-70   A      5´-TGCTGGCACTGCTGGCCC-3´
         G      5´-TGCTGGCGCTGCTGGCCC-3´
         
INS-28   C      5´-AGCCAACCGCCCATTGCT-3´
         T      5´-AGCCAACTGCCCATTGCT-3´
         
INS-31   C      5´-GTGGGCACGCTCCTYCCT-3´
         T      5´-GTGGGCATGCTCCTYCCT-3´
         
INS-32   C      5´-CTGCCTCCGGGCGAACAC-3´
         T      5´-CTGCCTCTGGGCGAACAC-3´
         
INS-34   C      5´-ACACCCACTGTGGGTGAC-3´
         G      5´-ACACCCAGTGTGGGTGAC-3´
         
INS-35   C      5´-GGGAGTGCGACCTAGGGC-3´
         T      5´-GGGAGTGTGACCTAGGGC-3´
         
INS-36   A      5´-CCTCGCCACTGTTCCGGA-3´
         G      5´-CCTCGCCGCTGTTCCGGA-3´
         
INS-37   C      5´-CTCTGCGCGGCACGTYCT-3´
         T      5´-CTCTGCGTGGCACGTYCT-3´
         
INS-38   C      5´-CGCAGCCCGCAGGCAGCC-3´
         T      5´-CGCAGCCTGCAGGCAGCC-3´
         
INS-39   A      5´-CAGCCCCACACCCGCCGC-3´
         C      5´-CAGCCCCCCACCCGCCGC-3´
         
INS-40   C      5´-TGCCTGTCGGCTGCCTGC-3´
         T      5´-TGCCTGTTGGCTGCCTGC-3´
         
INS-41   G      5´-GGGAGCTGCGGGGGTCTC-3´
         T      5´-GGGAGCTTCGGGGGTCTC-3´
         
INS-42   A      5´-GCCAGGGATGGTGGGGCC-3´
         G      5´-GCCAGGGGTGGTGGGGCC-3´
         
INS-43   C      5´-AGAGACCACGGCCAGGGT-3´
         G      5´-AGAGACCAGGGCCAGGGT-3´
         
INS-45   C      5´-CTTAGCCCACCCCCTCCC-3´
         T      5´-CTTAGCCTACCCCCTCCC-3´
         
INS-49   A      5´-GCTCCACCCAGGGCTGGG-3´
         T      5´-GCTCCACCCTGGGCTGGG-3´
         
INS-71   +      5´-GCTGGGCTGGGGATGGCT-3´
         -      5´-ACCCWGGGCTGGGGATGG-3´
         
INS-51   C      5´-GAGGCCCCTTCTGGGAGG-3´
         G      5´-GAGGCCCGTTCTGGGAGG-3´
         
INS-52   A      5´-GGACCGTATGTTGGAGTG-3´
         G      5´-GGACCGTGTGTTGGAGTG-3´
         
INS-53   A      5´-CTGGGGGATGAGGAGTGT-3´
         C      5´-CTGGGGGCTGAGGAGTGT-3´
         
INS-54   C      5´-GTGTCTTCYGAGGGGCCA-3´
         T      5´-GTGTCTTTYGAGGGGCCA-3´
         
INS-73   C      5´-GCAAGGCCGCCCACCCAA-3´
         T      5´-GCAAGGCTGCCCACCCAA-3´
         
INS-56   A      5´-GCCCTGGACCAGAGCTGG-3´
         G      5´-GCCCTGGGCCAGAGCTGG-3´
         
INS-74   A      5´-CCAGCACCTTGACCCCAC-3´
         G      5´-CCAGCGCCTTGACCCCAC-3´
         
INS-57   A      5´-GGAGACCACAGCCAGGGC-3´
         G      5´-GGAGACCGCAGCCAGGGC-3´
         
INS-60   A      5´-ATRAGAAACAGTTGGCCA-3´
         G      5´-ATRAGAAGCAGTTGGCCA-3´
         
INS-63   C      5´-GRCAGCCCTTCAGTGTCC-3´
         T      5´-GRCAGCCTTTCAGTGTCC-3´
         
INS-64   C      5´-GGAGCCTCGGYTTCACAT-3´
         G      5´-GGAGCCTGGGYTTCACAT-3´
         
INS-65   C      5´-GCCTSGGCTTCACATGCC-3´
         T      5´-GCCTSGGTTTCACATGCC-3´
         
INS-66   C      5´-TGCCCACCRGGCTGGCAG-3´
         T      5´-TGCCCACTRGGCTGGCAG-3´
         
INS-67   A      5´-GCCCACYAGGCTGGCAGG-3´
         G      5´-GCCCACYGGGCTGGCAGG-3´
         
INS-68   A      5´-CAGCCCCAGCGGTCACCC-3´
         G      5´-CAGCCCCGGCGGTCACCC-3´