A multiple-sequence alignment of the kit's HIV-1 subtype reference sequences is presented below in MSF/GCG format:

Note that half the HMA primers were reversed and complemented to match the strand orientation of the alignment.  These primers are indicated within their sequence names by "REVCOMP."  Subtypes are indicated after the hyphens.

PileUp   MSF: 1340  Type: N    Check:  3029   ..

 Name: sf170-A3 oo  Len: 1340  Check:  3165  Weight:  1.000
 Name: br20-B1 oo  Len: 1340  Check:  2267  Weight:  1.000
 Name: th14-B2 oo  Len: 1340  Check:  9878  Weight:  1.000
 Name: sf162-B3 oo  Len: 1340  Check:  2869  Weight:  1.000
 Name: ma959-C1 oo  Len: 1340  Check:  3493  Weight:  1.000
 Name: zm18-C2 oo  Len: 1340  Check:  3953  Weight:  1.000
 Name: in868-C3 oo  Len: 1340  Check:  7099  Weight:  1.000
 Name: ug21-D1 oo  Len: 1340  Check:  5919  Weight:  1.000
 Name: ug46-D3 oo  Len: 1340  Check:  6418  Weight:  1.000
 Name: th22-E1 oo  Len: 1340  Check:   716  Weight:  1.000
 Name: th06-E2 oo  Len: 1340  Check:  6676  Weight:  1.000
 Name: bz162-F1 oo  Len: 1340  Check:  7398  Weight:  1.000
 Name: bz163-F2 oo  Len: 1340  Check:   443  Weight:  1.000
 Name: ru131-G1 oo  Len: 1340  Check:  4399  Weight:  1.000
 Name: lbv21-G2 oo  Len: 1340  Check:  6773  Weight:  1.000
 Name: vi525-G3 oo  Len: 1340  Check:  3844  Weight:  1.000
 Name: vi557-H2 oo  Len: 1340  Check:  2113  Weight:  1.000
 Name: se9173-J1 oo  Len: 1340  Check:  6719  Weight:  1.000
 Name: se9280-J2 oo  Len: 1340  Check:  3905  Weight:  1.000
 Name: primer_ed5 oo  Len: 1340  Check:  7631  Weight:  1.000
 Name: primer_ed31 oo  Len: 1340  Check:  6931  Weight:  1.000
 Name: primer_es7 oo  Len: 1340  Check:  1696  Weight:  1.000
 Name: primer_ed33REVCOMP oo  Len: 1340  Check:  6033  Weight:  1.000
 Name: primer_es8REVCOMP oo  Len: 1340  Check:  2041  Weight:  1.000
 Name: primer_ed12REVCOMP oo  Len: 1340  Check:   650  Weight:  1.000

//
sf170-A3            ATGGGACCAG AGTCTAAAGC CATGTGTAAA GTTAACCCCT CTCTGCGTTA
br20-B1             ATGGGATCAA AGCCTAAAGC CTTGTGTAAA GTTAACCCCA CTCTGTGTTA
th14-B2             ATGGGATCAA AGCCTAAAGC CATGTGTAAA ATTAACCCCA CTCTGTGTTA
sf162-B3            ATGGGATCAA AGTCTAAAGC CATGTGTAAA GTTAACCCCA CTCTGTGTTA
ma959-C1            ATGGGATCAA AGCCTAAAGC CATGTGTAAA GTTGACCCCA CTCTGTGTCA
zm18-C2             ATGGGATCAA AGCTTAAAGC CATGTGTAAA GTTGACCCCA CTCTGTGTCA
in868-C3            ATGGGATCCA AGCCTGAAGC CATGTGTAAA GTTGACCCCA CTCTGTGTCA
ug21-D1             ATGGGATCAA AGCCTAAAAC CATGTGTAAA ATTACCCCCA CTCTGTGTCA
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             ATGGGATCAA AGTCTAAAGC CATGTGTAAA GTTAACTCCT CTCTGTGTTA
th06-E2             ATGGGATCAA AGTCTAAAGC CATGTGTAAA GTTAACTCCT CTCTGCGTTA
bz162-F1            ATGGGATCAA AGCCTAAAGC CATGTGTGAA GTTAACCCCA CTCTGTGTTA
bz163-F2            ATGGGATCAA AGCCTAAAGC CATGTGTGAA GTTAACCCCA CTCTGTGTTA
ru131-G1            ATGGGATGAA AGCCTAAAGC CATGTGTAAA GTTAACCCCT CTCTGTGTTA
lbv21-G2            ATGGGATGAA AGCCTAAAGC CATGTGTAAA GTTAACCCCT CTCTGTGTTA
vi525-G3            ATGGGATGAA AGCTTAAAGC CATGTGTAGA GCTAACCCCT CTCTGTGTTA
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           ATGGGATGAA AGCTTAAAGC CATGTGTAAA GATAACCCCT CTCTGTGTCA
se9280-J2           ATGGGATGAA AGCTTAAAGC CATGTGTAAA GATAACCCCT CTATGTGTCA
primer_ed5          ATGGGATCAA AGCCTAAAGC CATGTG.... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CTTTAAATTG TAGCCAT... AACATCACCA CC........ ..........
br20-B1             CTTTAAATTG CATTGATTTG AAT....... .......... ..........
th14-B2             CTTTAAACTG CACTGATTTG AGG....... .......... ..........
sf162-B3            CTCTACATTG CACTAATTTG AAG....... .......... ..........
ma959-C1            CTTTAAATTG TAGCAATGCT AAC....... .......... ..........
zm18-C2             CTTTAGAATG TGGAAATGTT AAT....... .......... ..........
in868-C3            CTTTAGAATG TAGAGAGGTT AAT....... .......... ..........
ug21-D1             CTTTAAACTG CACTGAATGG AAG....... .......... ..........
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             CTTTAAATTG TACCAATGCT AATTTGATCA AT........ ..........
th06-E2             CTTTAAATTG TACCAATGCT AAAGTGACCA AT........ ..........
bz162-F1            CTTTAAATTG TACTGATGCC ATC....... .......... ..........
bz163-F2            CTTTAAATTG TACTAATGCC ATT....... .......... ..........
ru131-G1            CTTTAAACTG TAGAAATGTA AGCTGTACTA ATTGTACTAA GGGAAAC...
lbv21-G2            CCTTAAACTG TACTAAT... .......... .....GCAAT CGCTAATGTA
vi525-G3            CTTTAAACTG TACTAAGGTA ACCTACAATA GCACTGCAGC CAACAATAGA
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           CTTTAAATTG TAGCGAC... .......... .......... .......GTC
se9280-J2           CTTTAAATTG TAGTAAC... .......... .......... .......ATC
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            .......... .....CATAA CATCACCACC AACAACCCCA ATATCACCAA
br20-B1             .........A ATAGTACTAA CAACAATAAT AGTAGTGGGG TAAAAACAGG
th14-B2             .........A ATGCTACTAA TACCAGTAGT ACA....... ..........
sf162-B3            .........A ATGCTACTAA TACCAAGAGT AGTAAT.... ..TGGAAAGA
ma959-C1            .......... ........AA CACTGCTACC AATAATGTAA CTGCTACCAA
zm18-C2             .......... .......... .......... ......GTTA CCCATGAGAA
in868-C3            .......... ........GA T......ACT AGAAATGGGG TTAATGTTAC
ug21-D1             .........A ATGCCACCAC TAATGCCACT AATGAGGGCA TA........
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             .......... .....GTCAA TAACATAACC AATGTCTCTA ACATAATAGG
th06-E2             .......... .....GTCAG TAATACAATC AATGCCCCTG ACATA...GG
bz162-F1            .........A ATAGCACT.. ....AAAAAC AGCACC.... .....CTGAT
bz163-F2            .........A ATGCCACTGC CATTCAAGAC GGGGAC.... .....CTGAA
ru131-G1            .......... .......... .......... ......AACA ATAGAACTGT
lbv21-G2            ACCAACAGCA ATAAGACTAG TAACAACAGC AGCCTTGGGA ATAGCACTGT
vi525-G3            TCATCCACTG TCACCACCCC TACTAGTACT GTAACCAACA ATAGCACTGT
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           AATAGTAACA ATAGTACAGA TAGTAATAGT AGTGCAAGCA ACAATAGTCC
se9280-J2           ACTAGTAACA GTAATACAAC TAGTAACAGT AGTGTAAGT. .....AGTCC
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            ATACATGGAA GGAGAAATAA AGAACTGCTC TTACAATATG ACCACAGAAC
br20-B1             GATAGACAAG GGAGAGATAA AAAACTGCTC TTTCAATACC ACCACAAGTG
th14-B2             .ATGGAGGGA GGAGAAATAA AAAACTGCTC TTTCAATATC ACCACGAGCA
sf162-B3            GATGGACAGA GGAGAAATAA AAAATTGCTC TTTCAAGGTC ACCACAAGCA
ma959-C1            TAATGTAACC AGTGACATGA AAAATTGTTC TTTCAATGCA ACCACAGAAT
zm18-C2             TAGCACGAAG GGGGAAATGA AAAATTGCTC TTTCAATGCA ACCACAGAAC
in868-C3            CAATAATGGG GAAGAAATAA AAAATTGCTC TTTCAATGCA ACCACAGAAA
ug21-D1             .......... ...GGAATGA AAAACTGCTC TTTC...... ...ACAGAAG
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             AAATATAACA GATGAAGTAA GAAACTGTAC TTTTAATATG ACCACAGAAA
th06-E2             AAATATAACA GATGAAGTAA GAAACTGTTC TTTTAATATG ACCACAGAAC
bz162-F1            GGAAGAGTCA GGGGCAATAC AAAACTGTTC TTTCAATATG ACCACAGAAG
bz163-F2            GGAAGGACCA GGGGCAATAC AAAACTGTTC TTTCAATGTG ACCATGGAAG
ru131-G1            GGAAGGCAAG GACGAAATGA AAAACTGCTC TTTCAATGTA ACTACAGAAA
lbv21-G2            GAGTAGCATA GAAGAAATGA AAAACTGCTC TTTCAATATA ACCACAGAAG
vi525-G3            GAGTGGCAAA GAAGAAATGA CAAACTGCTC TTTCAATGTA ACCACAGAAC
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           T......... GAAATCATGA AAAACTGCTC TTTCAATGTA ACTACAGAAA
se9280-J2           T......... GATATCATGA CAAACTGCTC TTTCAATATA ACTACAGAAA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TAAGGGATAA GAAACAGAAA GTGTATTCAC TTTTTTATAA ACTTGATGTA
br20-B1             TAAAAGATAA GGAGAAGAAG GAATATGCTC TCTTCTATAA TCTTGATGTA
th14-B2             TAAAAACTAA GGTA...AAA GACTATGCAC TTTTTTATAA ACTTGATGTA
sf162-B3            TAAGAAATAA GATGCAGAAA GAATATGCAC TTTTTTATAA ACTTGATGTA
ma959-C1            TAAGAGATAA GAGACAGAAA GTGTATGCAC TTTTTTATAA ACTTGATATA
zm18-C2             TAAAAGATAA AAAACAGAGA GTGTATGCAC TTTTTTATAA ACTTGATATA
in868-C3            TAAGAGATAG GAAGCAGACA GTGTATGCAC TTTTTTATAG ACTTGATATA
ug21-D1             TAAGAGATAA GAAGAAGCAA GCATATGCAC TTTTTTATAA GCTTGATGTG
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             TAAGAGATAA ACAGCAGAAG GTCCATGCAC TTTTTTATAG GCTTGATATA
th06-E2             TAAGAGATAA GAAGCAGAAG GTCCATGCAC TTTTTTATAA GCTTGATATA
bz162-F1            TAAGAGATAA GCAGAAGAGA GTACATGCAC TTTTTTATAA ACTTGATATA
bz163-F2            TAAGAGATAA GCAGCAGAAA GTACATGCAC TGTTT.ATAG ACTTGATATA
ru131-G1            TAAGAGATAA GAAAAAGACA GAATACGCGC TTTTCTATAA ACTTGATGTA
lbv21-G2            TAAGAGATAA GAGTAAGAAA GAATACGCTC TTTTCTATAG ACTTGATGTG
vi525-G3            TAAGAGATAA GCAGAAGGCA GAATACGCGC TTTTCTATAA ACTTGATGTA
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           TAAGAAATAA AAGGAAGCAA GAATACGCGC TTTTCTATAG ACAAGATGTA
se9280-J2           TAAGAAATAA AAGGAAGCAA GAGTACGCGC TTTTCTATAG ACAAGATGTA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            GTACCAATTG ATAAAAATAA TGGTAATAAC AATATAAGGA CTCAGTATAG
br20-B1             GTACAAAT.. .......AGG TAATGATAA. .....TACTA GC...TATAG
th14-B2             GTACCAAT.. .......AGA TAATGATAA. .....TACCA GC...TATAG
sf162-B3            GTACCAAT.. .......AGA TAATGATAA. .....TACAA GC...TATAA
ma959-C1            GTACCACTTA ATGAGAAGGA TAACAGCAG. .....CTCTG GAGAATATAG
zm18-C2             GTACCACTTA ATGAGAATAA CAACTCTAGT GAGGACTCTA GTGAGTATAG
in868-C3            GTACCACTTG ATAATAAGAA GAAGAACA.. .ACTCTAGTG AGTATTATAG
ug21-D1             GTACAAATGA ATG...ATGA TAATAGTAC. .....TAATA CCAGTTATAG
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             GTACAAAT.. .......GCA TAATGAAAA. .....TAGTA GTGAGTATAG
th06-E2             GTACAA.... .......... ....GTTAA. .....TAGTA GTGAGTACAG
bz162-F1            GTACCAAT.. .......CAA TGGCAGTAG. .....AACAT CA...TACAG
bz163-F2            GTACCAATTA GCAATGGAAG AAATGGCAG. .....TGGAG ACTACTACAG
ru131-G1            GTACCAATTA ......ATGA TGAAAGTAG. .....TAATA GTACTTATAG
lbv21-G2            GTACCAATTA ATGGTAATGA AAATAGTAG. .....TACAA CTGATTATAG
vi525-G3            GTACCAAT.. .......TGA TAATAATAG. .....AAATG ATAGTTATAG
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           GTACCAAT.. .......TAA TAGTGACAA. .....TAAAA GT...TATAT
se9280-J2           GTACCAAT.. .......TGA TAGTAACAA. .....TAAAA AT...TATAT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            ATTAATAAAT TGTAATACCT CAGCCATTAC ACAGGCTTGT CCAAAAGTAT
br20-B1             ATTGACAAGT TGTAATACCT CAGTCATTAC CCAGGCCTGT CCAAAGGTAA
th14-B2             GTTGATAAAT TGTAACACCT CAGTCATTAC ACAAGCTTGT CCAAAGGTAT
sf162-B3            ATTGATAAAT TGTAACACCT CAGTCATTAC ACAGGCCTGT CCAAAGGTAT
ma959-C1            ATTAATAAAT TGCAGTACCT CAACTGTAAC ACAAGCCTGT CCAAAGGTCT
zm18-C2             ATTAATAAAT TGTAATACCT CAGCCATAAC ACAAGCCTGT CCAAAGGTCA
in868-C3            ATTAATAAAT TGTAATACCT CAGCCATAAC ACAAGCCTGT CCAAAGGCCA
ug21-D1             ATTAATAAAT TGTAATGCCT CAACCATTAC ACAGGCGTGT CCAAAGATAT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             GTTAATAAAT TGTAATACTT CAGTCATTAA GCAGGCTTGT CCAAAGATAT
th06-E2             GTTAATAAAT TGTAATACTT CAGTCATTAA GCAGGCTTGT CCAAAGATAT
bz162-F1            GCTAATAAAT TGTAATACCT CAACCATTAC ACAGGCTTGT CCAAAGGTAT
bz163-F2            GCTAATAAAT TGCAATACCT CAACCATTAC ACAGGCTTGT CCAAAAGTAT
ru131-G1            GCTAATAAAT TGTAATGTCT CAACCATTAA ACAGGCTTGT CCAAAGGTGA
lbv21-G2            GCTAATAAAT TGTAATGCCT CAACCATTAA ACAAGCTTGT CCAAAGGTGA
vi525-G3            GCTAATACAT TGTAATGTCT CAACCATTAA ACAGGCTTGT CCCAAGGTAT
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           TCTAATAAAC TGTAATACCT CAGTTATTAA ACAGGCTTGT CCAAAGGTGT
se9280-J2           TCTAATAAAC TGTAATACCT CAGTCATTAA ACAAGCTTGT CCAAAGGTGT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......CCT CAGCCATTAC ACAGGCCTGT CCAAAG....
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CCTTTGAGCC AATTCCCATA CATTATTGTG CTCCAGCTGG TTTTGCGATT
br20-B1             CCTTTGAGCC AATTCCCATA CATTATTGTA CCCCGGCTGG TTATGCGATT
th14-B2             CCTTTGAGCC AATTCCCATA CATTATTGTA CCCCGGCTGG TTTTGCGATT
sf162-B3            CCTTTGAACC AATTCCCATA CATTATTGTG CCCCGGCTGG TTTTGCGATT
ma959-C1            CTTTTGACCC AATTCCTATA CATTATTGTA CTCCAGCTGG TTATGCGATT
zm18-C2             CTTTGGATCC AATTCCTATA CATTATTGTG CTCCAGCTGG ATATGCGATT
in868-C3            CTTTTGATCC AATTCCTATA CACTATTGTG CTCCAGCTGG TTTTGCGATT
ug21-D1             CCTTTGAGCC AATTCCCATA CATTATTGTG CCCCAGCTGG ATTTGCAATT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             CCTTTGATCC AATTCCTATA CATTATTGTA CTCCAGCTGG TTATGCGATT
th06-E2             CCTTTGATCC AATTCCTATA CATTATTGTG CTCCAGCTGG TTATGCGATT
bz162-F1            CTTGGGATCC TATTCCCATA CATTATTGTG CTCCAGCTGG TTATACGATT
bz163-F2            CTTGGGGTCC AATTCCCATA CATTATTGTG CTCCAGCTGG TTATGCGATT
ru131-G1            ATTTTGACCC AATTCCCATA CATTATTGTG CTCCAGCTGG TTTTGCGATT
lbv21-G2            CTTTTGACCC AATTCCCATA CATTATTGCG CTCCAGCTGG GTTTGCGATT
vi525-G3            CTTTTGAACC AATTCCCATA CATTATTGTG CTCCAGCTGG TTTTGCAATT
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           CTTTTCAACC AATTCCCATA CATTATTGTG CTCCAGCTGG TTTTGCGATT
se9280-J2           CTTTTCAACC AATTCCCATA CATTATTGTG CCCCAGCTGG TTTTGCGATT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CTAAAGTGTA ATGATGCAGA GTTCAATGGA ACAGGGCCAT GCAAGAATGT
br20-B1             CTAAAGTGTA ATGGTAAGAA GTTCAATGGA ACAGGACCCT GTACAAATGT
th14-B2             CTACAGTGTA ACAATAAAAA GTTCAATGGA ACAGGACCAT GTACAAATGT
sf162-B3            CTAAAGTGTA ATGATAAGAA GTTCAATGGA TCAGGACCAT GTACAAATGT
ma959-C1            CTAAAGTGTA ATAATAAGAC ATTCAATGGG ACAGGACCAT GCCATAATGT
zm18-C2             CTAAAGTGTA ATAATAAGAC ATTCAATGGG ACAGGACCAT GCCATAATGT
in868-C3            ATAAAGTGTA ATAATAAGAC ATTCAATGGG ACAGGACCAT GCAGTAATGT
ug21-D1             CTAAAATGTA ATGATAAAAA GTTCAATGGG ACAGGTCCAT GTAAAAATGT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             TTAAAGTGTA ATGACAAGAA TTTTACTGGG ACAGGGCCAT GTAAAAATGT
th06-E2             TTAAAGTGTA ATGATAAAAA CTTCAATGGG ACAGGGCCAT GTAAAAATGT
bz162-F1            CTAAAGTGTA AGGATAAAAA GTTCAATGGG ACAGGGCCAT GCGAGAATGT
bz163-F2            TTAAAGTGTA ATGATAAAAA GTTCAATGGG ACAGGGCCAT GCAAGAATGT
ru131-G1            TTAAAGTGTA GGGATAAGAA TTTCACTGGA ACAGGACCAT GTAAAAATGT
lbv21-G2            CTAACATGTA GGGATAAGAA GTTCAATGGA ACAGGACCGT GTAAAAATGT
vi525-G3            TTAAAGTGTA GGGAGAAGAA TTTCACTGGA ACAGGACTAT GTAAAAATGT
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           CTAAAATGTA ATAATAAGAC TTTCAATGGA ACAGGACCAT GCAAAAATGT
se9280-J2           CTAAAATGTA ATGATAAGAA TTTCAATGGA ACAGGATCAT GCAAAAATGT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CAGCACAGTA CAATGCACAC ATGGAATCAG GCCAGTA.AT ATCAACCCAA
br20-B1             CAGCACAGTA CAATGTACAC ATGGAATTAA GCCAGTA.GT GTCCACTCAA
th14-B2             CAGTACAGTA CAATGTACAC ATGGAATTAG GCCAGTA.GT ATCAACTCAA
sf162-B3            CAGCACAGTA CAATGTACAC ATGGAATTAG GCCAGTA.GT GTCAACTCAA
ma959-C1            CAGCACAGTA CAGTGTACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
zm18-C2             CAGCACAGTA CAATGTACAC ACGGAATCAA GCCAGTG.GT ATCAACTCAA
in868-C3            CAGCACAGTA CAATGTACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
ug21-D1             CAGCACAGTA CAGTGTACAC ATGGGATTAA GCCAGTA.GT GTCAACTCAA
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             CAGCTCAGTA CAATGCACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
th06-E2             CAGCTCAGTA CAATGCACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
bz162-F1            CAGCACAGTA CAATGTACAC ATGGAATTAA ACCAGTG.GT ATCAACTCAA
bz163-F2            CGC.ACAGTA CAGTGTACAC ATGGAATTAA ACCAGTG.GT ATCAACTCAA
ru131-G1            CAGTACAGTA CAATGTACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
lbv21-G2            CAGTACAGTG CAATGTACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
vi525-G3            CAGTACAGTA CAATGTACAC ATGGAATTAA GCCAGTG.GT ATCAACTCAA
vi557-H2            .......... .......... .......... .......... ..........
se9173-J1           CAGTACAGTA CAATGTACAC ACGGAATTAA GCCAGTG.GT ATCAACTCAA
se9280-J2           CAGTACAGTA CAATGTACAC ACGGAATTAA GCCAGTG.GT ATCAACTCAA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .....TGTAA AACGACGGCC
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CTGCTGTTAA ATGGCAGTCT AGCAGAAGGA AGGGTAAAGA TTAGATCTGA
br20-B1             CTGCTGTTAA ATGGCAGTCT AGCAGAAGAA GATATAGTAA TTAGATCTGA
th14-B2             CTGCTGTTAA ATGGCAGTTT AGCAGAAGAA GAGGTAGTAA TTAGATCTAG
sf162-B3            TTGCTGTTAA ATGGCAGTCT AGCAGAAGAA GGGGTAGTAA TTAGATCTGA
ma959-C1            CTACTGTTAA ATGGTAGCCT AGCAGAAGGA GAAATAATAA TTAGATCTGA
zm18-C2             CTACTGTTAA ATGGTAGCCT AGCAGAAGAA GAGATAATAA TTAGGTCTGA
in868-C3            CTACTGTTAG ATGGTAGCCT AGCAGAAGAA GGGATAATAA TTAGATCTGA
ug21-D1             CTGTTGTTGA ATGGCAGTCT AGCAGAAGAA GAGATAATAA TTAGATCTGA
ug46-D3             .......... .......... .......... ...ATAATAA TTAGATCTGA
th22-E1             TTGCTGTTAA ATGGCAGTCT AGCAGAAGAA GAGATAATAA TCAGATCTGA
th06-E2             TTGCTGTTAA ATGGCAGTCT AGCAGAAGAA GAGATAATAA TCAGATCTGA
bz162-F1            TTGTTGTTAA ATGGCAGCCT AGCAGAAGAA AGTATAGTAA TCAGATCTCA
bz163-F2            TTGTTGTTAA ATGGCAGCCT AGCAGAAGAA GATATAATAA TCAGATCTCA
ru131-G1            TTATTGCTGA ATGGCAGCTT AGCAGAAGAA GAAATAATAG TTAGATCTGA
lbv21-G2            TTACTGCTGA ATGGCAGTTT AGCAGAAGAA GAAATAATGA TTAGATCTGA
vi525-G3            CTACTGCTGA ATGGCAGTTT AGCAGAAAAA GAAATTATAA TTAGATCTGA
vi557-H2            .......... .......... .......AAC CATGTAATAA TTAGATCTAA
se9173-J1           CTACTGCTAA ATGGCAGTGT AGCAGAAGGA GACATAATAA TTAGATCTGA
se9280-J2           CTACTGCTAA ATGGCAGTAT AGCAGAAGGA GACATAATAA TTAGATCTGA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          AGTCTGTTAA ATGGCAGTCT AGC....... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AAATATCACA AACAATGCCA AAACCATAAT AGTACAACTT AACAAGACTG
br20-B1             AAATCTCACA AACAATGCTA AAACCATAAT AGTGCAGCTA AAGGACCCTG
th14-B2             CAATTTCACG GACAATGCTA GAGTCATAAT AGTACAGCTG AATGAATCTG
sf162-B3            AAATTTCACA GACAATGCTA AAACTATAAT AGTACAGCTG AAGGAATCTG
ma959-C1            AAATCTGACA AACAATGTCA AAACAATAAT AGTGCACCTT AATGAATCTG
zm18-C2             AAATCTAACA AACAATGCCA AAACAATAAT AGTACATCTT AATGAATCTG
in868-C3            AAATCTGACA AACAATGCCA AAATAATAAT AGTACATCTT GATCAACCTG
ug21-D1             AAATCTCACA AATAATGCTA AAATTATAAT AGTACATCTT AATGAGTCTG
ug46-D3             AAATCTCACA AATAATGCTA AAACCATAAT AGTACAGCTT AATGAGTCTG
th22-E1             AAATCTCACA AACAATGCCA AAACCATAAT AGTGCACCTT AATAAATCTG
th06-E2             AAATCTCACA AACAATGCCA AAACCATAAT AGTGTACCTT AATAAATCTG
bz162-F1            AAATATCTCA GATAATGCAA AAATCATAAT AGTACACCTT AATGAATCTG
bz163-F2            AAATATCTCA GATAATGCAA AAACCATAAT AGTACACTTT AATGAATCTG
ru131-G1            AAACTTCACA GACAATGCCA AAGTCATAAT AGTGCAGCTT AATAAATCTG
lbv21-G2            AAACTTCACA AACAATGCCA AAAACATAAT AGTGCAATTT AATAAATCTA
vi525-G3            AAACTTCACA AACAATGCCA AAGTCATAAT AGTGCAGCTT AATGAAACTG
vi557-H2            AAATATCACA GACAATACCA AAAACATAAT AGTACAGCTT AAAAGTCCTG
se9173-J1           AAATATCTCA GACAATGCTA AAAACATAAT AGTACAACTT AATGACACTG
se9280-J2           AAACATCTCA GACAATGCCA AAAACATAAT AGTACAACTT AATAAAACTG
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TAGAAATTAA TTGTACCAGA CCTAACAACA ATACAAGAAA AAGTGTACGT
br20-B1             TAGACATTAA TTGTACAAGA CCCAACAACA ATACAAGAAA GAGTATACAT
th14-B2             TAGAAATTAA TTGTACAAGA CCCAACAACA ATACAAGAAA AAGTATACAT
sf162-B3            TAGAAATTAA TTGTACAAGA CCTAACAATA ATACAAGAAA AAGTATAACT
ma959-C1            TAGAAATTGT GTGTACAAGA CCCAACAATA ATACAAGAAG AAGTATAAGA
zm18-C2             TAGAAATTGT GTGTACAAGA CCCAGCAATA ATACAAGAAA AAGTATAAGG
in868-C3            TAGAAATTGT GCGTACAAGA CCAAACAATA ATACAAGAAA AAGTATAAGG
ug21-D1             TACCAATTAA TTGCACAAGG CCCTACGATA AGGTAAGCTA CAGGACACCT
ug46-D3             TACCAATTAA TTGCTCAAGG CCCTACGAAA ATAAAAGACG ACGTACACCT
th22-E1             TAGAAATCAA TTGTACCAGA CCCTCCAACA ATACAAGAAC AAGTATAACT
th06-E2             TAGAAATCAA TTGTACCAGA CCCTCCAACA ATACAAGAAC AAGTATAACT
bz162-F1            TACAAATTAA TTGTACAAGA CCCAACAACA ATACAAGAAA AAGTATACAT
bz163-F2            TACAGATTAA TTGTACAAGA CCCAACAACA ATACAAGAAA AGGTATACAT
ru131-G1            TAGAAATTAC ATGTACCAGA CCTAATAACA ATACAAGAAA AAGTATAACT
lbv21-G2            TAGATATTGT GTGTACCAGA CCCAACAACA ATACAAGAAA AAGTATACAC
vi525-G3            TAGAAATTAA TTGTACCAGA CCCAACAACA ATACAAGAAA AAGTATAAAA
vi557-H2            TACCAATTAA CTGTACCAGA CCCAACAATA ATACGAGAAA AAGTATAAGT
se9173-J1           TAGAAATTGT GTGTACCAGA CCTAATAACA ATACAAGAAA AGGTATACAC
se9280-J2           TAGAAATTGT GTGTTACAGA CCTAATAACA ATACAAGGAA AGGTATACAC
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            ATAGGACCAG GACAAGCATT CTATGCAACA GGTGACATAA TAGGGGATAT
br20-B1             ATAGGACCAG GGAGAGCATT TTATGCAACA GGAGACATAA TAGGAGATAT
th14-B2             CTAGGACCAG GGCGAGCATG GTATACAACA GGACAAATAA TAGGAGATAT
sf162-B3            ATAGGACCGG GGAGAGCATT TTATGCAACA GGAGACATAA TAGGAGATAT
ma959-C1            ATAGGACCAG GACAAGTATT CTATGCAAAT AATGACATAA TAGGAGACAT
zm18-C2             ATAGGACCAG GACAAGCATT CTATGCAACA GGTGGCATAA TAGGAAACAT
in868-C3            ATAGGACCAG GACAAACATT CTATGCAACA GGAGACATAA TAGGAGACAT
ug21-D1             ATAGGAGTAG GGCGAGCATC CTATACAACA AG...AATAA AAGGAGATAT
ug46-D3             ATAGGACTAG GGCAAGCGTA CTATACAACA AA...ATTAA AAGGATATAT
th22-E1             ATAGGACCAG GACAAGTATT CTATAGAACA GGAGACATAA TAGGAGATAT
th06-E2             ATAGGACCAG GACAAGTATT CTATAGAACA GGAGACATAA TAGGAGATAT
bz162-F1            ATAGGACCAG GACGGGCACT TTATGCAACA GGAGACATAA TAGGAGACAT
bz163-F2            ATAGGACCAG GACGAGCATT TTATGCAACA GGAGACATAA TAGGAGACAT
ru131-G1            TTTGCACCAG GACAAGCGCT CTATGCAACA GGTGAAATAA TAGGAGATAT
lbv21-G2            ATAGGACCTG GACAAGCATT ATATGCAACA GGCGCCATAA TAGGCGATAT
vi525-G3            TTCGGAACAG GACGAGTGTT ATATGCAACA GGTGCCATAA TAGGAAATAT
vi557-H2            ATAGGGCCAG GACAAGCATT CTATGCAACA GGTGACATCA TAGGAGATAT
se9173-J1           ATGGGACCAG GACAAGTGCT CTACGCAACA GGGGAAATAA TAGGAGATAT
se9280-J2           ATGGGACCAG GACAAGTGCT CTACGCAACA GGAGAAATAA TAGGAAATAT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AAGACAAGCA TATTGTAATG TCAGTAGAGC AGACTGGAAT AAAACTTTAC
br20-B1             AAGACAAGCA CATTGTAACC TTAGCAGAGC ACAATGGAAT GACACTTTAA
th14-B2             AAGACAAGCA CATTGTAACC TTAGTAGCAC AAAATGGAAT AACACTTTAA
sf162-B3            AAGACAAGCA CATTGTAACA TTAGTGGAGA AAAATGGAAT AACACTTTAA
ma959-C1            AAGACAAGCA CATTGCAACA TTAGTAAGGA TGTCTGGAAC AGTACTTTAC
zm18-C2             AAGACAAGCA CATTGTAACA TTAGTAAAGA GAACTGGAAT AAAACTTTAC
in868-C3            AAGACGAGCA TATTGTAACA TTAGTGAAAA CAAATGGAAT GAAACTTTAC
ug21-D1             AAGACAAGCA CATTGTAACA TTAGTGGAGA AAAATGGAAT AAAACTTTAC
ug46-D3             AAGACCAGCA CATTGTAATA TTAGTGGAGC AGAATGGAAT AAAACTTTAC
th22-E1             AAGAAGAGCA TATTGTGAGA TTAATGGAAC AAAATGGAAT AAAGCTTTAA
th06-E2             AAGACAAGCA TATTGTGAGA TTAATGAAAC AAAATGGAAT GAAACTTTAA
bz162-F1            CAGAAAGGCA CATTGTAACG TTAGTAGAAC ACAATGGAAT AAGAAGTTAG
bz163-F2            CAGAAAGGCC CATTGTAATG TTAGTGGAAC ACAATGGAAT AAAACATTAG
ru131-G1            AAGACAAGCA CATTGTAATG TTAGTAGAAA AGATTGGAAT GAGATGTTGC
lbv21-G2            AAGACAAGCA CATTGTAATG TTAGTGAAAC AGACTGGAGA GACATGTTAC
vi525-G3            AAGACAAGCA CATTGTAATG TTAGTACAGA AAAATGGGGT AAGATGTTAC
vi557-H2            AAGAAAAGCA TATTGTAATA TTACTAGGGA AGATTGGAAA AGGACTTTAC
se9173-J1           AAGGAAAGCA TATTGTAACA TTAGTAGAAA AGATTGGAAT AACACTTTAC
se9280-J2           AAGAGAAACA CATTGTAACA TTAGTGAAAG AGATTGGAGT AACACTTTAC
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AAGGGGTAGC CAACCAATTA AAAAGTTACT TTAGTAACAA AACAATAATC
br20-B1             GCAAGATAGT TACAAAATTA AGAGAACAAT TTGAGAATAA AACAATAAAG
th14-B2             GACAGATAAC TGAAAAATTA AGAGAACAAT TTGGGAACAA AACAATAGTC
sf162-B3            AACAGATAGT TACAAAATTA CAAGCACAAT TTGGGAATAA AACAATAGTC
ma959-C1            AAAAGGTAGG TAAAAAATTA AAAGAACACT TCCCTAATAA AACAATAACA
zm18-C2             AAAAGGTAGG AAAAAAATTA GCAGAGCACT TCCCTAATAA AACAATAAAA
in868-C3            AAAGGGTGAG TAAAAAATTA GCAGAATACT TCCCTAATAA AACAATACAA
ug21-D1             AACAGGTAGC TGCGAAATTA AGAGACCTTC TTAACCAAAC AGCAATAATT
ug46-D3             AACAGGTAGC TAAAAAATTA GGAGACCTTT TCAACCAGAC AACAATAATT
th22-E1             AACAGGTAAC TGAAAAATTA AAAGAGCACT TTAAT...AA GACAATAATC
th06-E2             AACAGGTAAC TAAAAAATTA AAAGAGCACT TTAATAATAA GACAATAATC
bz162-F1            ACCAGGTAAA GGCAGAGTTA AAGTCTCATT TCCCTAATGC AACAATACAA
bz163-F2            AACAAGTAAG GGCAAAGTTA AAGTCTCATT TTCCTAATGC AACAATAAAA
ru131-G1            AGAATGTGAC TACAAAACTA AAAGGAATCT TTAACAACAC AAACATAACA
lbv21-G2            AGAAGGTAAA AGCACAACTA CAAGGAATCT ACAACAAAAG C...ATAACC
vi525-G3            AGAATGTAGC TGCAAAACTA CAAAAAGAAT TTAATAAA.. .AACATAACC
vi557-H2            ATGAGGTAGT TCAGCAATTA AGAGAACACT TTAATAATCA AACAATAATT
se9173-J1           GTAGAGTAGC TAAAAAACTA AGAGAACACT TTAATAAAAC A...ATAGAC
se9280-J2           GTAGAGTAGC TACAAAACTA AGAGAACACT TTAATAAAAC A...ATAAAC
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TTTGCTAGCT CCTCAGGAGG GGATTTAGAA ATTACAACAC ATAGTTTTAA
br20-B1             TTTCAGCCAC CCTCAGGAGG GGATCCAGAA ATTGTATTTC ACAGTTTTAA
th14-B2             TTTAATCAAT CCTCAGGAGG GGACCCAGAG ATTGTAATGC ACAGTTTTAA
sf162-B3            TTTAAGCAAT CCTCAGGAGG GGACCCAGAA ATTGTAATGC ACAGTTTTAA
ma959-C1            TTTGAACCAC ACTCAGGAGG AGATCTAGAA ATTACAACAC ATAGTTTTAA
zm18-C2             TTTGACCAAC ACTCAGGAGG GGACCTAGAA ATTACAACAC ATAGCTTTAA
in868-C3            TTTGCATCAT CCTCAGGAGG GGACCTAGAA ATTACAACAC ATAGCTTTAA
ug21-D1             TTTAAACCAT CCTCGGGAGG GGACCCAGAA ATTACAACAC ACAGCTTTAA
ug46-D3             TTTCAACCA. .......... .......... .......... ..........
th22-E1             TTTCAACCAC CCTCAGGAGG AGATCTAGAA ATTACAATGC ATCATTTTAA
th06-E2             TTTCACCCAC CCTCAGGAGG AGATCTAGAA ATTATAACGC ATCATTTTAA
bz162-F1            TTTAACTCAT CCTCAGGAGG GGACCTAGAA GTTACAATGC ATCATTTTAT
bz163-F2            TTTAATTCAT CCTCAGGAGG GGACCTAGAA ATTACAATGC ATAGTTTTAA
ru131-G1            TATAACTCAG CTGCAGGAGG AGATCTAGAA ATTACAACAC ATAGTTTTAA
lbv21-G2            TTTAACTCAT CCTCAGGAGG GGACCTAGAA ATTACAGCAC ATAGTTTTAA
vi525-G3            TTTAACTCAT CCTCAGGAGG GGACCTAGAA ATTACAACAC ATAGTTTTAA
vi557-H2            TTCGAACCAT CCTCAGGAGG GGACATGGAA ATTACAATGC ATACTTTTAA
se9173-J1           TTTACATCAC CCTCAGGAGG GGACATAGAA ATTACAACAC ATAGTTTTAA
se9280-J2           TTTACATCAC CCTCAGGAGG GGATATAGAA ATTGTGACAC ATAGTTTTAA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TTGTGGAGGA GAATTTTTTT ATTGTGATAC ATCAGGCCTG TTTAATAGCA
br20-B1             TTGTGGAGGG GAATTTTTCT ACTGTAATAC AACACAACTG TTTAATAGTA
th14-B2             TTGTGGAGGG GAATTTTTCT ACTGTAATAC AACACAACTG TTTAATAGTA
sf162-B3            TTGTGGAGGG GAATTTTTCT ACTGTAATTC AACACAGCTT TTTAATAGTA
ma959-C1            TTGTAGAGGA GAATTTTTCT ATTGCAATAC ATCAGGGCTG TTTAATAGTA
zm18-C2             TTGTAGAGGA GAATTTTTCT ATTGCAATAC ATCAAACCTG TTTAATAGTA
in868-C3            TTGTAGAGGA GAATTTTTCT ATTGCAATAC ATCAAACCTG TTTAATGGTA
ug21-D1             TTGTGGAGGG GAATTTTTCT ACTGCAATAC ATCAGGACTG TTTAACAATA
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             TTGTAGAGGG GAATTTTTCT ATTGCAATAC AACACGACTG TTTAGTAATA
th06-E2             TTGTAGAGGG GAATTTTTCT ATTGCAATAC ACCAAAATTG TTTAATGGAA
bz162-F1            TTGTAAAGGA GAATTTTTCT ACTGCGATAC ATCAAGACTG TTCAGTAACA
bz163-F2            TTGTAGAGGA GAATTTTTCT ACTGCAATAC ATCAGGACTG TT........
ru131-G1            TTGTAGAGGA GAATTTTTCT ATTGCAATAC ATCAGGACTG TTTAATAATA
lbv21-G2            TTGTAGAGGA GAATTTTTCT ATTGTAATAC ATCAGGACTG TTTAATAGTA
vi525-G3            TTGTAGAGGA GAATTTTTTT ATTGTAAGAC ATCAGAGCTG TTTAATAGTA
vi557-H2            TTGTAGAGGA GAATTTTTCT ATTGCAATAC ATCAAAATTG TTTAACAGTA
se9173-J1           TTGTGGAGGA GAATTTTTCT ATTGTAATAC ATCAACACTG TTCAATAGTA
se9280-J2           TTGTGGAGGA GAATTTTTAT ATTGTAATAC ATCAAAACTG TTCAATAGTA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .....GAGGG GAATTTTTCT ACTGTAA... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CATGGGGGGG AAATAGCACT GACAGCATAC AGGAGTCAAA TAGCACAGAG
br20-B1             CCTGGACAAA TAACAC...T GAAGGGACAA GTAACACTAC AGGGAATGAC
th14-B2             CTTGGAATGA TACTAG...T ACTTGG...A ATAATAATAC AGGAAATGGC
sf162-B3            CTTGGA...A TAATAC...T ATAGGGCCAA ATAACACT.. ....AATGGA
ma959-C1            .........A CTTTAA...T GATACAGAAG GTAATTCA.. ....ACTTTA
zm18-C2             CATATA...A GCCTAA...T GATACAAATA GTACATATAA TCCTAATGAT
in868-C3            ......CATA CATGAA...T GGTACAAAAA GTAATTCA.. ....AGCTCA
ug21-D1             GTGTATGGAC ATCAAA...T AGT...ACGA TAGGGGCA.. ....AATGGG
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             CTTGCATAAA AAATGA...A ACCATGGCGG GG...TGT.. ....AACGGC
th06-E2             CCATGGAGGG GCCTAA...T AACACGGAGG GGCCTAAT.. ....AACACT
bz162-F1            C......... .......... ..AGAATCCA ATGGCACAGA ATCCAATGGC
bz163-F2            .......... .......... ........TA ACGACACAGG ATCCAATGGC
ru131-G1            G......... TGAGAA...T AACTCCACTA TCGAGAAT.. ....AACTCC
lbv21-G2            GTATATTATC TAACAA...T AATGCACCAT CTAATAGC.. ....AGTAAG
vi525-G3            CTTGGTTGTT TAATAGTACT G...GGCTGG TTAATAGTAC TTGGAATGAT
vi557-H2            CTTGGG...T TAACAG...T ACATCAAATG ATATCTCAAA TGGCACAACA
se9173-J1           GTTGGGATGA GAATAACATT AAGGACACAA ATAGTACAAA TGACAACACA
se9280-J2           GTTGGGATAA GAATAGCATT GAAGCTACAA ATGACACAAG T...NACGCA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TCAAATGACA CTATAATTCT CCCATGCAGA ATAAAGCAAA TTATAAATAT
br20-B1             AC........ .AATCACACT CCCATGTAGA ATAAAACAAA TTGTAAACAT
th14-B2             AC........ .TATCACGCT CCCTTGCAGA ATAAAACAAA TTGTAAACAT
sf162-B3            AC........ .TATCACACT CCCATGCAGA ATAAAACAAA TTATAAACAG
ma959-C1            AG........ .CATAACCCT CCCATGCAGA ATAAAACAAA TTATAAACAT
zm18-C2             AC........ .AATCACACT CCCATGCAGA ATAAAACAAA TTATAAACAT
in868-C3            AC........ .CATCACAAT CCTATGCAGA ATAAAACAAG TTGTAAACAT
ug21-D1             AC........ .AATCACACT CCCATGCAGA ATAAAACAAA TTATAAATAT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             AC........ .TATCATACT TCCATGCAAG ATAAAGCAAA TTATAAACAT
th06-E2             AC........ .TATCATACT TCCATGCAAG ATAAAGCAAA TTGTAAACAT
bz162-F1            AC........ .TATCACTCT CCCATGTCGA ATAAAACAAA TGGTAAACAT
bz163-F2            AC........ .TATCACTCT CCTATGTCGA ATAAAACAAA TGGTAAACAT
ru131-G1            AC........ .TATCACACT CCCATGTAGG ATAAAACAAA TTATAATAAT
lbv21-G2            AA........ .TATCACACT CCCATGTAGA ATAAAACAAA TTGTAAGAAT
vi525-G3            ACACGAAAAG ATATTACACT GCAATGCAAA ATAAAACAAA TTGTGAGAAT
vi557-H2            AT........ .AATTGAACT GCCATGCAGA ATAAAACAAA TTATAAACAT
se9173-J1           AC........ .TATCACAAT ACCATGTAAA ATAAAACAAA TTGTGAGAAT
se9280-J2           AC........ .TATCACAAT ACCATGTAAA ATAAAACAAA TTGTGAGAAT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            GTGGCAGAGA GTAGGACAAG CAATGTATGC CCCTCCCATC ...CAAGGAG
br20-B1             GTGGCAGGAA GTAGGAAAAG CAATGTATGC CCCTCCCATC ...AAGGGAA
th14-B2             GTGGCAGGAA GTAGGAAAAG CAATGTATGC CCCTCCCATC ...AGAGGAC
sf162-B3            GTGGCAGGAA GTAGGAAAAG CAATGTATGC CCCTCCCATC ...AGAGGAC
ma959-C1            GTGGCAGGAG GTAGGACGAG CAATGTATGC CCCTCCCATT ...GAAGGAA
zm18-C2             GTGGCAGGGG GTAGGACAAG CAATGTATGC CCCTCCCATT ...GCAGGAA
in868-C3            GTGGCAGGAG GTAGGACGAG CAATGTATGC CCCTCCCATT ...GAAGGAA
ug21-D1             GTGGCAGGGA GTAGGAAAAG CAATGTATAC CCCTCCCATT ...GAAGGAC
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             GTGGCAGGGA GCAGGACAAG CAATGTATGC TCCTCCCATT ...AGGGGAA
th06-E2             GTGGCAGGGA GCAGGACAAG CAATGTATGC TCCTCCCATC ...AGTGGAA
bz162-F1            GTGGCAGGAA GTAGGACGAA CAATGTATGC CGCTCCCATC ...GCAGGAA
bz163-F2            GTGGCAGGAA GTGGGACGAG CAATGTATGC CGCTCCCATC ...TCAGAAA
ru131-G1            GTGGCAGAGA GTGGGGCAAG CAATGTATGC CCCTCCCATC ...GCAGGAA
lbv21-G2            GTGGCAGAGG GTGGGACAAG CAATGTATGC CCCTCCCATT ...GCAGGAA
vi525-G3            GTGGCAGAGA GTGGGACAAG CAATGTATGC CCCTCCCATC GCAGCAGGAA
vi557-H2            GTGGCAGAGA GTAGGACAAG CAATGTATGC CCCTCCCATC ...AAAGGAA
se9173-J1           GTGGCAAAGA ACAGGACAAG CAATATATGC CCCTCCCATC ...GCAGGAA
se9280-J2           GTGGCAAAGG ACAGGACAAG CAATCTATGC CCCTCCCATT ...GCAGGAA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            TAATAAAGTG TATATCAAAT ATTACAGGAC TTCTATTAAC AAGAGATGGT
br20-B1             AAATTAAATG TTCATCAAAC ATTACAGGGC TACTATTGAC AAGGGATGGT
th14-B2             AAATTAGATG TTCATCAAAT ATTACAGGGT TGCTATTAAC AAGAGATGGT
sf162-B3            AAATTAGATG CTCATCAAAT ATTACAGGAC TGCTATTAAC AAGAGATGGT
ma959-C1            ACATAACATG TAAATCAAAT ATCACAGGAC TACTATTGAC ACGTGGTGGA
zm18-C2             ACATAACATG TAAATCAAAT ATCACAGGAC TACTATTGAC ACGGGATGGA
in868-C3            ACATAACATG TAAATCAAAT ATCACAGGAC TACTATTGGC ACGTGATGGA
ug21-D1             AAATCAACTG TTCATCAACT ATTACAGGAC TATTGTTGAC AAGAGATGGT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             GAATTAATTG TGTATCAAAT ATTACAGGAA TACTATTGAC AAGGGATGGT
th06-E2             GAATTAATTG TGTATCAAAT ATTACAGGAA TACTATTAAC AAGAGATGGT
bz162-F1            ACATTACCTG TAACTCAAAT ATTACAGGTC TACTATTGAC AAGAGACGGT
bz163-F2            ACATTACCTG TAACTCGAAT ATTACAGGTC TACTATTGAC AAGAGATGGT
ru131-G1            ACATCACATG TATTTCAAAC ATTACAGGAC TACTATTAAC AAGAGATGGT
lbv21-G2            ACATTACATG TAAATCAAAC ATTACAGGAC TAATATTAAC AAGAGATGGT
vi525-G3            ACATTGAATG TAGATCAAGC ATTACAGGAC TAATATTAAC AAGAGATGGT
vi557-H2            AAATTACATG TGAATCAAAT ATTACAGGGC TAATATTGAC AAGTGATCAT
se9173-J1           ACATTACATG CAAATCAAAT ATTACAGGAT TATTATTGAC ACGTGATGGA
se9280-J2           ACATTACGTG CACATCAAAT ATTACAGGAT TACTATTGAC ACGTGATGGA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            GG........ .GGA...... TAATAACAGT GCA......A ATGAAACCTT
br20-B1             GG........ .TAA...... TAATGAGATG AAC...ACGA CCGAGATCTT
th14-B2             GG........ .TAA...... TAGTGAGAAC AAG...ACCA CCGAGACCTT
sf162-B3            GG........ .TAA...... AGAGATCAGT AAC...ACCA CCGAGATCTT
ma959-C1            GG........ .TCC...... A...ACTAAC ACA...AAGA CAGAGACATT
zm18-C2             GG........ .GTC...... AAATGATACC ACA...AACA CAGAGACATT
in868-C3            GG........ .AAC...... A...GAGTCA AAT...CATA CAGAGATATT
ug21-D1             GG........ .TGT...... GAAAAATAAT AGT...CAGA ACGAGACCTT
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             GG........ .TGC...... TAATAATGCG .........A ACGAGACCTT
th06-E2             GG........ .TGC...... TAATAATACG AC......TA ACGAGACCTT
bz162-F1            GGGTTAGATG ATGGTAGGAA TACTAGTCAG ACTAATCGGA CTGAGATCTT
bz163-F2            GG........ .TCA...... GAATAATAAT CAG......A CTGAGACCTT
ru131-G1            GG........ .GAA...... CAATAATAAC AGCACAAATA ATGAGACCTT
lbv21-G2            GG........ .GAA...... TAGTACCAAT GGA......A ATGAGACCTT
vi525-G3            GG........ .GAA...... TAATAATAAT ACC......A ATGAGACCTT
vi557-H2            G......... .......... ..TTAATTCT GCAGAAAGTA ATGTTACCTT
se9173-J1           GG........ .AAACA...G GAATGGCAGT GAGAATGGCA CTGAGACCTT
se9280-J2           GG........ .AAACAGGGG GAATGGCAGT GAGAATGGCA CTGAGACCTT
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            CAGACCTACA GGAGGAAATA TGAGGGACAA TTGGAGAAGT GAATTATATA
br20-B1             CAGACCTGGA GGAGGAGATA TGAGGGACAA TTGGAGGAGT GAATTATATA
th14-B2             CAGACCTGGA GGAGGAGATA TGAGGGACAA TTGGAGAAGT GAATTATATA
sf162-B3            CAGACCTGGA GGTGGAGATA TGAGGGACAA TTGGAGAAGT GAATTATATA
ma959-C1            CAGGCCTGGA GGAGGAGATA TGAGGGACAA TTGGAGAAGT GAATTATATA
zm18-C2             CAGACCTGGA GGAGGAGATA TGAGGGACAA TTGGAGAAGT GAACTATATA
in868-C3            CAGACCTGGA GGAGGAGATA TGAGGAACAA TTGGAGAAGT GAATTATATA
ug21-D1             CAGACCTGGA GGGGGAGATA TGAGAGACAA CTGGAGAAAT GAATTATACA
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             CAGACCTGGA GGAGGAAATA TAAAGGACAA TTGGAGAAGT GAATTATATA
th06-E2             CAGACCTGGA GGAGGAAATA TAAAGGACAA TTGGAGAAGT GAATTATATA
bz162-F1            CAGACCTGGG GGAGGAAATA TGAAAGACAA TTGGAGAAGT GAATTATATA
bz163-F2            CAGACCTGGG GGTGGTGATA TGAAAGACTA TTGGAGAAGT GTATTATATA
ru131-G1            CAGACCTGGA GGAGGAGATA TGAGGGACAA TTGGAGAAGT GAATTATATA
lbv21-G2            CAGACCTGCA GGAGGAGACA TGAGGGACAA TTGGAGAAGT GAATTATATA
vi525-G3            CAGACCTGGA GGAGGAGACA TGAGGGGCAA TTGGAGAAGT GAATTATATA
vi557-H2            CAGACCTGGA GGAGGAGATA TGAGGGACAA TTGGAGAAGT GAATTATATA
se9173-J1           CAGACCTACA GGAGGAAATA TGAAAGATAA TTGGAGAAGT GAATTATATA
se9280-J2           CAGACCTACA GGAGGAAATA TGAAGGACAA TTGGAGAAGT GAATTATATA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... TGAGGGACAA TTGGAGAAGT GGGTCATAGC
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AGTATAAAGT AGTAAAAATT GAACCACTAG GAGTAGCACC CACCCCGGCA
br20-B1             AATATAAAGT AGTAAGAATT GAACCATTAG GAATAGCACC CACCAGGGCA
th14-B2             AATATAAAGT AGTGAAAATT GAACCATTAG GAGTAGCACC CACCAAGCCA
sf162-B3            AATATAAAGT AGTAAAAATT GAGCCATTAG GAGTAGCACC CACCAAGGCA
ma959-C1            AGTATAAAGT GGTAGAAATT AAGCCATTGG GAGTAGCACC CACTAAGGCA
zm18-C2             AATATAAAGT GGTAGAAATT AAACCATTGG GCATAGCACC CACTGCGGCA
in868-C3            AATACAAAGT GGTAGAAATT AAGCCATTGG GAGTAGTACC CACTACAGCA
ug21-D1             AATATAAAGT AGTAAGAATT GAACCACTAG GTCTAGCACC CACCAAGGCA
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             AATATAAAGT AGTACAAATT GAACCACTAG GAATAGCACC CACCAGGGCA
th06-E2             AATATAAAGT AGTACAAATT GAACCACTAG GAATAGCACC CACCAGGGCA
bz162-F1            AATATAAAGT AGTAGAAATT GAACCACTAG GAGTAGCACC CACCAAGGCA
bz163-F2            AGTATAAAGT AGTAGAAATT GAACCACTAG GAGTAGCACC CACCAGGGCA
ru131-G1            AGTATAAAGT AGTAAGAATT AAACCACTAG GAGTAGCACC CACCAGG...
lbv21-G2            AGTATAAAGT AATAAAAATT AAACCACTAG GAGTAGCACC CACCAAGGCA
vi525-G3            AGTATAAAGT AGTAAAAATC AAATCACTAG GAGTAGCACC CACCAGGGCA
vi557-H2            AATATAAAGT AGTAAGAGTC GAACCACTAG GATTAGCACC CACCAGGGCA
se9173-J1           AATATAAAGT AGTAGAGCTT GAGCCACTAG GAGTAGCACC CACCAAGGCA
se9280-J2           AATATAAAGT AGTAGAGATT GAGCCACTAG GAGTAGCACC CACCAAGGCA
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   TGTTTCCTG. .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AAGAGAAGAG TGGTGCAG.. .AGAGAAAAA AGAGCAGTTG GA...ATAGG
br20-B1             AAGAGAAGAG TGGTGCAA.. .AGAGAAAAA AGAGCAGTGG GAACATTAGG
th14-B2             AAGAGAAGAG TGGTGCAG.. .AGAGAAAAA AGAGCAGTGG GAACGATAGG
sf162-B3            AAGAGAAGAG TGGTGCAG.. .AGAGAAAAA AGAGCAGTG. ..ACGCTAGG
ma959-C1            AAAAGGAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
zm18-C2             AAAAGGAGAG TGGTGGAGAC GAGAGAAAAA AGAGCAGTGG GA...ATAGG
in868-C3            AAAAGGAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATGGG
ug21-D1             AGGAGAAGAG TGGTGGAA.. .AGAGAAAAA AGAGCAATAG GA...CTGGG
ug46-D3             .......... .......... .......... .......... ..........
th22-E1             AAGAGAAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
th06-E2             AAGAGAAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
bz162-F1            AAAAGACAAG TGGTGAAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
bz163-F2            AAAAGACAAG TGGTGAGG.. .AGAGAAAAA AGAGCAGTGG GA...ATGGG
ru131-G1            .......... .......... .......... .......... ..........
lbv21-G2            AGGAGAAGAG TGGTGGGG.. .AGAGAAAAA AGAGCAATTA CT......GG
vi525-G3            AGGAGAAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAATTG GA...CTGGG
vi557-H2            AGGAGAAGAG TGGTGGAA.. .AGAGAAAAA AGAGCTGTGG GA...CTGGA
se9173-J1           AAAAGAAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
se9280-J2           AAAAGAAGAG TGGTGGAG.. .AGAGAAAAA AGAGCAGTGG GA...ATAGG
primer_ed5          .......... .......... .......... .......... ..........
primer_ed31         .......... .......... .......... .......... ..........
primer_es7          .......... .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... .......... ..........
primer_ed12REVCOMP  .......... .......... .......... .......... ..........


sf170-A3            AGCTGTATTC ATTGGGTTCT TAGGAGCAGC CGGAAGCACT
br20-B1             AGCTATGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCACT
th14-B2             AGCTATGTTC CTTGGGTTCT TGGGAACAGC AGGAAGCACT
sf162-B3            AGCTATGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCACT
ma959-C1            AGCTGTGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCACT
zm18-C2             AGCTGTGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCACT
in868-C3            AGCTGTGTTC CTTGGGTTCT TGGGAGCAGC AGGAACCACT
ug21-D1             AGCTTTGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCACG
ug46-D3             .......... .......... .......... ..........
th22-E1             AGCTATGATC TTTGGGTTCT TAGGAGCAGC AGGAAGCACT
th06-E2             AGCTATGATC TTTGGGTTCT TAGGAGCAGC AGGAAGCACT
bz162-F1            AGCTATGTTC CTTGGGTTCT TGGGAGCAGC AGGAAGCTCT
bz163-F2            AGCTTTGTTC CTTGGGTTCT TGAGCGCGGC AGGAAGCACT
ru131-G1            .......... .......... .......... ..........
lbv21-G2            AGCTGTCTTC CTTGGGTTCT TAGGAGCAGC TGGGAGCACT
vi525-G3            AGCTGTCTTC CTTGGGTTCT TAGGAGCAGC AGGAAGCACT
vi557-H2            AGCTGTTTTC CTTGGGTTCT TGGGAGCAGC AGGGAGCACT
se9173-J1           AGCTGTGTTC CTTGGGTTCT TGGGAACAGC AGGAAGCACT
se9280-J2           AGCTGTGTTC CTTGGGTTCT TGGGAACAGC AGGAAGTACT
primer_ed5          .......... .......... .......... ..........
primer_ed31         .......... .......... .......... ..........
primer_es7          .......... .......... .......... ..........
primer_ed33REVCOMP  .......... .......... .......... ..........
primer_es8REVCOMP   .......... .......... .......... ..........
primer_ed12REVCOMP  .......... CTTGGGTTCT TGGGAGCAGC AGGAAGCACT