6. Mark the conserve region of C2 and C3 in 4., then use it in designing a pair of PCR primers. The V3 region of HIV-1 subtype-B and E must be able to amplified by your PCR primers.

>PCRtemp:
GCCAGTGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATC
AGATCTGAAATCTCACAAACAATGCAAAACCATAATAGTCACTAATGAATCTGTAGAAAT
AATTGTACAGACCCCAACAACAATACAAGAAAAAGTATAAATATAGGACCAGGGAGAGCA
TATTCTATAACAGGAGACATAATAGGAGATATAAGACAAGCATATTGTAATTATGGAACA
AAATGGAATAAACTTTAAAACAGGTAGCTAAAATTAAAAGACATTTAAAAAAATAAGAAA
AAAAAACAATAATCTTTAACACCTCAGGAGGGACCAGAAATTCAATGCATTTTTAATTGT
GAGGGGAATTTTTCTATGAATACAACACAACTGTTTAATAGTACTTGGAAAATGAAAAAA
AAAAACCAGAGGGGTAATGACACAAAAAAAAAAATATCACACTCCATGCAGAATAAAACA
AATTATAAACATGTGGCAGGAGTAGGAAAGCAATGTATGCCCTCCCATCAGTGGAAATTA
ATGTTATCAAATATTACAGGAATACTATTACAAGAGATGGTGGTA

>V3:
tgtacaagacccaacaacaatataagaaaaagaatacatatagggccagggagagcattt

tatacaacaggaaaaataataggaggtataagacaagcacat
 
 

Sequence Length: 585 bases

  

A - 268 (45.81%)
 
C - 84 (14.36%)
 
G - 99 (16.92%)
 
T - 134 (22.91%)
 
N - 0 ( 0.00%)
 

1 
GCCAGTGTAT CAACTCAACT GCTGTTAAAT GGCAGTCTAG CAGAAGAAGA GATAATAATC
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
CGGTCACATA GTTGAGTTGA CGACAATTTA CCGTCAGATC GTCTTCTTCT CTATTATTAG
61 
AGATCTGAAA TCTCACAAAC AATGCAAAAC CATAATAGTC ACTAATGAAT CTGTAGAAAT
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TCTAGACTTT AGAGTGTTTG TTACGTTTTG GTATTATCAG TGATTACTTA GACATCTTTA
121 
AATTGTACAG ACCCCAACAA CAATACAAGA AAAAGTATAA ATATAGGACC AGGGAGAGCA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTAACATGTC TGGGGTTGTT GTTATGTTCT TTTTCATATT TATATCCTGG TCCCTCTCGT
181 
TATTCTATAA CAGGAGACAT AATAGGAGAT ATAAGACAAG CATATTGTAA TTATGGAACA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
ATAAGATATT GTCCTCTGTA TTATCCTCTA TATTCTGTTC GTATAACATT AATACCTTGT
241 
AAATGGAATA AACTTTAAAA CAGGTAGCTA AAATTAAAAG ACATTTAAAA AAATAAGAAA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTACCTTAT TTGAAATTTT GTCCATCGAT TTTAATTTTC TGTAAATTTT TTTATTCTTT
301 
AAAAAACAAT AATCTTTAAC ACCTCAGGAG GGACCAGAAA TTCAATGCAT TTTTAATTGT
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTTTTGTTA TTAGAAATTG TGGAGTCCTC CCTGGTCTTT AAGTTACGTA AAAATTAACA
361 
GAGGGGAATT TTTCTATGAA TACAACACAA CTGTTTAATA GTACTTGGAA AATGAAAAAA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
CTCCCCTTAA AAAGATACTT ATGTTGTGTT GACAAATTAT CATGAACCTT TTACTTTTTT
421 
AAAAACCAGA GGGGTAATGA CACAAAAAAA AAAATATCAC ACTCCATGCA GAATAAAACA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTTTGGTCT CCCCATTACT GTGTTTTTTT TTTTATAGTG TGAGGTACGT CTTATTTTGT
481 
AATTATAAAC ATGTGGCAGG AGTAGGAAAG CAATGTATGC CCTCCCATCA GTGGAAATTA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTAATATTTG TACACCGTCC TCATCCTTTC GTTACATACG GGAGGGTAGT CACCTTTAAT
541 
ATGTTATCAA ATATTACAGG AATACTATTA CAAGAGATGG TGGTA
|||||||||| |||||||||| |||||||||| |||||||||| |||||
TACAATAGTT TATAATGTCC TTATGATAAT GTTCTCTACC ACCAT

 
  


Forward Primer
GCCAGTGTATCAACTCAACTGC
A - 6 (27.27%) C - 7 (31.82%)
G - 4 (18.18%) T - 5 (22.73%)
N - 0 ( 0.00%)
Coordinates: 1 .. 22
Tm
Nearest Neighbor Tm (standard): 59.81oC
%GC Method Tm: 54.84oC
2(A+T) + 4(G+C) Tm: 66.00oC
 
Reverse Primer
AACATTAATTTCCACTGATGGG
A - 7 (31.82%) C - 4 (18.18%)
G - 4 (18.18%) T - 7 (31.82%)
N - 0 ( 0.00%)
Coordinates: 545 .. 524
Tm
Nearest Neighbor Tm (standard): 57.86oC
%GC Method Tm: 49.25oC
2(A+T) + 4(G+C) Tm: 60.00oC
 

1 
GCCAGTGTAT CAACTCAACT GCTGTTAAAT GGCAGTCTAG CAGAAGAAGA GATAATAATC
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
CGGTCACATA GTTGAGTTGA CGACAATTTA CCGTCAGATC GTCTTCTTCT CTATTATTAG
61 
AGATCTGAAA TCTCACAAAC AATGCAAAAC CATAATAGTC ACTAATGAAT CTGTAGAAAT
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TCTAGACTTT AGAGTGTTTG TTACGTTTTG GTATTATCAG TGATTACTTA GACATCTTTA
121 
AATTGTACAG ACCCCAACAA CAATACAAGA AAAAGTATAA ATATAGGACC AGGGAGAGCA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTAACATGTC TGGGGTTGTT GTTATGTTCT TTTTCATATT TATATCCTGG TCCCTCTCGT
181 
TATTCTATAA CAGGAGACAT AATAGGAGAT ATAAGACAAG CATATTGTAA TTATGGAACA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
ATAAGATATT GTCCTCTGTA TTATCCTCTA TATTCTGTTC GTATAACATT AATACCTTGT
241 
AAATGGAATA AACTTTAAAA CAGGTAGCTA AAATTAAAAG ACATTTAAAA AAATAAGAAA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTACCTTAT TTGAAATTTT GTCCATCGAT TTTAATTTTC TGTAAATTTT TTTATTCTTT
301 
AAAAAACAAT AATCTTTAAC ACCTCAGGAG GGACCAGAAA TTCAATGCAT TTTTAATTGT
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTTTTGTTA TTAGAAATTG TGGAGTCCTC CCTGGTCTTT AAGTTACGTA AAAATTAACA
361 
GAGGGGAATT TTTCTATGAA TACAACACAA CTGTTTAATA GTACTTGGAA AATGAAAAAA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
CTCCCCTTAA AAAGATACTT ATGTTGTGTT GACAAATTAT CATGAACCTT TTACTTTTTT
421 
AAAAACCAGA GGGGTAATGA CACAAAAAAA AAAATATCAC ACTCCATGCA GAATAAAACA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTTTTGGTCT CCCCATTACT GTGTTTTTTT TTTTATAGTG TGAGGTACGT CTTATTTTGT
481 
AATTATAAAC ATGTGGCAGG AGTAGGAAAG CAATGTATGC CCTCCCATCA GTGGAAATTA
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
TTAATATTTG TACACCGTCC TCATCCTTTC GTTACATACG GGAGGGTAGT CACCTTTAAT
541 
ATGTTATCAA ATATTACAGG AATACTATTA CAAGAGATGG TGGTA
|||||||||| |||||||||| |||||||||| |||||||||| |||||
TACAATAGTT TATAATGTCC TTATGATAAT GTTCTCTACC ACCAT
>PCRproduct:
GCCAGTGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGATAATAATCA

GATCTGAAATCTCACAAACAATGCAAAACCATAATAGTCACTAATGAATCTGTAGAAATAA

TTGTACAGACCCCAACAACAATACAAGAAAAAGTATAAATATAGGACCAGGGAGAGCATAT

TCTATAACAGGAGACATAATAGGAGATATAAGACAAGCATATTGTAATTATGGAACAAAAT

GGAATAAACTTTAAAACAGGTAGCTAAAATTAAAAGACATTTAAAAAAATAAGAAAAAAAA

ACAATAATCTTTAACACCTCAGGAGGGACCAGAAATTCAATGCATTTTTAATTGTGAGGGG

AATTTTTCTATGAATACAACACAACTGTTTAATAGTACTTGGAAAATGAAAAAAAAAAACC

AGAGGGGTAATGACACAAAAAAAAAAATATCACACTCCATGCAGAATAAAACAAATTATAA

ACATGTGGCAGGAGTAGGAAAGCAATGTATGCCCTCCCATCAGTGGAAATTAATGTT
 
 
 
H1 H2 H3 H4 H5 H6 H7 H8 H9-H13