<< Worksheet Section 4.2: Choose your primers >>

Choose a left (forward) primer and right (reverse) primer from the primer list generated in the previous step:

Action:
Step 4.1 (Create left and right primer list)

Make sure starting postion + length of left primer is lower than number noted in #11a above.
Make sure starting postion of right primer is higher than number noted in #11b above.

12. After choosing your primer pair:
        a. Write down your Left primer in 5' to 3' direction, its length and its starting position.
        a. Write down your Right primer in 5' to 3' direction, its length and its starting position.
The primers will bracket the region to be amplified.

Extended Hyper-variable Segment I (15919 - 16569)

   |15919    |         |         |         |         |         |         |         |         |         |  16027|
5'-TGTAAaCCggAgAtGAAAACCtttTtCcAAGGaCAaaTCAGAGAAAAAGtCTTTAACTCCACCATTAGCACCCaAAGCTAAGATtCTAATTTAAACTAtTCTCTGTtCT-3'
3'-ACATTtGGccTcTaCTTTTGGaaaAaGgTTCCtGTttAGTCTCTTTTTCaGAAATTGAGGTGGTAATCGTGGGtTTCGATTCTAaGATTAAATTTGATaAGAGACAaGA-5'
   |1        |         |         |         |         |         |         |         |         |         |    109|
   |16028    |         |         |         |         |         |         |         |         |         |  16136|
5'-TTCaTGGGGaagCagATTTGgGtacCACCCAagtAtTGacTcaccCatcAAcaaccgctATgTAtttcGtaCATtActgccagcCaccAtgaaTattGtaCagtaccat-3'
3'-AAGtACCCCttcGtcTAAACcCatgGTGGGTtcaTaACtgAgtggGtagTTgttggcgaTAcATaaagCatGTAaTgacggtcgGtggTacttAtaaCatGtcatggta-5'
   |110      |         |         |         |         |         |         |         |         |         |    218|
   |16137    |         |         |         |         |         |         |         |         |         |  16245|
5'-aaatAcTtgaccAcCtgtagtaCataaaaacccaatccacatcaaaaccctccccccatgctTAcAagcaagtacagcaatcaaccttcAactgtcacacaTcaaCtgc-3'  
3'-tttaTgAactggTgGacatcatGtatttttgggttaggtgtagttttgggaggggggtacgaATgTtcgttcatgtcgttagttggaagTtgacagtgtgtAgttGacg-5'
   |219      |         |         |         |         |         |         |         |         |         |    327|
   |16246    |         |         |         |         |         |         |         |         |         |  16354|
5'-aactcCaaagccacccctcacCcactaggaTatcaaCAaacctacccacccttaacagtacAtagcacaTaaagccatttaccGtacatagcacaTtacagtcaaatcc-3'
3'-ttgagGtttcggtggggagtgGgtgatcctAtagttGTttggatgggtgggaattgtcatgTatcgtgtAtttcggtaaatggCatgtatcgtgtAatgtcagtttagg-5'
   |328      |         |         |         |         |         |         |         |         |         |    436|
   |16355    |         |         |         |         |         |         |         |         |         |  16463|
5'-cttctcgtccccatGGaTGAcCcCCctCAgATAggggTCCcTTgacCACCATCCTCCGTGAAAtcAAtAtCCCgcACAAGAGTgCtACTCTCCTCGCTCCGgGCCCATa-3'
3'-gaagagcaggggtaCCtACTgGgGGgaGTcTATccccAGGgAActgGTGGTAGGAGGCACTTTAgTTaTaGGGcgTGTTCTCAcGaTGAGAGGAGCGAGGCcCGGGTAt-5'
   |437      |         |         |         |         |         |         |         |         |         |    545|
   |16464    |         |         |         |         |         |         |         |         |         16569|
5'-AcACtTggGgGTAGCTAAagTGAAcTGTATCCGaCAtCTGGTTCCTACTTCAGGgcCATAaAgcCTAAATAGCCCAcACGTTCCcCTTAAATAAGACATCACGaTG-3'-end
3'-TgTGaAccCcCATCGATTtcACTTgACATAGGCtGTaGACCAAGGATGAAGTCCcgGTATtTcgGATTTATCGGGTgTGCAAGGgGAATTTATTCTGTAGTGCtAC-5'-end
   |546      |         |         |         |         |         |         |         |         |         | 651|
 
    16037 - 16368   highly variable region in HVSI