<< Worksheet Section 4.1 Identify Region to amplify >>

11. Based on the order of your SNPs (your answer to question #10 on page 3)
identify the base positions of your lowest and highest expected mutations on the diagram below.
This will be the area you need to PCR-amplify and sequence to identify your haplogroup.

a. Note Base pair position of the first mtDNA mutation of your haplogroup.
b. Note Base pair position of the last mtDNA mutation of your haplogroup.

Action: Now run Primer-3 to create the left&right primer list:

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