You can ignore the *_hap* alternate chromosomes. Use this alignment:
chr6:31323962-31324314 -Galt 6/28/2011 7:34 AM, Ying Li: > Hi > > I have two primers that I used as input for in silico PCR. The search ended > giving me several PCR products (listed below). As I am not familiar with > human genome sequences, I was just wondering if the multiple results meant > that my primers will anneal to multiple sites on human genome or these > multiple results are actually the same sites but with different names. > > > >> chr6_ssto_hap7:2657722-2658074<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=200335593&db=hg19&position=chr6_ssto_hap7:2657722-2658074&hgPcrResult=pack> >> 353bp CCCGGTTTCATTTTCAGTTG CCTTCCCGTTCTCCAGGTAT > > CCCGGTTTCATTTTCAGTTGaggccaaaatccccgcgggttggtcggggc > > ggggcggggctcgggggacggggctgaccgcggggccggggccagggtct > > cacatcatccagaggatgtacggctgcgacgtggggccggacgggcgcct > > cctccgcgggtatgaccaggacgcctacgacggcaaggattacatcgccc > > tgaacgaggacctgagctcctggaccgcggcggacaccgcggctcagatc > > acccagcgcaagtgggaggcggcccgtgtggcggagcaggacagagccta > > cctggagggcctgtgcgtggagtcgctccgcagATACCTGGAGAACGGGA > > AGG > >> chr6_mcf_hap5:2703754-2704106<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=200335593&db=hg19&position=chr6_mcf_hap5:2703754-2704106&hgPcrResult=pack> >> 353bp CCCGGTTTCATTTTCAGTTG CCTTCCCGTTCTCCAGGTAT > > CCCGGTTTCATTTTCAGTTGaggccaaaatccccgcgggttggtcggggc > > ggggcggggctcgggggacggggctgaccgcggggcctgggccagggtct > > cacaccctccagaggatgtacggctgcgacgtggggccggacgggcgcct > > cctccgcgggcatgaccagtccgcctacgacggcaaggattacatcgccc > > tgaacgaggacctgagctcctggaccgcggcggacacggcggctcagatc > > acccagcgcaagtgggaggcggcccgtgaggcggagcagtggagagccta > > cctggagggcctgtgcgtggagtggctccgcagATACCTGGAGAACGGGA > > AGG > >> chr6_mann_hap4:2670418-2670770<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=200335593&db=hg19&position=chr6_mann_hap4:2670418-2670770&hgPcrResult=pack> >> 353bp CCCGGTTTCATTTTCAGTTG CCTTCCCGTTCTCCAGGTAT > > CCCGGTTTCATTTTCAGTTGaggccaaaatccccgcgggttggtcggggc > > ggggcggggctcgggggacggggctgaccgcggggccggggccagggtct > > cacatcatccagaggatgtacggctgcgacgtggggccggacgggcgcct > > cctccgcgggtatgaccaggacgcctacgacggcaaggattacatcgccc > > tgaacgaggacctgagctcctggaccgcggcggacaccgcggctcagatc > > acccagcgcaagtgggaggcggcccgtgtggcggagcagctgagagccta > > cctggagggcctgtgcgtggagtcgctccgcagATACCTGGAGAACGGGA > > AGG > >> chr6:31323962-31324314<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=200335593&db=hg19&position=chr6:31323962-31324314&hgPcrResult=pack> >> 353bp CCCGGTTTCATTTTCAGTTG CCTTCCCGTTCTCCAGGTAT > > CCCGGTTTCATTTTCAGTTGaggccaaaatccccgcgggttggtcggggc > > ggggcggggctcgggggactgggctgaccgcggggccggggccagggtct > > cacaccctccagagcatgtacggctgcgacgtggggccggacgggcgcct > > cctccgcgggcatgaccagtacgcctacgacggcaaggattacatcgccc > > tgaacgaggacctgcgctcctggaccgccgcggacacggcggctcagatc > > acccagcgcaagtgggaggcggcccgtgaggcggagcagcggagagccta > > cctggagggcgagtgcgtggagtggctccgcagATACCTGGAGAACGGGA > > AGG > >> chr6_cox_hap2:2836649-2837002<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=200335593&db=hg19&position=chr6_cox_hap2:2836649-2837002&hgPcrResult=pack> >> 354bp CCCGGTTTCATTTTCAGTTG CCTTCCCGTTCTCCAGGTAT > > CCCGGTTTCATTTTCAGTTGaggccaaaatccccgcgggttggtcggggc > > ggggcggggctcggggggacggggctgaccgcggggccggggccagggtc > > tcacaccctccagagcatgtacggctgcgacgtggggccggacgggcgcc > > tcctccgcgggcataaccagtacgcctacgacggcaaggattacatcgcc > > ctgaacgaggacctgcgctcctggaccgcggcggacaccgcggctcagat > > cacccagcgcaagtgggaggcggcccgtgtggcggagcaggacagagcct > > acctggagggcacgtgcgtggagtggctccgcagATACCTGGAGAACGGG > > AAGG > > > Thanks. > > Ying > > Ying Li, PhD > Senior Scientist > > BioHelix Corporation > 500 Cummings Ctr > Suite 5550 > Beverly MA 01915 > Tel: 866-800-5458 > Fax: 978-927-3382 > www.biohelix.com > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
