UCSC In-Silico PCR
  
>chr21_GL383581v2_alt:31340+31687 348bp AAAGGTCTGGTATACTGAACTGGTAAAC CCATGAGACCTGCTGTCTCT
AAAGGTCTGGTATACTGAACTGGTAAACtaattacaattttgctttccaa
cctcctcaagtatttaaaagacccaactcagcccatcttagaggccttgg
acaaggacagctcaccaaaggatgacgtctgggactctgtgtccattatc
tcgtttccggaaaaggagcaagaagatgttctccaaacgctttgaaccaa
agcatgggcctagcccactggctccctggaagagatcaagccatcggagc
tgctagagttctgtctggactttccagagaccagtattcccttttgctgc
ctctaaaaggcctgtccctgcagacatgAGAGACAGCAGGTCTCATGG
>chr21:33436768+33437115 348bp AAAGGTCTGGTATACTGAACTGGTAAAC CCATGAGACCTGCTGTCTCT
AAAGGTCTGGTATACTGAACTGGTAAACtaattacaattttgctttccaa
cctcctcaagtatttaaaagacccaactcagcccatcttagaggccttgg
acaaggacagctcaccaaaggatgacgtctgggactctgtgtccattatc
tcgtttccggaaaaggagcaagaagatgttctccaaacgctttgaaccaa
agcatgggcctagcccactggctccctggaagagatcaagccatcggagc
tgctagagttctgtctggactttccagagaccagtattcccttttgctgc
ctctaaaaggcctgtccctgcagacatgAGAGACAGCAGGTCTCATGG

Notes on the results above
  What is chrom_alt?

Primer Melting Temperatures
  Forward: 60.4 C aaaggtctggtatactgaactggtaaac
Reverse: 57.9 C ccatgagacctgctgtctct
The temperature calculations are done assuming 50 mM salt and 50 nM annealing oligo concentration. The code to calculate the melting temp comes from Primer3, the formula by Rychlik W, Spencer WJ and Rhoads RE NAR 1990, which can be activated in Primer3 with PRIMER_TM_FORMULA=0.

Help
  What is chr_alt & chr_fix?
Replicating in-Silico PCR results on local machine