UCSC In-Silico PCR
 
>chrI:3879889-3880534 646bp TTGTACCGTTTTACCGGCTC TGAACAAAACGACGCAAAAA
TTGTACCGTTTTACCGGCTCcacgtacaaatgaaatatttcctttgttca
ttgagacctgagtaattgatcctgctccatccgaaggttgctgctgttgc
tgatccaatgaatccatcggattcgacgaagtcgtagtctcctgtgcctt
tcgttcagcatccacacgcatttgtacagatgtcagtgtgacattcacgt
tgtatgacgcttcgactgatctacgaacacgaagcatgtcacgaacagtt
gcctcgtttccatgagcaacttcaaagtttttccacgtatcccagaactt
tacatgaacttttggatcggaaatctcggcggcgtgcgcgtagatcgctc
gggctcggtcaatctctccgaccgtcgtctcgagctgagcataccgcaag
ctcattgctcgagacttatcctctggcaattcggaaatcgctcgttcaaa
gatgggccggcactgcgcgattccatacatttcctggacctttttgatgt
agatattgtacatctaaaatgacaattttgaagaatttgcgggttttatc
gggttttatcgtgatttttcgtttgaaaaattgaatttcgcgaaattttg
ttgttttgaagtgtttttaactataaTTTTTGCGTCGTTTTGTTCA

Primer Melting Temperatures
  Forward: 60.0 C ttgtaccgttttaccggctc
Reverse: 60.3 C tgaacaaaacgacgcaaaaa
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