UCSC In-Silico PCR
 
>chrX:955403-956393 991bp TACCTCCCAGCGCTTGTATC CCCTCATGGTCATCGAATTT
TACCTCCCAGCGCTTGTATCtgacacatggatggaaggatacatcatcta
gaagtcttgggttgataagggtcattgtgagatcaggcattccggacagt
ttacagcaaacgtcaacctgaaatttgtcaaggataagatgaatatattc
ttaatatttccaaatatttttcagaatttttacctccagaacacatgcta
gttcaaaacgtcagcacccaaatttggtggtgtgaagtattatattatta
aaatattttcatttggtttatttataattttgtatttaaatctttagagg
tgcacagaactaaacaattttgcaatccgatattcactacaattacaaat
tgatagagattatcagtagccataatcgctttatttccgcaaaatacgtt
ttaagttttgaagtttaaaagattttggcatataatactactacaaaggt
ccgcaaacctctggttctacaaaaatgttttaataaacaggacaaaatag
tatgttcaatatgaaggcataatttgattttttgtttcaaatactcaaaa
ctcacatatccctgaatctcggcaaaaacagtggatccttgcttatcaac
aatcacgtcaatttcctcaatcacatcaaaatacgcttcattatttgtgt
acttcactccttgtcgcctccatggaatatttgatagctgccccgttggc
agggtttcagaaaggtttgtacggccggtgacctgattagcaatattgcg
cagaaagttgggcggcttgatcaaatcttgaaggatgttcatttccgtca
ccagtggaaagccgttgtccagcatttcatcgagcaactggaaatcggaa
tgttaagcctcaattttgaagttataaagctcacctcaaaaaccatcacg
caattttctttcatagaagaatccgaaaattcatcaaagtattgtgtgaa
ggtttgaattactctgtgtaaAAATTCGATGACCATGAGGG

Primer Melting Temperatures
  Forward: 60.2 C tacctcccagcgcttgtatc
Reverse: 59.8 C ccctcatggtcatcgaattt
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