| Primer ID | Sequence (5' → 3') | Size (bp) | GC (%) | Tm (°C) | ΔG (kcal/mol) | PBN* | MBN* |
|---|---|---|---|---|---|---|---|
| P1 | AAGTCAATAGAAGCCGGCGTA | 21 | 47.62 | 60.04 | -22.40 | 7 | 6 |
| P2 | ACAGGCTCCTCTAGAGGGATAT | 22 | 50.00 | 59.54 | -22.23 | 7 | 12 |
| P3 | TTTGCAAGGAGAGCCAAAGC | 20 | 50.00 | 59.83 | -21.78 | 35 | 30 |
| P4 | AGAGGGTTCTGTGGGCAAAT | 20 | 50.00 | 59.74 | -21.42 | 35 | 30 |
| P5 | CTAGGGATAACAGCGCAATCCT | 22 | 50.00 | 60.49 | -23.10 | 16 | 19 |
| P6 | TCTCTTGTCCTTTCGTACAGGG | 22 | 50.00 | 59.96 | -22.82 | 14 | 13 |
No hairpins found.
No dimers found.
| Amp ID | Product Name | Fp x Rp | Product Size (bp) | Fp Tm (°C) | Rp Tm (°C) | Fp ΔG (kcal/mol) | Rp ΔG (kcal/mol) |
|---|---|---|---|---|---|---|---|
| 1 | chrM | P1 x P2 | 290 | 61.11 | 60.34 | -23.09 | -23.07 |
| 2 | chrM | P5 x P6 | 212 | 60.65 | 60.15 | -23.83 | -23.57 |
| 3 | chrM | P3 x P4 | 196 | 59.32 | 61.04 | -21.66 | -22.31 |
Size = 290 bp, GC content = 43.45%
F: Tm = 61.11 °C, ΔG = -23.09 kcal/mol
R: Tm = 60.34 °C, ΔG = -23.07 kcal/mol
Binding sites: 918(21/21) ... 1207(22/22)
>>>P1
1 21
5' AAGTCAATAGAAGCCGGCGTA 3'
::::::::::::::::::::: 1207
5' AAGTCAATAGAAGCCGGCGTAaagagtgttttagat...acctggcggtgcttcATATCCCTCTAGAGGAGCCTGT 3'
918 ::::::::::::::::::::::
3' ATATCCCTCTAGAGGAGCCTGT 5'
22 1
P2<<<
>Amp_1 P1 + P2 ==> spec/db/hg38.fa:chrM:917-1207
AAGTCAATAGAAGCCGGCGTAaagagtgttttagatcaccccctccccaataaagctaaaactcacctgagttgtaaaaa
actccagttgacacaaaatagactacgaaagtggctttaacatatctgaacacacaatagctaagacccaaactgggatt
agataccccactatgcttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccacagct
taaaactcaaaggacctggcggtgcttcATATCCCTCTAGAGGAGCCTGT
Size = 212 bp, GC content = 44.81%
F: Tm = 60.65 °C, ΔG = -23.83 kcal/mol
R: Tm = 60.15 °C, ΔG = -23.57 kcal/mol
Binding sites: 2929(22/22) ... 3140(22/22)
>>>P5
1 22
5' CTAGGGATAACAGCGCAATCCT 3'
:::::::::::::::::::::: 3140
5' CTAGGGATAACAGCGCAATCCTattctagagtccata...tacnttcaaattcctCCCTGTACGAAAGGACAAGAGA 3'
2929 ::::::::::::::::::::::
3' CCCTGTACGAAAGGACAAGAGA 5'
22 1
P6<<<
>Amp_2 P5 + P6 ==> spec/db/hg38.fa:chrM:2928-3140
CTAGGGATAACAGCGCAATCCTattctagagtccatatcaacaatagggtttacgacctcgatgttggatcaggacatcc
cgatggtgcagccgctattaaaggttcgtttgttcaacgattaaagtcctacgtgatctgagttcagaccggagtaatcc
aggtcggtttctatctacnttcaaattcctCCCTGTACGAAAGGACAAGAGA
Size = 196 bp, GC content = 45.41%
F: Tm = 59.32 °C, ΔG = -21.66 kcal/mol
R: Tm = 61.04 °C, ΔG = -22.31 kcal/mol
Binding sites: 1876(20/20) ... 2071(20/20)
>>>P3
1 20
5' TTTGCAAGGAGAGCCAAAGC 3'
:::::::::::::::::::: 2071
5' TTTGCAAGGAGAGCCAAAGCtaagacccccgaaac...ttagttcaactttaaATTTGCCCACAGAACCCTCT 3'
1876 ::::::::::::::::::::
3' ATTTGCCCACAGAACCCTCT 5'
20 1
P4<<<
>Amp_3 P3 + P4 ==> spec/db/hg38.fa:chrM:1875-2071
TTTGCAAGGAGAGCCAAAGCtaagacccccgaaaccagacgagctacctaagaacagctaaaagagcacacccgtctatg
tagcaaaatagtgggaagatttataggtagaggcgacaaacctaccgagcctggtgatagctggttgtccaagatagaat
cttagttcaactttaaATTTGCCCACAGAACCCTCT
| Database | canFam6.fa, hg38.fa, GCF_000005845.2_ASM584v2_genomic.fna |
| Kvalue | 9 |
| MisMatch | 0 |
| Product Min Size (bp) | 0 |
| Product Max Size (bp) | 500 |
| Tm (°C) | 47 |
| Concentration of monovalent cations (mM) | 50 |
| Concentration of divalent cations (mM) | 1.5 |
| Concentration of dNTPs (mM) | 0.25 |
| Concentration of annealing oligos (nM) | 50 |