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BjornFJohansson/gist:73ad364ac5617dd7d8b4c3df99bced1c

Last active November 16, 2025 16:21
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gistfile1.txt
This is the assumed sequence: https://www.ncbi.nlm.nih.gov/nuccore/U25676.1
Pydnaweb PCR simulation with original primers:
---
limit: 13
---
# pcr
| Component | Name | Size | Seguid |
|-------------|----------------|--------|--------------------------------------|
| fw primer | Forward | 36 | lsseguid=8o4wVLIKd0hFeJxoKr5zfDoKmGQ |
| rv primer | Reverse | 30 | lsseguid=z3lPrqDVs6xvSDfqzbt_Nu4HDS4 |
| template | HSU25676 | 825 | ldseguid=7XiWQtFc80Br1m3ETGnU9JIMUag |
| pcr product | 497bp_PCR_prod | 497 | ldseguid=i3qqZAa2A-F94tZCL0L0kdvwhmQ |
```
5ATGTACAGGATGCAACTCCT...TCATCTCAACACT3
|||||||||||||
3agtagagttgtgactgaactCCCGGGCGCG5
5GCGCGCTAGCGCCACCatgtacaggatgcaactcct3
||||||||||||||||||||
3TACATGTCCTACGTTGAGGA...AGTAGAGTTGTGA5
```
Suggested program for Taq DNA polymerase.
```
|95°C|95°C | |tmf:59.1
|____|_____ 72°C|72°C|tmr:40.4
|3min|30s \ 50.0°C _____|____|45s/kb
| | \______/ 0:30|5min|GC 41%
| | 30s | |497bp
```
```
>Forward lsseguid=8o4wVLIKd0hFeJxoKr5zfDoKmGQ (fw)
GCGCGCTAGCGCCACCatgtacaggatgcaactcct
>Reverse lsseguid=z3lPrqDVs6xvSDfqzbt_Nu4HDS4 (rv)
GCGCGGGCCCtcaagtcagtgttgagatga
>HSU25676 ldseguid=7XiWQtFc80Br1m3ETGnU9JIMUag (template)
ATCACTCTCTTTAATCACTACTCACATTAACCTCAACTCCTGCCACAATGTACAGGATGCAACTCCTGTCTTGCATTGCACTAATTCTTGCACTTGTCACAAACAGTGCACCTACTTCAAGTTCGACAAAGAAAACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGATTTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTCACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACAGCTTCAGTGTCTAGAAGAAGAACTCAAACCTCTGGAGGAAGTGCTGAATTTAGCTCAAAGCAAAAACTTTCACTTAAGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAAACAACATTCATGTGTGAATATGCAGATGAGACAGCAACCATTGTAGAATTTCTGAACAGATGGATTACCTTTTGTCAAAGCATCATCTCAACACTAACTTGATAATTAAGTGCTTCCCACTTAAAACATATCAGGCCTTCTATTTATTTATTTAAATATTTAAATTTTATATTTATTGTTGAATGTATGGTTGCTACCTATTGTAACTATTATTCTTAATCTTAAAACTATAAATATGGATCTTTTATGATTCTTTTTGTAAGCCCTAGGGGCTCTAAAATGGTTTACCTTATTTATCCCAAAAATATTTATTATTATGTTGAATGTTAAATATAGTATCTATGTAGATTGGTTAGTAAAACTATTTAATAAATTTGATAAATATAAAAAAAAAAAACAAAAAAAAAAA
>497bp_PCR_prod ldseguid=i3qqZAa2A-F94tZCL0L0kdvwhmQ (pcr product)
GCGCGCTAGCGCCACCatgtacaggatgcaactcctGTCTTGCATTGCACTAATTCTTGCACTTGTCACAAACAGTGCACCTACTTCAAGTTCGACAAAGAAAACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGATTTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTCACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACAGCTTCAGTGTCTAGAAGAAGAACTCAAACCTCTGGAGGAAGTGCTGAATTTAGCTCAAAGCAAAAACTTTCACTTAAGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAAACAACATTCATGTGTGAATATGCAGATGAGACAGCAACCATTGTAGAATTTCTGAACAGATGGATTACCTTTTGTCAAAGCAtcatctcaacactgacttgaGGGCCCGCGC
DNA sequence for a His-tag 5'-CAT CAC CAT CAC CAT CAC-3'
PCR with histag reverse primer, the last sequence is the PCR product with histag.
---
limit: 13
---
# pcr
| Component | Name | Size | Seguid |
|-------------|----------------|--------|--------------------------------------|
| fw primer | Forward | 36 | lsseguid=8o4wVLIKd0hFeJxoKr5zfDoKmGQ |
| rv primer | Reverse | 48 | lsseguid=OPMs2nuWvGwXfUCyAxTbqJY6ZnA |
| template | HSU25676 | 825 | ldseguid=7XiWQtFc80Br1m3ETGnU9JIMUag |
| pcr product | 515bp_PCR_prod | 515 | ldseguid=3G9oH0hELkNNx6fy3rIHzNBMaio |
```
5ATGTACAGGATGCAACTCCT...TCATCTCAACACT3
|||||||||||||
3agtagagttgtgactgaGTAGTGGTAGTGGTAGTGactCCCGGGCGCG5
5GCGCGCTAGCGCCACCatgtacaggatgcaactcct3
||||||||||||||||||||
3TACATGTCCTACGTTGAGGA...AGTAGAGTTGTGA5
```
Suggested program for Taq DNA polymerase.
```
|95°C|95°C | |tmf:59.1
|____|_____ 72°C|72°C|tmr:40.4
|3min|30s \ 50.2°C _____|____|45s/kb
| | \______/ 0:30|5min|GC 41%
| | 30s | |515bp
```
```
>Forward lsseguid=8o4wVLIKd0hFeJxoKr5zfDoKmGQ (fw)
GCGCGCTAGCGCCACCatgtacaggatgcaactcct
>Reverse lsseguid=OPMs2nuWvGwXfUCyAxTbqJY6ZnA (rv)
GCGCGGGCCCtcaGTGATGGTGATGGTGATGagtcagtgttgagatga
>HSU25676 ldseguid=7XiWQtFc80Br1m3ETGnU9JIMUag (template)
ATCACTCTCTTTAATCACTACTCACATTAACCTCAACTCCTGCCACAATGTACAGGATGCAACTCCTGTCTTGCATTGCACTAATTCTTGCACTTGTCACAAACAGTGCACCTACTTCAAGTTCGACAAAGAAAACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGATTTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTCACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACAGCTTCAGTGTCTAGAAGAAGAACTCAAACCTCTGGAGGAAGTGCTGAATTTAGCTCAAAGCAAAAACTTTCACTTAAGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAAACAACATTCATGTGTGAATATGCAGATGAGACAGCAACCATTGTAGAATTTCTGAACAGATGGATTACCTTTTGTCAAAGCATCATCTCAACACTAACTTGATAATTAAGTGCTTCCCACTTAAAACATATCAGGCCTTCTATTTATTTATTTAAATATTTAAATTTTATATTTATTGTTGAATGTATGGTTGCTACCTATTGTAACTATTATTCTTAATCTTAAAACTATAAATATGGATCTTTTATGATTCTTTTTGTAAGCCCTAGGGGCTCTAAAATGGTTTACCTTATTTATCCCAAAAATATTTATTATTATGTTGAATGTTAAATATAGTATCTATGTAGATTGGTTAGTAAAACTATTTAATAAATTTGATAAATATAAAAAAAAAAAACAAAAAAAAAAA
>515bp_PCR_prod ldseguid=3G9oH0hELkNNx6fy3rIHzNBMaio (pcr product)
GCGCGCTAGCGCCACCatgtacaggatgcaactcctGTCTTGCATTGCACTAATTCTTGCACTTGTCACAAACAGTGCACCTACTTCAAGTTCGACAAAGAAAACAAAGAAAACACAGCTACAACTGGAGCATTTACTGCTGGATTTACAGATGATTTTGAATGGAATTAATAATTACAAGAATCCCAAACTCACCAGGATGCTCACATTTAAGTTTTACATGCCCAAGAAGGCCACAGAACTGAAACAGCTTCAGTGTCTAGAAGAAGAACTCAAACCTCTGGAGGAAGTGCTGAATTTAGCTCAAAGCAAAAACTTTCACTTAAGACCCAGGGACTTAATCAGCAATATCAACGTAATAGTTCTGGAACTAAAGGGATCTGAAACAACATTCATGTGTGAATATGCAGATGAGACAGCAACCATTGTAGAATTTCTGAACAGATGGATTACCTTTTGTCAAAGCAtcatctcaacactgactCATCACCATCACCATCACtgaGGGCCCGCGC
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