Consensus sequences

Hello, I am aligning about 100 sequences in order to identify some primer targets for a long range PCR. I used the ... sequence with degerate codes allowed. I can not find any option to get such a consensus sequence in the aligned areas. Please let me know if this is possible and ...

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... sites necessary for transcription to happen. They usually have sequences called consensus sequence like TATA box in eukaryote or prinbow box in prokaryotes, which initiates ...

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try the NCBI BLAST, it should automatically set for short sequences. There are also some algoritms for searching consensus sequences, whit AAs far from each other.

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I second mith until the last sentence. If your sequences are too short, it will be nearimpossible to get a consensus because they won't differ enough to provide enough significant overlap. Sequences the size ...

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... these interactions may be transient (as occurring at degenerate consensus sequences). The apparatus may detect levels of more than one transcription factor for fidelity. ...

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