I want to using the online sit (http://www.cbs.dtu.dk/services/Promoter/) to predict my DNA sequence's promoter. I have no idea what's means. Here is the result of the prediction:
Sequence, 1932 nucleotides
Position Score Likelihood 1400 1.077 Highly likely prediction
What's this result means? If I want to clone this promoter for my research, where should I start to clone it? How long of the flank should I chose?
The result tells you that it is likely that your fragment includes a promoter. The position tells you that they predict a promoter activity when you clone base pairs 1-1400 into the reporter vector. You may include putative 5'-utr sequence by adding sequence beyond position 1400 but avoid including an ATG. I guess that you do luciferase or a similar assay. The first ATG should be the one from your reporter.
However, I would not completely rely on a prediction. Try to get more information about your gene of interest, e.g. from ensemble.org. You would also expect some conserved elements which you may identify at http://meme-suite.org.
The predictions are always a multiple of 100, so I suppose that is the precision of the computation, it does not seem to attempt precise prediction of the transcription start site (TSS). 1.077 is a score that gives you an idea about relative strength of individual predictions.
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