RSAT - position-analysis

Calculates the positional distribution of oligonucleotides in a set of sequences, and detects those which significantly discard from a homogeneous distribution.

Warning: this program is useful for large data sets (some hundreds or thousands of sequences), pre-aligned on some signal (e.g. start codon).

Reference: van Helden, J., del Olmo, M. and Perez-Ortin, J. E. (2000). Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 28, 1000-10.


Sequence       Format Paste your sequence in the box below

Or select a file to upload (.gz compressed files supported)


Mask 
Sequence type
 purge sequences (highly recommended)

Oligonucleotide size   prevent overlapping matches
Count on   return reverse complements together in the output
Positions       window size      Origin     Offset

Background model


Homogeneous distribution across windows.
Window-specific background model          Markov order: 

Output fields

Return Lower
Threshold
Upper
Threshold
Occurrences
          chi2 significance
 
 

 Applicability condition for the chi2 test 

 Sort patterns by significance. 


Output 
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