RSAT - position-analysis

Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.
Warning: this program is appropriate for data sets containing hundreds or thousands of sequences, with a given reference position (e.g. transcription start sites of co-expressed genes, centers of ChIP-seq peaks).
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.

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Sequence       Format  fasta ig wconsensus raw ncbi tab multi Paste your sequence in the box below Or select a file to upload (.gz compressed files supported) Mask  none upper lower non-dna

Sequence type dna protein other

 purge sequences (highly recommended)

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Oligonucleotide size  1 2 3 4 5 6 7 8  prevent overlapping matches
Count on  single strand both strands  return reverse complements together in the output
Positions       window size      Origin start center end     Offset
Position limits for chi2:        min:      max: 

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Background model

Homogeneous distribution across windows.
Window-specific background model          Markov order:  0 1 2

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Output fields

Return	Lower Threshold	Upper Threshold
Occurrences
Chi2 statistics
chi2 significance
Rank
Position distribution
Expected occurrences
Clusters (words clustered by position profiles)
Position-specific scoring matrices
Graphs

 Applicability condition for the chi2 test  check filter

 Sort patterns by significance. 

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Output displayemail 

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