SSA

FindM

Find Motifs around Functional Sites

SSA Input Data
Select available Data Sets
         Genome :   
         Data Type :   
         Series :   
         Sample :   

Sequence input via server-resident FPS file(s)
        Name(s) of FPS file(s) (up to four):
       
        Feature  :

Upload Sequence Set in Fasta Format


Internal position of functional site :

Functional Position Set (FPS) name :

FPS type (e.g. TSS) :

Upload custom Data
     
      from a FILE (gzip or zip formats are also accepted):
     
      or from a URL:
     
      Experiment  :
      Feature  :
 Genomes
Additional Input Data Options
 Repeat Masker      
Sequence Range
Entire sequence range (for uploaded sequences only)

5' border:       3' border:
Sequence Selection and Search Criteria

Search mode:       forward    bidirectional

Sequence Selection mode :
Signal Description
PWMs from Library     
        Motif Library:  
        Motif :  
Custom Weight Matrix
        Format  
        PWM text  

      

  Cut-off
absolute    percentage    p-value
  value
  
  Bg base composition
  

Consensus seq
  

  Mismatches

  Name (max 20 chars)
  Reference position
Sequence Output Format
Retrieve sequences in : FASTA     FPS

Sequence extraction range around matches (FASTA only) :

5' border:       3' border:      

 

    

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Last update October 2017