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Table 1 Motif discovery example.

From: Discovering multiple realistic TFBS motifs based on a generalized model

Sequences S SIM A TFBSs R PFM Θ (4 × w(= 7))
S1: acgtCGATTGCctaag 0000100000000000 CGATTGC  
S2: taTGATCGAtgacgca 0010000000000000 TGATCGA A: 0.0 0.2 0.6 0.1 0.1 0.0 0.7
S3: cgaCAATTGAgcttac 0001000000000000 CAATTGA C: 0.8 0.0 0.2 0.3 0.3 0.2 0.3
S4: gCGCTCGAcaagctgt 0100000000000000 CGCTCGA G: 0.0 0.8 0.0 0.0 0.0 0.8 0.0
S5: cgttTGTCACAgtcta 0000100000000000 TGTCACA T: 0.2 0.0 0.2 0.6 0.6 0.0 0.0
S6: tcagcCACACCCagct 0000010000000000 CACACCC  
S7: ccagagCGTCTGAttg 0000001000000000 CGTCTGA Background: Θ0:
S8: gacttcaCGACTGAgc 0000000100000000 CGACTGA θ0A= 0.24 θ0C= 0.29
S9: gctgcccatCGATTGA 0000000001000000 CGATTGA θ0G= 0.24 θ0T= 0.23
S10: ccaggtacCGATTGCa 0000000010000000 CGATTGC  
  1. An artificial example of motif discovery. It shows the sequences S, the SIM A, the motif instances R, the PFM Θ and the background frequencies Θ0. In sequences S, the nucleotides from the background are shown in lower case, while the nucleotides from the motif instances in upper case.