. 2009 Nov 11;38(2):e12. doi: 10.1093/nar/gkp907

Table 2.

Prediction by Cosmo and MEME on the E. coli dataset

Transcription factor	Known motifs (L and N)^a	Cosmo (BIC)^d result (L, N)	MEME result (L, N)
ArgR	`TGAATAATAATTCA (14,24)`	`TGTGTGTATTAAAATTCATG^b (20,22)`	`CTTTATGAATAAAAATTCAC (20,12)`
CpxR	`GTAAAATTTTGTAA (14,44)`	`GTAAAATTATGTAAC (15,8)`	`AAAATGTAAAAAAATGTAAA (20,7)`
CRP	`TGTGANNNNNNTCACA (16,281)`	`TGTGAGACTGATCACATT (18,55)`	`TGTGATCCAGCTCACA (16,154)`
DnaA	`TTATGCACAA (10,21)`	`GCAAAAACTGTGACAGAGA^c (19,0)`	`TAGCAACAACTGTGCCAGAG^c (20,0)`
Fnr	`TTGATCTATATCAA (14,92)`	`TTGAAATTGATCAATATCAA (20,49)`	`AATTGATATTTATCAATG (18,27)`
FruR	`TGAATCGTTTCAGC (14,11)`	`GCTGAATCGACAGT (14,11)`	`GCTGAATCGATT (12,11)`
Fur	`AATGATAATCATTATC (16,89)`	`GCCTGACCCGAGCTCTCAC^c (19,0)`	`ATAATTATTTTCATTTTCAT (20,24)`
GntR	`TGTTACCCATAACA (14,24)`	`TGTTGTCACTAGTAACA (17,11)`	`GCGATACTACGCCTGGCGGC^c (20,0)`
LexA	`CTGTATATATATACAG (16,25)`	`ACTGTGTATATATACAGAAT (20,11)`	`TACTGTATAAATAAACAGT (19,11)`
MetJ	`AGACGTCTAAACGTCT (16,65)`	`TCTGGACGACTAAACGGATA (20,43)`	`ATCTGGACGTCTAAACGGAT (20,34)`
NarP	`TACCCCTAAAGGGGTA (16,38)`	`TACCTACCCAGTGATAGTTA (20,16)`	`AAAAATAAAATTATGAACAT^c (20,4)`
NtrC	`TGCACCAAAATGGTGC (16,33)`	`TGCACCACTATAATGCTGCA (20,19)`	`TGCACCATTCTGGGGCACCA (20,9)`
PhoB	`TGTCATAAATCTGTCA (16,17)`	`GCCGGAGCCGGC^c (12,1)`	`ATCTGTCATAAATCTGTCA (19,2)`
PurR	`GAAAACGTTTGC (12,18)`	`ACGGAAACCGTTTCCTT (17,15)`	`AGGAAAACGTTTGCG (15,15)`
TrpR	`GTACTAGTTAACTAGT (16,34)`	`GTAATTCAGTACTGAAGAGC (20,10)`	`CGTACTAGTTAACTAGTTCG (20,14)`
TyrR	`TGTAAACTTATATATACA (18,15)`	`GTGAAAATTAATTTTTACA (19,10)`	`TGTAAATTTTTATTTACAC (19,7)`
Total	Number of binding sites: 831	Detected binding sites: 281	Detected binding sites: 331

^aThe number in parenthesis (L, N) denotes the length and binding sites number of a motif, respectively.

^bThe segments with underline is the overlap part with real motifs.

^cThe actual motif was completely missed.

^dBayesian Information Criterion used by Cosmo for identifying the motif length.