Table 3 Discovered motifs using positive and negative data
Transcription factors | Known motifs | Â | Â | WordSpy | Â | MEME | AlignACE |
|---|---|---|---|---|---|---|---|
ACE2 | CCAGCA | GCTGG(1) | CCAGC(2) | GCTGGC(1) | AACCAGC(2) | AACCAGCA(7) | AACCAGC(12) |
Fkh1 | GTAAACA | GTAAACA(1) | TGTTTAC(2) | GTAAACAA(1) | TTGTTTAC(2) | GTAAACAA(1) | AAANGTAAACA(5) |
Fkh2 | GTAAACA | GTAAACA(1) | TGTTTAC(2) | GTAAACAA(1) | TTGTTTAC(2) | TTGTTTAC(1) | AANRWAAACA(3) |
Mbp1 | ACGCGT | ACGCGT(1) | AACGCGT(1) | ACGCGTT(2) | Â | AACGCGTT(2) | RACGCGWY(3) |
| Â | CRCGAAA | GACGCGA(3) | TCGCGTC(5) | ACGCGAA(6) | Â | n/a | ACGCGWAAAA(9) |
Mcm1 | TTTCCTAATTAGGAAA | TAGGAAA(1) | TTTCCTAA(9) | TTAGGAAA(10) | Â | CCTAATTAGG(1) | TTNCCNNNTNNGGAAA(1) |
Met4 | TCACGTG | CACGTGA(1) | TCACGTG(2) | Â | Â | CACGTGA(1) | CACGTGAY(2) |
| Â | AAACTGTGG | GTGGC(1) | CCACA(3) | TGTGG(5) | CTGTG(6) | CCACAGTT(3) | AAACTGTGG(4) |
| Â | Â | TGTGGC(2) | CCACAGT(3) | GCCACAC(4) | ACTGTGG(5) | AACTGTGG(7) | Â |
Met31 | AAACTGTGG | TGTGGC(1) | GCCACA(2) | GCCACAC(2) | Â | TGTGGCG(10) | AAAANTGTGGC(4) |
| Â | TCACGTG | CACGTGA(1) | TCACGTG(3) | Â | Â | GCACGTGA(2) | CACGTGANNT(7) |
Stb1 | ACGCGA | AACGCG(4) | TCGCGTT(3) | TCGCGTT(3) | Â | TTCGCGTT(3) | AACGCSAAAA(3) |
| Â | CRCGAAA | TTCGCG(1) | TTTCGCG(1) | TTTGGCG(2) | TTTCGTG(5) | CGCGAAAA(1) | AACGCSAAAA(3) |
| Â | ACGCGT | ACGCGT(3) | Â | Â | Â | n/a | n/a |
Ste12 | TGAAACA | TGAAACA(1) | ATGAAAC(2) | TGAAACAA(2) | Â | TGAAACA(2) | ATGMAAC(13) |
Swi4 | CGCGAAA | ACGCGAA(1) | GACGCGA(2) | AAACGCG(3) | CACGAAA(7) | GACGCGAA(1) | RACGCGAAAA(2) |
| Â | ACGCGT | AACGCGT(10) | Â | Â | Â | n/a | n/a |
Swi5 | CCAGCA | GCTGG(1) | CCAGC(2) | Â | Â | n/a | n/a |
Swi6 | ACGCGT | ACGCGT(1) | AACGCGT(2) | ACGCGTT(3) | Â | AACGCGTT(2) | AAACGCGW(4) |
| Â | ACGCGA | AAACGCG(5) | CGCGTTT(6) | ACGCGAA(10) | TTCGCGT(12) | TTTCGCG(3) | AAACGCGW(4) |