SMOTIF: efficient structured pattern and profile motif search

Table 11 Potential Binding Sites

Genes	UASH		URS1H		Hamming Distance
	Site	Pos	Site	Pos
MES1	GATTTTGAAGTAGGA	-438	TTAGCCGCCGA	-246	5:MER1
YJL045W	TTTTGTGAAGAGATA	-407	TTAGCCGCTCA	-273	4:DMC1
HSP60	GTTTTTGTAGGTATA	-329	ATAGCCGCCCA	-252	5:MER1
SPO1	ATTTTTGAAGTTAAC	-192	TCAGCGGCTAT	-90	5:RED1
MEK1	TCATTTGTAGTTTAT	-233	TCGGCGGCTAT	-136	3:MEK1
YIG1	ATTTCCGGAGTTTTC	-183	TCGGCGGCTAT	-140	5:RED1
^†AGP1	CCTTTTGATGACTTT	-786	TCGGCGGCTAA	-699	5:SPO16
^†AGPl	CCTTTTGATGACTTT	-786	TCGGCGGCTAA	-668	5:SPO16
^†REC114	CATTTTGGTGGGTTC	-158	TGGGCGGCTAA	-94	5:SPO16
^†GNTl	TCATTTGGAGAATAT	-340	ATAGCCGCCAT	-299	5:SPO13
^‡MEK1	TTATATGCAGTATAT	-276	ATGGCGGCTAA	-150	4:MEK1
^‡MMS1	AACTCTGTAGTTATA	-643	TGGGCGGCTAA	-497	5:REC114

For each occurrence we give the gene names corresponding to the upstream region, the sites and positions for UASH and URS1H, and also the hamming distance and the closest known gene with the cooperative binding sites. For example, 5:SPO16 in the first row means that the hamming distance between AGP1 and SPO16 was 5. ^†: found only by IUPAC pattern search, ^‡: found only by profile search.

ISSN: 1748-7188