Thank you for your quick resonse Here are some samples: 
 genes saved in sequence file look like this:
>hg18_refGene_NM_006511 range=chr1:15857951-15860804  
cctagtcacctgctaattaatctttttcctttcccctgtgttccatatagagaaaagtggtaaagaatct
+acctcactgggaATGTCATCATTACCAACTTCAGATGGGTTTAACCATCC
>hg18_refGene_NR_027268 range=chr1:28294033-28296656 
tttttttttttcttcttcttttttgtggagttgctttttttttttttcttcttttttgtgtcattgtttt
+tttaccatgtcctcagagtctggaattttacaaagtagttgctgagtaaacaggTAGATACAAATCAAG
+ATGAACTTTTCCGCAGGAGCTCTTATCATGAACAT

and the binding motifs:
>mot1
tttgtagatttt
>mot2
ggatcctttaag
>mot3
gtttaccccaa

[download]

In reply to Re^2: How to find any of many motifs? by Nikulina
in thread How to find any of many motifs? by Nikulina

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