BMC Genomics 2006, 7:133 Additional material Additional File 1 Sixty six binding motifs whose scores pass T5 on at least one major Alu subfamily sequence. The consensus sites of the PSSMs (from the IUPAC convention [33]) is in the second column and the the target sequences with the highest scores among all the major Alu consensus sequences – in the third, with nucleotides that agree with the consensus denoted by capi- tal letters. The fourth column contains the locations of the putative target sites on the Alu sequences of the subfamily with the highest score (in case the same sequence appears on several Alu elements, we choose the one with the highest number of copies in the 5 kb upstream regions). Two Alu subsequences serve as putative target sites of several TFs (designated by *, and **). The fifth column contains the p-values (see text and methods) and the number of subfamilies on which the BSs of the third column resides is listed in column 6. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-133-S1.xls] Additional File 2 We present for 66 PSSMs the number of putative BSs in the 5 Kbp region upstream, averaged over the genes that belong to various biological proc- esses. The PSSMs that are shown are those for which Tmax>T5. The number of genes in each biological process is given in column 2. The Alu density and number of Alu repeats per gene are given in columns 3 and 4 respectively. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-133-S2.xls] Acknowledgements The authors wish to thank Tal Shay for help identifying the Alu elements and with the intial genomic mapping of Alu elements, Yuval Tabach for use- ful comments and fruitful discussions, Or Zuk and Assif Yitzhaky for help with writing computer scripts for searching BSs on the genes' promoters. 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