Additional file 5.
Sequence context at regulatory motifs for Argonaute (AGO) 1 to 4. Non-redundant seed-matches in coding regions for the top 20 expressed miRNAs in the Argonaute dataset. 8 mer-m1 is a seed-match between the mRNA and nucleotides 1 to 8 of the miRNA seed sequence, 8 mer-A1 matches nucleotides 2 to 8 of the seed sequence paired with an A at position 1. 7 mer-1 m and 7 mer-A1 are similarly defined for nucleotides 1 to 7; 7 mer-m8 is a match utilizing nucleotides 2 to 8 of the seed sequence. 6 mer2-7 is a match utilizing nucleotides 2 to 7 of the seed sequence, and 6 mer3-8 utilizes nucleotides 3 to 8 of the sequence. Heatmap: nucleotide composition, relative to a uniform background, of each individual binding site found in the coding region of a gene. Barplot: likelihood of a T = > C conversion given that there is a 'T' at the given position. Unlike the heatmap, the barplot is not normalized by the number of reads mapping to an individual binding site. The horizontal dotted red line indicates the background conversion probability for all 'T's within the respective coding region.
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Corcoran et al. Genome Biology 2011 12:R79 doi:10.1186/gb-2011-12-8-r79