Additional File 2. Description of Y-patch, AuxRE-like and ABRE-like coupling motifs, revealed by de novo motif search on the flanks of experimentally proven AuxREs. For each motif we compiled the frequency matrix with the estimated threshold; #seq denotes the number of the sequence in the Additional file 1; position, strand, PWM score, and sequences that passed the threshold. Logos constructed for these three sequence sets are shown on Figure 1D-F. Name of motif Y-patch Frequency matrix and threshold for the respective PWM A 0 0 0 1 0 0 0 1 C 0 25 0 22 25 0 12 7 G 0 0 0 0 0 0 0 0 T 25 0 25 2 0 25 13 17 0.91 AuxRE-like A C G T 9 0 0 0 0 0 7 0 0 9 25 25 2 0 0 0 7 0 25 0 7 0 0 0 9 25 0 25 9 7 0 9 0.9997 ABRE-like A C G T 9 7 0 9 9 1 9 0 0 0 1 0 12 0 12 12 0 12 7 12 7 0 12 12 12 9 0 9 13 1 13 0 0.9949 #seq 18 12 24 10 13 17 21 7 2 11 5 12 15 18 20 23 24 3 9 11 13 21 6 13 22 8 23 9 Position, strand 89+ 81+ 4396+ 61+ 32+ 62+ 11+ 6585+ 77+ 1690+ 30+ 96100+ 2286+ 7115+ 12+ 73+ 22+ 102+ 95+ 724586+ PWM score 1 0.9957 0.9825 0.9782 0.9301 0.9301 0.9301 0.9274 0.9231 0.9139 1 1 1 1 1 1 1 0.9997 0.9997 0.9997 0.9997 0.9997 1 1 1 0.9997 0.9997 0.9949 Sequence TCTCCTCT TCTCCTTT TCTCCTCC TCTCCTTC TCTTCTCT TCTTCTCT TCTTCTCT TCTCCTCA TCTCCTTA TCTACTCT ATTTTCTT TTTTTCTT ATTTTCTT ATTTTCTT TTTTTCTA TTTTTCTT TTTTTCTT ATTGTCTA TTTGTCTA ATTGTCTT ATTCTCTT ATTCTCTT ATGTCGGC TTCTCGGG ATGTCGGG TGGTCGGC TGCTCCGG ATGTCCTC