Table 2.

Predicted miRNA target sites

mRNA	miRNA	RNAhybrid (G r p)	RNAplex (G r p)	RIsearch (G r p)
AGTR1	miR-155	−20.90 1 11	−14.37 1 11	−14.06 1 9
BCL2	miR-16	−24.10 1 1	−18.90 2 1	−18.69 1 1
SLC7A1	miR-122	−29.00 1 2	−23.80 1 2	−23.04 1 4
TPPP3	miR-16	−26.00 2 0	−20.80 2 1	−19.95 1 1
CLOCK	miR-141	−22.10 1 0	−16.40 1 0	−15.37 1 7
CXCL12	miR-23a	−25.90 1 38	−19.80 2 37	−18.00 2 38
CYP1B1	miR-27b	−33.60 1 1	−28.20 1 1	−26.91 1 1
E2F3	miR-34a	−25.10 2 10	−19.10 2 10	−18.31 2 1
EZH2	miR-101	−22.40 1 1	−16.90 1 1	−15.65 1 1
PARP8	miR-145	−27.40 1 3	−21.80 1 3	−20.00 1 1
FSTL1	miR-206	−23.20 3 0	−18.40 4 0	−15.87 6 2
GJA1	miR-1	−20.60 1 1	−14.30 2 1	−12.76 2 12
GJA1	miR-206	−21.00 4 11	−15.03 6 11	−12.55 8 0
HAND2	miR-1	−18.10 1 1	−12.20 1 1	−9.61 2 5
HOXA1	miR-10a	−23.30 1 14	−15.93 4 12	−12.71 4 13
KIT	miR-221	−23.40 3 0	−17.70 3 0	−15.18 2 2
KIT	miR-222	−23.70 3 58	−18.60 4 56	−15.38 5 56
KRAS	let-7a	−21.30 5 2	−16.30 3 3	−15.03 3 3
LIN28A	let-7b	−33.50 1 1	−27.40 1 1	−25.20 1 5
MAPK14	miR-24	−32.20 1 1	−27.10 1 0	−25.98 1 1
MYCN	miR-101	−20.70 1 1	−13.85 2 16	−12.19 1 1
NRAS	let-7a	−21.60 4 6	−17.70 2 22	−13.96 4 8
PTEN	miR-19a	−23.20 1 1	−17.70 1 1	−16.74 1 1
ARHGAP32	miR-132	−25.10 1 3	−18.80 1 3	−18.55 1 1
SMC1A	let-7e	−27.70 1 1	−22.20 1 1	−21.49 1 2
TMSB4X	miR-1	−21.90 1 1	−16.90 1 1	−16.76 1 1
TPM1	miR-21	−20.00 1 13	−15.00 1 8	−13.44 1 7
Average rank and position		1.67/6.74	1.93/7.56	2.07/6.81

Column 1: HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] symbol, column 2: miRNA ID (all human), columns 3–5: Results shown for each of the tools include the G (kcal/mol) of the interaction, its rank (r) within all predictions and the deviation [nt] of the predicted target position pred from the reported one lit (p) with p = . Note, that for RNAhybrid the energies are usually lower, because the initiation energy of 4.1 kcal/mol is not included. The last row contains the average of the rank and the deviation in position.