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Figure 4 | BMC Bioinformatics

Figure 4

From: siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect

Figure 4

Calculated Tm values and appearances of 7-nt seed sequences. (A) Calculated Tm values of the duplex formed by all possible 7-nt sequences. The dotted line indicates that the number of 7-nt sequences with duplex Tm below 21.5°C is 4,488 (27.4%). (B) Appearance of 7-nt seed sequences in human 3' UTRs. The numbers of 3' UTR sequences containing at least one given 7-nt sequence are shown. (C) Relationship between the appearance of each 7-nt sequence in the 3' UTRs containing at least one 7-nt sequence and its calculated Tm. Histograms in the right panel show the appearance of each 7-nt sequence in human 3' UTR, divided into 10°C Tm intervals. The seed sequence whose duplex has lower Tm (colored blue) is more frequently observed in the 3' UTRs as compared to those with higher Tm (colored orange).

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