miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
5480	3'	-52.8	NC_001798.1	+	26794	0.66	0.982589
	Target:  5'- uGUGUGGUUuauucgggGGUCGggcgggcgggGGUCgGGCGgGCg -3' miRNA:   3'- -CACACCAG--------CCAGCa---------UCAGgUUGCaCG- -5'
5480	3'	-52.8	NC_001798.1	+	128089	0.67	0.964066
	Target:  5'- aUGUGGUCGGcgUCGgcGauccCCAACGcacUGCc -3' miRNA:   3'- cACACCAGCC--AGCauCa---GGUUGC---ACG- -5'
5480	3'	-52.8	NC_001798.1	+	14316	0.67	0.96059
	Target:  5'- -aGUGGggGGUgCGUGGggaGGCGUGCg -3' miRNA:   3'- caCACCagCCA-GCAUCaggUUGCACG- -5'
5480	3'	-52.8	NC_001798.1	+	92399	0.68	0.944385
	Target:  5'- -cGUGGccgCGGUCGUcgGGUCCcgcacGACGgGCc -3' miRNA:   3'- caCACCa--GCCAGCA--UCAGG-----UUGCaCG- -5'
5480	3'	-52.8	NC_001798.1	+	71977	0.68	0.934852
	Target:  5'- -gGUGGUCGGggacgCGcugAGggCC-ACGUGCa -3' miRNA:   3'- caCACCAGCCa----GCa--UCa-GGuUGCACG- -5'
5480	3'	-52.8	NC_001798.1	+	125682	0.69	0.929721
	Target:  5'- -aGgggGGUCGGggCGaaggAGUCCGACGUcggGCg -3' miRNA:   3'- caCa--CCAGCCa-GCa---UCAGGUUGCA---CG- -5'
5480	3'	-52.8	NC_001798.1	+	36829	0.75	0.659901
	Target:  5'- -aGUGGUCGG-CGUGGggaCCGGCuGUGUg -3' miRNA:   3'- caCACCAGCCaGCAUCa--GGUUG-CACG- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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